Daily Papers

Computed Tomography (CT) is one of the most widely used and diagnostically information-dense imaging modalities, covering critical organs such as the heart, lungs, liver, and colon. Clinical interpretation relies on both slice-driven local features (e.g., sub-centimeter nodules, lesion boundaries) and volume-driven spatial representations (e.g., tumor infiltration, inter-organ anatomical relations). However, existing Large Vision-Language Models (LVLMs) remain fragmented in CT slice versus volumetric understanding: slice-driven LVLMs show strong generalization but lack cross-slice spatial consistency, while volume-driven LVLMs explicitly capture volumetric semantics but suffer from coarse granularity and poor compatibility with slice inputs. The absence of a unified modeling paradigm constitutes a major bottleneck for the clinical translation of medical LVLMs. We present OmniCT, a powerful unified slice-volume LVLM for CT scenarios, which makes three contributions: (i) Spatial Consistency Enhancement (SCE): volumetric slice composition combined with tri-axial positional embedding that introduces volumetric consistency, and an MoE hybrid projection enables efficient slice-volume adaptation; (ii) Organ-level Semantic Enhancement (OSE): segmentation and ROI localization explicitly align anatomical regions, emphasizing lesion- and organ-level semantics; (iii) MedEval-CT: the largest slice-volume CT dataset and hybrid benchmark integrates comprehensive metrics for unified evaluation. OmniCT consistently outperforms existing methods with a substantial margin across diverse clinical tasks and satisfies both micro-level detail sensitivity and macro-level spatial reasoning. More importantly, it establishes a new paradigm for cross-modal medical imaging understanding. Our project is available at https://github.com/ZJU4HealthCare/OmniCT.

Speech language models align with human brain responses to natural language to an impressive degree. However, current models rely heavily on low-level speech features, indicating they lack brain-relevant semantics which limits their utility as model organisms of semantic processing in the brain. In this work, we address this limitation by inducing brain-relevant bias directly into the models via fine-tuning with fMRI recordings of people listening to natural stories, a process we name brain-tuning. After testing it on 3 different pretrained model families, we show that brain-tuning not only improves overall alignment with new brain recordings in semantic language regions, but also reduces the reliance on low-level speech features for this alignment. Excitingly, we further show that brain-tuning leads to 1) consistent improvements in performance on a range of downstream tasks and 2) a representational space with increased semantic preference. Our results provide converging evidence, for the first time, that incorporating brain signals into the training of language models improves the models' semantic understanding.

Multi-organ medical segmentation is a crucial component of medical image processing, essential for doctors to make accurate diagnoses and develop effective treatment plans. Despite significant progress in this field, current multi-organ segmentation models often suffer from inaccurate details, dependence on geometric prompts and loss of spatial information. Addressing these challenges, we introduce a novel model named CRISP-SAM2 with CRoss-modal Interaction and Semantic Prompting based on SAM2. This model represents a promising approach to multi-organ medical segmentation guided by textual descriptions of organs. Our method begins by converting visual and textual inputs into cross-modal contextualized semantics using a progressive cross-attention interaction mechanism. These semantics are then injected into the image encoder to enhance the detailed understanding of visual information. To eliminate reliance on geometric prompts, we use a semantic prompting strategy, replacing the original prompt encoder to sharpen the perception of challenging targets. In addition, a similarity-sorting self-updating strategy for memory and a mask-refining process is applied to further adapt to medical imaging and enhance localized details. Comparative experiments conducted on seven public datasets indicate that CRISP-SAM2 outperforms existing models. Extensive analysis also demonstrates the effectiveness of our method, thereby confirming its superior performance, especially in addressing the limitations mentioned earlier. Our code is available at: https://github.com/YU-deep/CRISP\_SAM2.git.

Understanding the functional organization of higher visual cortex is a central focus in neuroscience. Past studies have primarily mapped the visual and semantic selectivity of neural populations using hand-selected stimuli, which may potentially bias results towards pre-existing hypotheses of visual cortex functionality. Moving beyond conventional approaches, we introduce a data-driven method that generates natural language descriptions for images predicted to maximally activate individual voxels of interest. Our method -- Semantic Captioning Using Brain Alignments ("BrainSCUBA") -- builds upon the rich embedding space learned by a contrastive vision-language model and utilizes a pre-trained large language model to generate interpretable captions. We validate our method through fine-grained voxel-level captioning across higher-order visual regions. We further perform text-conditioned image synthesis with the captions, and show that our images are semantically coherent and yield high predicted activations. Finally, to demonstrate how our method enables scientific discovery, we perform exploratory investigations on the distribution of "person" representations in the brain, and discover fine-grained semantic selectivity in body-selective areas. Unlike earlier studies that decode text, our method derives voxel-wise captions of semantic selectivity. Our results show that BrainSCUBA is a promising means for understanding functional preferences in the brain, and provides motivation for further hypothesis-driven investigation of visual cortex.

Natural Language Inference (NLI) relies heavily on adequately parsing the semantic content of the premise and hypothesis. In this work, we investigate whether adding semantic information in the form of an Abstract Meaning Representation (AMR) helps pretrained language models better generalize in NLI. Our experiments integrating AMR into NLI in both fine-tuning and prompting settings show that the presence of AMR in fine-tuning hinders model generalization while prompting with AMR leads to slight gains in GPT-4o. However, an ablation study reveals that the improvement comes from amplifying surface-level differences rather than aiding semantic reasoning. This amplification can mislead models to predict non-entailment even when the core meaning is preserved.

Vision-and-language models (VLMs) have been increasingly explored in the medical domain, particularly following the success of CLIP in general domain. However, unlike the relatively straightforward pairing of 2D images and text, curating large-scale paired data in the medical field for volumetric modalities such as CT scans remains a challenging and time-intensive process. This difficulty often limits the performance on downstream tasks. To address these challenges, we propose a novel vision-language pre-training (VLP) framework, termed as VELVET-Med, specifically designed for limited volumetric data such as 3D CT and associated radiology reports. Instead of relying on large-scale data collection, our method focuses on the development of effective pre-training objectives and model architectures. The key contributions are: 1) We incorporate uni-modal self-supervised learning into VLP framework, which are often underexplored in the existing literature. 2) We propose a novel language encoder, termed as TriBERT, for learning multi-level textual semantics. 3) We devise the hierarchical contrastive learning to capture multi-level vision-language correspondence. Using only 38,875 scan-report pairs, our approach seeks to uncover rich spatial and semantic relationships embedded in volumetric medical images and corresponding clinical narratives, thereby enhancing the generalization ability of the learned encoders. The resulting encoders exhibit strong transferability, achieving state-of-the-art performance across a wide range of downstream tasks, including 3D segmentation, cross-modal retrieval, visual question answering, and report generation.

Generative universal speech enhancement (USE) methods aim to leverage generative models to improve speech quality under various types of distortions. Diffusion- or flow-based generative models are capable of producing enhanced speech with high quality and fidelity. However, they typically achieve speech enhancement by learning an acoustic feature mapping from degraded speech to clean speech, while lacking awareness of high-level semantic information. This deficiency tends to cause semantic ambiguity and acoustic discontinuities in the enhanced speech. In contrast, humans can often comprehend heavily corrupted speech by relying on semantic priors, suggesting that semantics play a crucial role in speech enhancement. Therefore, in this paper, we propose SenSE, which leverages a language model to capture the semantic information of distorted speech and effectively integrates it into a flow-matching-based speech enhancement framework. Specifically, we introduce a semantic-aware speech language model to capture the semantics of degraded speech and generate semantic tokens. We then design a semantic guidance mechanism that incorporates semantic information into the flow-matching-based speech enhancement process, effectively mitigating semantic ambiguity. In addition, we propose a prompt guidance mechanism, which leverages a short reference utterance to alleviate the loss of speaker similarity under severe distortion conditions. The results of several benchmark data sets demonstrate that SenSE not only ensures high perceptual quality but also substantially improves speech fidelity while maintaining strong robustness under severe distortions. Codes and demos are available.

Understanding how humans process visual information is one of the crucial steps for unraveling the underlying mechanism of brain activity. Recently, this curiosity has motivated the fMRI-to-image reconstruction task; given the fMRI data from visual stimuli, it aims to reconstruct the corresponding visual stimuli. Surprisingly, leveraging powerful generative models such as the Latent Diffusion Model (LDM) has shown promising results in reconstructing complex visual stimuli such as high-resolution natural images from vision datasets. Despite the impressive structural fidelity of these reconstructions, they often lack details of small objects, ambiguous shapes, and semantic nuances. Consequently, the incorporation of additional semantic knowledge, beyond mere visuals, becomes imperative. In light of this, we exploit how modern LDMs effectively incorporate multi-modal guidance (text guidance, visual guidance, and image layout) for structurally and semantically plausible image generations. Specifically, inspired by the two-streams hypothesis suggesting that perceptual and semantic information are processed in different brain regions, our framework, Brain-Streams, maps fMRI signals from these brain regions to appropriate embeddings. That is, by extracting textual guidance from semantic information regions and visual guidance from perceptual information regions, Brain-Streams provides accurate multi-modal guidance to LDMs. We validate the reconstruction ability of Brain-Streams both quantitatively and qualitatively on a real fMRI dataset comprising natural image stimuli and fMRI data.

Multi-modal data abounds in biomedicine, such as radiology images and reports. Interpreting this data at scale is essential for improving clinical care and accelerating clinical research. Biomedical text with its complex semantics poses additional challenges in vision--language modelling compared to the general domain, and previous work has used insufficiently adapted models that lack domain-specific language understanding. In this paper, we show that principled textual semantic modelling can substantially improve contrastive learning in self-supervised vision--language processing. We release a language model that achieves state-of-the-art results in radiology natural language inference through its improved vocabulary and novel language pretraining objective leveraging semantics and discourse characteristics in radiology reports. Further, we propose a self-supervised joint vision--language approach with a focus on better text modelling. It establishes new state of the art results on a wide range of publicly available benchmarks, in part by leveraging our new domain-specific language model. We release a new dataset with locally-aligned phrase grounding annotations by radiologists to facilitate the study of complex semantic modelling in biomedical vision--language processing. A broad evaluation, including on this new dataset, shows that our contrastive learning approach, aided by textual-semantic modelling, outperforms prior methods in segmentation tasks, despite only using a global-alignment objective.

Semantic information refers to the meaning conveyed through words, phrases, and contextual relationships within a given linguistic structure. Humans can leverage semantic information, such as familiar linguistic patterns and contextual cues, to reconstruct incomplete or masked speech signals in noisy environments. However, existing speech enhancement (SE) approaches often overlook the rich semantic information embedded in speech, which is crucial for improving intelligibility, speaker consistency, and overall quality of enhanced speech signals. To enrich the SE model with semantic information, we employ language models as an efficient semantic learner and propose a comprehensive framework tailored for language model-based speech enhancement, called GenSE. Specifically, we approach SE as a conditional language modeling task rather than a continuous signal regression problem defined in existing works. This is achieved by tokenizing speech signals into semantic tokens using a pre-trained self-supervised model and into acoustic tokens using a custom-designed single-quantizer neural codec model. To improve the stability of language model predictions, we propose a hierarchical modeling method that decouples the generation of clean semantic tokens and clean acoustic tokens into two distinct stages. Moreover, we introduce a token chain prompting mechanism during the acoustic token generation stage to ensure timbre consistency throughout the speech enhancement process. Experimental results on benchmark datasets demonstrate that our proposed approach outperforms state-of-the-art SE systems in terms of speech quality and generalization capability.

Deep learning classifiers face significant challenges when dealing with heterogeneous multi-modal and multi-organ biomedical datasets. The low-level feature distinguishability limited to imaging-modality hinders the classifiers' ability to learn high-level semantic relationships, resulting in sub-optimal performance. To address this issue, image augmentation strategies are employed as regularization techniques. While additive noise input during network training is a well-established augmentation as regularization method, modern pipelines often favor more robust techniques such as dropout and weight decay. This preference stems from the observation that combining these established techniques with noise input can adversely affect model performance. In this study, we propose a novel pretraining pipeline that learns to generate conditional noise mask specifically tailored to improve performance on multi-modal and multi-organ datasets. As a reinforcement learning algorithm, our approach employs a dual-component system comprising a very light-weight policy network that learns to sample conditional noise using a differentiable beta distribution as well as a classifier network. The policy network is trained using the reinforce algorithm to generate image-specific noise masks that regularize the classifier during pretraining. A key aspect is that the policy network's role is limited to obtaining an intermediate (or heated) model before fine-tuning. During inference, the policy network is omitted, allowing direct comparison between the baseline and noise-regularized models. We conducted experiments and related analyses on RadImageNet datasets. Results demonstrate that fine-tuning the intermediate models consistently outperforms conventional training algorithms on both classification and generalization to unseen concept tasks.

Universal Multimodal Retrieval (UMR) seeks any-to-any search across text and vision, yet modern embedding models remain brittle when queries require latent reasoning (e.g., resolving underspecified references or matching compositional constraints). We argue this brittleness is often data-induced: when images carry "silent" evidence and queries leave key semantics implicit, a single embedding pass must both reason and compress, encouraging spurious feature matching. We propose a data-centric framework that decouples these roles by externalizing reasoning before retrieval. Using a strong Vision--Language Model, we make implicit semantics explicit by densely captioning visual evidence in corpus entries, resolving ambiguous multimodal references in queries, and rewriting verbose instructions into concise retrieval constraints. Inference-time enhancement alone is insufficient; the retriever must be trained on these semantically dense representations to avoid distribution shift and fully exploit the added signal. Across M-BEIR, our reasoning-augmented training method yields consistent gains over strong baselines, with ablations showing that corpus enhancement chiefly benefits knowledge-intensive queries while query enhancement is critical for compositional modification requests. We publicly release our code at https://github.com/AugmentedRetrieval/ReasoningAugmentedRetrieval.

Image enhancement improves visual quality and helps reveal details that are hard to see in the original image. In medical imaging, it can support clinical decision-making, but current models often over-edit. This can distort organs, create false findings, and miss small tumors because these models do not understand anatomy or contrast dynamics. We propose SMILE, an anatomy-aware diffusion model that learns how organs are shaped and how they take up contrast. It enhances only clinically relevant regions while leaving all other areas unchanged. SMILE introduces three key ideas: (1) structure-aware supervision that follows true organ boundaries and contrast patterns; (2) registration-free learning that works directly with unaligned multi-phase CT scans; (3) unified inference that provides fast and consistent enhancement across all contrast phases. Across six external datasets, SMILE outperforms existing methods in image quality (14.2% higher SSIM, 20.6% higher PSNR, 50% better FID) and in clinical usefulness by producing anatomically accurate and diagnostically meaningful images. SMILE also improves cancer detection from non-contrast CT, raising the F1 score by up to 10 percent.

The rapid advancement of large language models (LLMs) has significantly impacted various domains, including healthcare and biomedicine. However, the phenomenon of hallucination, where LLMs generate outputs that deviate from factual accuracy or context, poses a critical challenge, especially in high-stakes domains. This paper conducts a scoping study of existing techniques for mitigating hallucinations in knowledge-based task in general and especially for medical domains. Key methods covered in the paper include Retrieval-Augmented Generation (RAG)-based techniques, iterative feedback loops, supervised fine-tuning, and prompt engineering. These techniques, while promising in general contexts, require further adaptation and optimization for the medical domain due to its unique demands for up-to-date, specialized knowledge and strict adherence to medical guidelines. Addressing these challenges is crucial for developing trustworthy AI systems that enhance clinical decision-making and patient safety as well as accuracy of biomedical scientific research.

Video multimodal large language models (Video-MLLMs) have achieved remarkable progress in video understanding. However, they remain vulnerable to hallucination-producing content inconsistent with or unrelated to video inputs. Previous video hallucination benchmarks primarily focus on short-videos. They attribute hallucinations to factors such as strong language priors, missing frames, or vision-language biases introduced by the visual encoder. While these causes indeed account for most hallucinations in short videos, they still oversimplify the cause of hallucinations. Sometimes, models generate incorrect outputs but with correct frame-level semantics. We refer to this type of hallucination as Semantic Aggregation Hallucination (SAH), which arises during the process of aggregating frame-level semantics into event-level semantic groups. Given that SAH becomes particularly critical in long videos due to increased semantic complexity across multiple events, it is essential to separate and thoroughly investigate the causes of this type of hallucination. To address the above issues, we introduce ELV-Halluc, the first benchmark dedicated to long-video hallucination, enabling a systematic investigation of SAH. Our experiments confirm the existence of SAH and show that it increases with semantic complexity. Additionally, we find that models are more prone to SAH on rapidly changing semantics. Moreover, we discuss potential approaches to mitigate SAH. We demonstrate that positional encoding strategy contributes to alleviating SAH, and further adopt DPO strategy to enhance the model's ability to distinguish semantics within and across events. To support this, we curate a dataset of 8K adversarial data pairs and achieve improvements on both ELV-Halluc and Video-MME, including a substantial 27.7% reduction in SAH ratio.

Since commonsense information has been recorded significantly less frequently than its existence, language models pre-trained by text generation have difficulty to learn sufficient commonsense knowledge. Several studies have leveraged text retrieval to augment the models' commonsense ability. Unlike text, images capture commonsense information inherently but little effort has been paid to effectively utilize them. In this work, we propose a novel Multi-mOdal REtrieval (MORE) augmentation framework, to leverage both text and images to enhance the commonsense ability of language models. Extensive experiments on the Common-Gen task have demonstrated the efficacy of MORE based on the pre-trained models of both single and multiple modalities.

Large Multimodal Models (LMMs) have achieved impressive progress in visual perception and reasoning. However, when confronted with visually ambiguous or non-semantic scene text, they often struggle to accurately spot and understand the content, frequently generating semantically plausible yet visually incorrect answers, which we refer to as semantic hallucination. In this work, we investigate the underlying causes of semantic hallucination and identify a key finding: Transformer layers in LLM with stronger attention focus on scene text regions are less prone to producing semantic hallucinations. Thus, we propose a training-free semantic hallucination mitigation framework comprising two key components: (1) ZoomText, a coarse-to-fine strategy that identifies potential text regions without external detectors; and (2) Grounded Layer Correction, which adaptively leverages the internal representations from layers less prone to hallucination to guide decoding, correcting hallucinated outputs for non-semantic samples while preserving the semantics of meaningful ones. To enable rigorous evaluation, we introduce TextHalu-Bench, a benchmark of over 1,730 samples spanning both semantic and non-semantic cases, with manually curated question-answer pairs designed to probe model hallucinations. Extensive experiments demonstrate that our method not only effectively mitigates semantic hallucination but also achieves strong performance on public benchmarks for scene text spotting and understanding.

While deep networks have achieved broad success in analyzing natural images, when applied to medical scans, they often fail in unexcepted situations. We investigate this challenge and focus on model sensitivity to domain shifts, such as data sampled from different hospitals or data confounded by demographic variables such as sex, race, etc, in the context of chest X-rays and skin lesion images. A key finding we show empirically is that existing visual backbones lack an appropriate prior from the architecture for reliable generalization in these settings. Taking inspiration from medical training, we propose giving deep networks a prior grounded in explicit medical knowledge communicated in natural language. To this end, we introduce Knowledge-enhanced Bottlenecks (KnoBo), a class of concept bottleneck models that incorporates knowledge priors that constrain it to reason with clinically relevant factors found in medical textbooks or PubMed. KnoBo uses retrieval-augmented language models to design an appropriate concept space paired with an automatic training procedure for recognizing the concept. We evaluate different resources of knowledge and recognition architectures on a broad range of domain shifts across 20 datasets. In our comprehensive evaluation with two imaging modalities, KnoBo outperforms fine-tuned models on confounded datasets by 32.4% on average. Finally, evaluations reveal that PubMed is a promising resource for making medical models less sensitive to domain shift, outperforming other resources on both diversity of information and final prediction performance.

Medical imaging is critical to the diagnosis and treatment of numerous medical problems, including many forms of cancer. Medical imaging reports distill the findings and observations of radiologists, creating an unstructured textual representation of unstructured medical images. Large-scale use of this text-encoded information requires converting the unstructured text to a structured, semantic representation. We explore the extraction and normalization of anatomical information in radiology reports that is associated with radiological findings. We investigate this extraction and normalization task using a span-based relation extraction model that jointly extracts entities and relations using BERT. This work examines the factors that influence extraction and normalization performance, including the body part/organ system, frequency of occurrence, span length, and span diversity. It discusses approaches for improving performance and creating high-quality semantic representations of radiological phenomena.

Large Vision and Language Models (LVLMs) have shown strong performance across various vision-language tasks in natural image domains. However, their application to remote sensing (RS) remains underexplored due to significant domain differences in visual appearances, object scales, and semantics. These discrepancies hider the effective understanding of RS scenes, which contain rich, multi-level semantic information spanning from coarse-to-fine levels. Hence, it limits the direct adaptation of existing LVLMs to RS imagery. To address this gap, we propose a novel LVLM framework tailored for RS understanding, incorporating two core components: Semantic-augmented Multi-level Alignment and Semantic-aware Expert Modeling. First, to align multi-level visual features, we introduce the retrieval-based Semantic Augmentation Module which enriches the visual features with relevant semantics across fine-to-coarse levels (e.g., object- and scene-level information). It is designed to retrieve relevant semantic cues from a RS semantic knowledge database, followed by aggregation of semantic cues with user query and multi-level visual features, resulting in semantically enriched representation across multiple levels. Second, for Semantic-aware Expert Modeling, we design semantic experts, where each expert is responsible for processing semantic representation at different levels separately. This enables hierarchical semantic understanding from coarse to fine levels. Evaluations across multiple RS tasks-including scene classification and VQA, etc.-demonstrate that the proposed framework achieves consistent improvements across multiple semantic levels. This highlights its capability and effectiveness in bridging the gap between general LVLMs and unique demands of RS-specific vision-language understanding.

Masked Language Models (MLMs) have achieved remarkable success in many self-supervised representation learning tasks. MLMs are trained by randomly masking portions of the input sequences with [MASK] tokens and learning to reconstruct the original content based on the remaining context. This paper explores the impact of [MASK] tokens on MLMs. Analytical studies show that masking tokens can introduce the corrupted semantics problem, wherein the corrupted context may convey multiple, ambiguous meanings. This problem is also a key factor affecting the performance of MLMs on downstream tasks. Based on these findings, we propose a novel enhanced-context MLM, ExLM. Our approach expands [MASK] tokens in the input context and models the dependencies between these expanded states. This enhancement increases context capacity and enables the model to capture richer semantic information, effectively mitigating the corrupted semantics problem during pre-training. Experimental results demonstrate that ExLM achieves significant performance improvements in both text modeling and SMILES modeling tasks. Further analysis confirms that ExLM enriches semantic representations through context enhancement, and effectively reduces the semantic multimodality commonly observed in MLMs.

Recent advances in causal interpretability have extended from language models to vision-language models (VLMs), seeking to reveal their internal mechanisms through input interventions. While textual interventions often target semantics, visual interventions typically rely on coarse pixel-level perturbations, limiting semantic insights on multimodal integration. In this study, we introduce V-SEAM, a novel framework that combines Visual Semantic Editing and Attention Modulating for causal interpretation of VLMs. V-SEAM enables concept-level visual manipulations and identifies attention heads with positive or negative contributions to predictions across three semantic levels: objects, attributes, and relationships. We observe that positive heads are often shared within the same semantic level but vary across levels, while negative heads tend to generalize broadly. Finally, we introduce an automatic method to modulate key head embeddings, demonstrating enhanced performance for both LLaVA and InstructBLIP across three diverse VQA benchmarks. Our data and code are released at: https://github.com/petergit1/V-SEAM.

Recent advances in context optimization (CoOp) guided by large language model (LLM)-distilled medical semantic priors offer a scalable alternative to manual prompt engineering and full fine-tuning for adapting biomedical CLIP-based vision-language models (VLMs). However, prompt learning in this context is challenged by semantic misalignment between LLMs and CLIP variants due to divergent training corpora and model architectures; it further lacks scalability across continuously evolving families of foundation models. More critically, pairwise multimodal alignment via conventional Euclidean-space optimization lacks the capacity to model unified representations or apply localized geometric constraints, which tends to amplify modality gaps in complex biomedical imaging and destabilize few-shot adaptation. In this work, we propose vMFCoOp, a framework that inversely estimates von Mises-Fisher (vMF) distributions on a shared Hyperspherical Manifold, aligning semantic biases between arbitrary LLMs and CLIP backbones via Unified Semantic Anchors to achieve robust biomedical prompting and superior few-shot classification. Grounded in three complementary constraints, vMFCoOp demonstrates consistent improvements across 14 medical datasets, 12 medical imaging modalities, and 13 anatomical regions, outperforming state-of-the-art methods in accuracy, generalization, and clinical applicability. This work aims to continuously expand to encompass more downstream applications, and the corresponding resources are intended to be shared through https://github.com/VinyehShaw/UniEqui.

Large Language Models (LLMs) are known to hallucinate, whereby they generate plausible but inaccurate text. This phenomenon poses significant risks in critical applications, such as medicine or law, necessitating robust hallucination mitigation strategies. While recent works have proposed fine-tuning methods to teach LLMs to abstain from answering questions beyond their knowledge or capabilities, these methods rely on the existence of ground-truth labels or are limited to short-form responses. To address these limitations, we propose fine-tuning using semantic entropy, an uncertainty measure derived from introspection into the model which does not require external labels. We demonstrate that our approach matches or outperforms models fine-tuned using prior work and achieves strong performance for both short and long-form generations on a range of datasets.

Reinforcement learning (RL) with rule-based rewards has demonstrated strong potential in enhancing the reasoning and generalization capabilities of vision-language models (VLMs) and large language models (LLMs), while reducing computational overhead. However, its application in medical imaging remains underexplored. Existing reinforcement fine-tuning (RFT) approaches in this domain primarily target closed-ended visual question answering (VQA), limiting their applicability to real-world clinical reasoning. In contrast, open-ended medical VQA better reflects clinical practice but has received limited attention. While some efforts have sought to unify both formats via semantically guided RL, we observe that model-based semantic rewards often suffer from reward collapse, where responses with significant semantic differences receive similar scores. To address this, we propose ARMed (Adaptive Reinforcement for Medical Reasoning), a novel RL framework for open-ended medical VQA. ARMed first incorporates domain knowledge through supervised fine-tuning (SFT) on chain-of-thought data, then applies reinforcement learning with textual correctness and adaptive semantic rewards to enhance reasoning quality. We evaluate ARMed on six challenging medical VQA benchmarks. Results show that ARMed consistently boosts both accuracy and generalization, achieving a 32.64% improvement on in-domain tasks and an 11.65% gain on out-of-domain benchmarks. These results highlight the critical role of reward discriminability in medical RL and the promise of semantically guided rewards for enabling robust and clinically meaningful multimodal reasoning.

Large Language Models (LLMs) have demonstrated a remarkable potential in medical knowledge acquisition and question-answering. However, LLMs can potentially hallucinate and yield factually incorrect outcomes, even with domain-specific pretraining. Previously, retrieval augmented generation (RAG) has limited success in addressing hallucinations. Unlike previous methods in RAG where the retrieval model was trained separately from the LLM, we introduce JMLR (for Jointly trains LLM and information Retrieval) during the fine-tuning phase. The synchronized training mechanism enhances JMLR's ability to retrieve clinical guidelines and leverage medical knowledge to reason and answer questions and reduces the demand for computational resources. We evaluated JMLR on the important medical question-answering application. Our experimental results demonstrate that JMLR-13B (70.5%) outperforms a previous state-of-the-art open-source model using conventional pre-training and fine-tuning Meditron-70B (68.9%) and Llama2-13B with RAG (67.7%) on a medical question-answering dataset. Comprehensive evaluations reveal JMLR-13B enhances reasoning quality and reduces hallucinations better than Claude3-Opus. Additionally, JMLR-13B (148 GPU hours) also trains much faster than Meditron-70B (42630 GPU hours). Through this work, we provide a new and efficient knowledge enhancement method for healthcare, demonstrating the potential of integrating retrieval and LLM training for medical question-answering systems.

Low-level enhancement and high-level visual understanding in low-light vision have traditionally been treated separately. Low-light enhancement improves image quality for downstream tasks, but existing methods rely on physical or geometric priors, limiting generalization. Evaluation mainly focuses on visual quality rather than downstream performance. Low-light visual understanding, constrained by scarce labeled data, primarily uses task-specific domain adaptation, which lacks scalability. To address these challenges, we build a generalized bridge between low-light enhancement and low-light understanding, which we term Generalized Enhancement For Understanding (GEFU). This paradigm improves both generalization and scalability. To address the diverse causes of low-light degradation, we leverage pretrained generative diffusion models to optimize images, achieving zero-shot generalization performance. Building on this, we propose Semantically Consistent Unsupervised Fine-tuning (SCUF). Specifically, to overcome text prompt limitations, we introduce an illumination-aware image prompt to explicitly guide image generation and propose a cycle-attention adapter to maximize its semantic potential. To mitigate semantic degradation in unsupervised training, we propose caption and reflectance consistency to learn high-level semantics and image-level spatial semantics. Extensive experiments demonstrate that our proposed method outperforms current state-of-the-art methods in traditional image quality and GEFU tasks including classification, detection, and semantic segmentation.

Large language models (LLM) hold significant potential for applications in biomedicine, but they struggle with hallucinations and outdated knowledge. While retrieval-augmented generation (RAG) is generally employed to address these issues, it also has its own set of challenges: (1) LLMs are vulnerable to irrelevant or incorrect context, (2) medical queries are often not well-targeted for helpful information, and (3) retrievers are prone to bias toward the specific source corpus they were trained on. In this study, we present RAG^2 (RAtionale-Guided RAG), a new framework for enhancing the reliability of RAG in biomedical contexts. RAG^2 incorporates three key innovations: a small filtering model trained on perplexity-based labels of rationales, which selectively augments informative snippets of documents while filtering out distractors; LLM-generated rationales as queries to improve the utility of retrieved snippets; a structure designed to retrieve snippets evenly from a comprehensive set of four biomedical corpora, effectively mitigating retriever bias. Our experiments demonstrate that RAG^2 improves the state-of-the-art LLMs of varying sizes, with improvements of up to 6.1\%, and it outperforms the previous best medical RAG model by up to 5.6\% across three medical question-answering benchmarks. Our code is available at https://github.com/dmis-lab/RAG2.

Recent advances in Large Multimodal Models (LMMs) lead to significant breakthroughs in both academia and industry. One question that arises is how we, as humans, can understand their internal neural representations. This paper takes an initial step towards addressing this question by presenting a versatile framework to identify and interpret the semantics within LMMs. Specifically, 1) we first apply a Sparse Autoencoder(SAE) to disentangle the representations into human understandable features. 2) We then present an automatic interpretation framework to interpreted the open-semantic features learned in SAE by the LMMs themselves. We employ this framework to analyze the LLaVA-NeXT-8B model using the LLaVA-OV-72B model, demonstrating that these features can effectively steer the model's behavior. Our results contribute to a deeper understanding of why LMMs excel in specific tasks, including EQ tests, and illuminate the nature of their mistakes along with potential strategies for their rectification. These findings offer new insights into the internal mechanisms of LMMs and suggest parallels with the cognitive processes of the human brain.

The development of Neural Radiance Fields (NeRFs) has provided a potent representation for encapsulating the geometric and appearance characteristics of 3D scenes. Enhancing the capabilities of NeRFs in open-vocabulary 3D semantic perception tasks has been a recent focus. However, current methods that extract semantics directly from Contrastive Language-Image Pretraining (CLIP) for semantic field learning encounter difficulties due to noisy and view-inconsistent semantics provided by CLIP. To tackle these limitations, we propose OV-NeRF, which exploits the potential of pre-trained vision and language foundation models to enhance semantic field learning through proposed single-view and cross-view strategies. First, from the single-view perspective, we introduce Region Semantic Ranking (RSR) regularization by leveraging 2D mask proposals derived from SAM to rectify the noisy semantics of each training view, facilitating accurate semantic field learning. Second, from the cross-view perspective, we propose a Cross-view Self-enhancement (CSE) strategy to address the challenge raised by view-inconsistent semantics. Rather than invariably utilizing the 2D inconsistent semantics from CLIP, CSE leverages the 3D consistent semantics generated from the well-trained semantic field itself for semantic field training, aiming to reduce ambiguity and enhance overall semantic consistency across different views. Extensive experiments validate our OV-NeRF outperforms current state-of-the-art methods, achieving a significant improvement of 20.31% and 18.42% in mIoU metric on Replica and Scannet, respectively. Furthermore, our approach exhibits consistent superior results across various CLIP configurations, further verifying its robustness.

In medical scenarios, effectively retrieving external knowledge and leveraging it for rigorous logical reasoning is of significant importance. Despite their potential, existing work has predominantly focused on enhancing either retrieval or reasoning capabilities of the models in isolation, with little attention given to their joint optimization, which leads to limited coordination between the two processes. Additionally, current methods rely heavily on supervised fine-tuning (SFT), which can cause models to memorize existing problem-solving pathways, thereby restricting their generalization ability when confronted with novel problem contexts. Furthermore, while some studies have explored to improve retrieval-augmented reasoning in general domains via reinforcement learning, their reward function designs do not adequately capture the specific demands of the medical domain. To address these challenges, we introduce **Med-R^3**, a **Med**ical **R**etrieval-augmented **R**easoning framework driven by progressive **R**einforcement learning. In this framework, we first develop the model's ability to perform logical reasoning over medical problems. Subsequently, on the basis of this foundation, we adaptively optimize the retrieval capability to better align with the characteristics of knowledge corpus and external information utilization throughout the reasoning process. Finally, we conduct joint optimization of the model's retrieval and reasoning coordination. Extensive experiments indicate that **Med-R^3** could achieve state-of-the-art performances, with LLaMA3.1-8B-Instruct + Med-R^3 surpassing closed-sourced GPT-4o-mini by 3.93\% at a comparable parameter scale, while Qwen2.5-14B augmented with Med-R^3 shows a more substantial gain of 13.53\%.

In computational pathology, understanding and generation have evolved along disparate paths: advanced understanding models already exhibit diagnostic-level competence, whereas generative models largely simulate pixels. Progress remains hindered by three coupled factors: the scarcity of large, high-quality image-text corpora; the lack of precise, fine-grained semantic control, which forces reliance on non-semantic cues; and terminological heterogeneity, where diverse phrasings for the same diagnostic concept impede reliable text conditioning. We introduce UniPath, a semantics-driven pathology image generation framework that leverages mature diagnostic understanding to enable controllable generation. UniPath implements Multi-Stream Control: a Raw-Text stream; a High-Level Semantics stream that uses learnable queries to a frozen pathology MLLM to distill paraphrase-robust Diagnostic Semantic Tokens and to expand prompts into diagnosis-aware attribute bundles; and a Prototype stream that affords component-level morphological control via a prototype bank. On the data front, we curate a 2.65M image-text corpus and a finely annotated, high-quality 68K subset to alleviate data scarcity. For a comprehensive assessment, we establish a four-tier evaluation hierarchy tailored to pathology. Extensive experiments demonstrate UniPath's SOTA performance, including a Patho-FID of 80.9 (51% better than the second-best) and fine-grained semantic control achieving 98.7% of the real-image. The meticulously curated datasets, complete source code, and pre-trained model weights developed in this study will be made openly accessible to the public.

Incentivizing the reasoning ability of Multimodal Large Language Models (MLLMs) is essential for medical applications to transparently analyze medical scans and provide reliable diagnosis. However, existing medical MLLMs rely solely on internal knowledge during reasoning, leading to hallucinated reasoning and factual inaccuracies when encountering cases beyond their training scope. Although recent Agentic Retrieval-Augmented Generation (RAG) methods elicit the medical model's proactive retrieval ability during reasoning, they are confined to unimodal LLMs, neglecting the crucial visual information during reasoning and retrieval. Consequently, we propose the first Multimodal Medical Reasoning-with-Retrieval framework, Med-RwR, which actively retrieves external knowledge by querying observed symptoms or domain-specific medical concepts during reasoning. Specifically, we design a two-stage reinforcement learning strategy with tailored rewards that stimulate the model to leverage both visual diagnostic findings and textual clinical information for effective retrieval. Building on this foundation, we further propose a Confidence-Driven Image Re-retrieval (CDIR) method for test-time scaling when low prediction confidence is detected. Evaluation on various public medical benchmarks demonstrates Med-RwR's significant improvements over baseline models, proving the effectiveness of enhancing reasoning capabilities with external knowledge integration. Furthermore, Med-RwR demonstrates remarkable generalizability to unfamiliar domains, evidenced by 8.8% performance gain on our proposed EchoCardiography Benchmark (ECBench), despite the scarcity of echocardiography data in the training corpus. Our data, model, and codes will be made publicly available at https://github.com/xmed-lab/Med-RwR.

Psychological research consistently finds that human ratings of words across diverse semantic scales can be reduced to a low-dimensional form with relatively little information loss. We find that the semantic associations encoded in the embedding matrices of large language models (LLMs) exhibit a similar structure. We show that the projections of words on semantic directions defined by antonym pairs (e.g. kind - cruel) correlate highly with human ratings, and further find that these projections effectively reduce to a 3-dimensional subspace within LLM embeddings, closely resembling the patterns derived from human survey responses. Moreover, we find that shifting tokens along one semantic direction causes off-target effects on geometrically aligned features proportional to their cosine similarity. These findings suggest that semantic features are entangled within LLMs similarly to how they are interconnected in human language, and a great deal of semantic information, despite its apparent complexity, is surprisingly low-dimensional. Furthermore, accounting for this semantic structure may prove essential for avoiding unintended consequences when steering features.

Multimodal Large Language Models (MLLMs) have demonstrated impressive capabilities in understanding common visual elements, largely due to their large-scale datasets and advanced training strategies. However, their effectiveness in medical applications remains limited due to the inherent discrepancies between data and tasks in medical scenarios and those in the general domain. Concretely, existing medical MLLMs face the following critical limitations: (1) limited coverage of medical knowledge beyond imaging, (2) heightened susceptibility to hallucinations due to suboptimal data curation processes, (3) lack of reasoning capabilities tailored for complex medical scenarios. To address these challenges, we first propose a comprehensive data curation procedure that (1) efficiently acquires rich medical knowledge data not only from medical imaging but also from extensive medical texts and general-domain data; and (2) synthesizes accurate medical captions, visual question answering (VQA), and reasoning samples. As a result, we build a multimodal dataset enriched with extensive medical knowledge. Building on the curated data, we introduce our medical-specialized MLLM: Lingshu. Lingshu undergoes multi-stage training to embed medical expertise and enhance its task-solving capabilities progressively. Besides, we preliminarily explore the potential of applying reinforcement learning with verifiable rewards paradigm to enhance Lingshu's medical reasoning ability. Additionally, we develop MedEvalKit, a unified evaluation framework that consolidates leading multimodal and textual medical benchmarks for standardized, fair, and efficient model assessment. We evaluate the performance of Lingshu on three fundamental medical tasks, multimodal QA, text-based QA, and medical report generation. The results show that Lingshu consistently outperforms the existing open-source multimodal models on most tasks ...

Representational spaces learned via language modeling are fundamental to Natural Language Processing (NLP), however there has been limited understanding regarding how and when during training various types of linguistic information emerge and interact. Leveraging a novel information theoretic probing suite, which enables direct comparisons of not just task performance, but their representational subspaces, we analyze nine tasks covering syntax, semantics and reasoning, across 2M pre-training steps and five seeds. We identify critical learning phases across tasks and time, during which subspaces emerge, share information, and later disentangle to specialize. Across these phases, syntactic knowledge is acquired rapidly after 0.5% of full training. Continued performance improvements primarily stem from the acquisition of open-domain knowledge, while semantics and reasoning tasks benefit from later boosts to long-range contextualization and higher specialization. Measuring cross-task similarity further reveals that linguistically related tasks share information throughout training, and do so more during the critical phase of learning than before or after. Our findings have implications for model interpretability, multi-task learning, and learning from limited data.

Reinforcement learning (RL) is often credited with improving language model reasoning and generalization at the expense of degrading memorized knowledge. We challenge this narrative by observing that RL-enhanced models consistently outperform their base and supervised fine-tuned (SFT) counterparts on pure knowledge recall tasks, particularly those requiring traversal of hierarchical, structured knowledge (e.g., medical codes). We hypothesize these gains stem not from newly acquired data, but from improved procedural skills in navigating and searching existing knowledge hierarchies within the model parameters. To support this hypothesis, we show that structured prompting, which explicitly guides SFTed models through hierarchical traversal, recovers most of the performance gap (reducing 24pp to 7pp on MedConceptsQA for DeepSeek-V3/R1). We further find that while prompting improves final-answer accuracy, RL-enhanced models retain superior ability to recall correct procedural paths on deep-retrieval tasks. Finally our layer-wise internal activation analysis reveals that while factual representations (e.g., activations for the statement "code 57.95 refers to urinary infection") maintain high cosine similarity between SFT and RL models, query representations (e.g., "what is code 57.95") diverge noticeably, indicating that RL primarily transforms how models traverse knowledge rather than the knowledge representation itself.

Neural decoding, the process of understanding how brain activity corresponds to different stimuli, has been a primary objective in cognitive sciences. Over the past three decades, advancements in functional Magnetic Resonance Imaging and machine learning have greatly improved our ability to map visual stimuli to brain activity, especially in the visual cortex. Concurrently, research has expanded into decoding more complex processes like language and memory across the whole brain, utilizing techniques to handle greater variability and improve signal accuracy. We argue that "seeing" involves more than just mapping visual stimuli onto the visual cortex; it engages the entire brain, as various emotions and cognitive states can emerge from observing different scenes. In this paper, we develop algorithms to enhance our understanding of visual processes by incorporating whole-brain activation maps while individuals are exposed to visual stimuli. We utilize large-scale fMRI encoders and Image generative models pre-trained on large public datasets, which are then fine-tuned through Image-fMRI contrastive learning. Our models hence can decode visual experience across the entire cerebral cortex, surpassing the traditional confines of the visual cortex. We first compare our method with state-of-the-art approaches to decoding visual processing and show improved predictive semantic accuracy by 43%. A network ablation analysis suggests that beyond the visual cortex, the default mode network contributes most to decoding stimuli, in line with the proposed role of this network in sense-making and semantic processing. Additionally, we implemented zero-shot imagination decoding on an extra validation dataset, achieving a p-value of 0.0206 for mapping the reconstructed images and ground-truth text stimuli, which substantiates the model's capability to capture semantic meanings across various scenarios.

Large language models (LLM) have demonstrated remarkable capabilities in various biomedical natural language processing (NLP) tasks, leveraging the demonstration within the input context to adapt to new tasks. However, LLM is sensitive to the selection of demonstrations. To address the hallucination issue inherent in LLM, retrieval-augmented LLM (RAL) offers a solution by retrieving pertinent information from an established database. Nonetheless, existing research work lacks rigorous evaluation of the impact of retrieval-augmented large language models on different biomedical NLP tasks. This deficiency makes it challenging to ascertain the capabilities of RAL within the biomedical domain. Moreover, the outputs from RAL are affected by retrieving the unlabeled, counterfactual, or diverse knowledge that is not well studied in the biomedical domain. However, such knowledge is common in the real world. Finally, exploring the self-awareness ability is also crucial for the RAL system. So, in this paper, we systematically investigate the impact of RALs on 5 different biomedical tasks (triple extraction, link prediction, classification, question answering, and natural language inference). We analyze the performance of RALs in four fundamental abilities, including unlabeled robustness, counterfactual robustness, diverse robustness, and negative awareness. To this end, we proposed an evaluation framework to assess the RALs' performance on different biomedical NLP tasks and establish four different testbeds based on the aforementioned fundamental abilities. Then, we evaluate 3 representative LLMs with 3 different retrievers on 5 tasks over 9 datasets.

Current approaches to learning semantic representations of sentences often use prior word-level knowledge. The current study aims to leverage visual information in order to capture sentence level semantics without the need for word embeddings. We use a multimodal sentence encoder trained on a corpus of images with matching text captions to produce visually grounded sentence embeddings. Deep Neural Networks are trained to map the two modalities to a common embedding space such that for an image the corresponding caption can be retrieved and vice versa. We show that our model achieves results comparable to the current state-of-the-art on two popular image-caption retrieval benchmark data sets: MSCOCO and Flickr8k. We evaluate the semantic content of the resulting sentence embeddings using the data from the Semantic Textual Similarity benchmark task and show that the multimodal embeddings correlate well with human semantic similarity judgements. The system achieves state-of-the-art results on several of these benchmarks, which shows that a system trained solely on multimodal data, without assuming any word representations, is able to capture sentence level semantics. Importantly, this result shows that we do not need prior knowledge of lexical level semantics in order to model sentence level semantics. These findings demonstrate the importance of visual information in semantics.

Expanding multimodal representations to novel modalities is constrained by reliance on large-scale paired datasets (e.g., text-image, text-audio, text-3D, text-molecule), which are costly and often infeasible in domains requiring expert annotation such as medical imaging and molecular analysis. We introduce TextME, the first text-only modality expansion framework, to the best of our knowledge, projecting diverse modalities into LLM embedding space as a unified anchor. Our approach exploits the geometric structure of pretrained contrastive encoders to enable zero-shot cross-modal transfer using only text descriptions, without paired supervision. We empirically validate that such consistent modality gaps exist across image, video, audio, 3D, X-ray, and molecular domains, demonstrating that text-only training can preserve substantial performance of pretrained encoders. We further show that our framework enables emergent cross-modal retrieval between modality pairs not explicitly aligned during training (e.g., audio-to-image, 3D-to-image). These results establish text-only training as a practical alternative to paired supervision for modality expansion.

Recent text-to-image generative models have demonstrated an unparalleled ability to generate diverse and creative imagery guided by a target text prompt. While revolutionary, current state-of-the-art diffusion models may still fail in generating images that fully convey the semantics in the given text prompt. We analyze the publicly available Stable Diffusion model and assess the existence of catastrophic neglect, where the model fails to generate one or more of the subjects from the input prompt. Moreover, we find that in some cases the model also fails to correctly bind attributes (e.g., colors) to their corresponding subjects. To help mitigate these failure cases, we introduce the concept of Generative Semantic Nursing (GSN), where we seek to intervene in the generative process on the fly during inference time to improve the faithfulness of the generated images. Using an attention-based formulation of GSN, dubbed Attend-and-Excite, we guide the model to refine the cross-attention units to attend to all subject tokens in the text prompt and strengthen - or excite - their activations, encouraging the model to generate all subjects described in the text prompt. We compare our approach to alternative approaches and demonstrate that it conveys the desired concepts more faithfully across a range of text prompts.

Large language models (LLMs) have demonstrated remarkable performance across diverse tasks by encoding vast amounts of factual knowledge. However, they are still prone to hallucinations, generating incorrect or misleading information, often accompanied by high uncertainty. Existing methods for hallucination detection primarily focus on quantifying internal uncertainty, which arises from missing or conflicting knowledge within the model. However, hallucinations can also stem from external uncertainty, where ambiguous user queries lead to multiple possible interpretations. In this work, we introduce Semantic Volume, a novel mathematical measure for quantifying both external and internal uncertainty in LLMs. Our approach perturbs queries and responses, embeds them in a semantic space, and computes the determinant of the Gram matrix of the embedding vectors, capturing their dispersion as a measure of uncertainty. Our framework provides a generalizable and unsupervised uncertainty detection method without requiring white-box access to LLMs. We conduct extensive experiments on both external and internal uncertainty detection, demonstrating that our Semantic Volume method consistently outperforms existing baselines in both tasks. Additionally, we provide theoretical insights linking our measure to differential entropy, unifying and extending previous sampling-based uncertainty measures such as the semantic entropy. Semantic Volume is shown to be a robust and interpretable approach to improving the reliability of LLMs by systematically detecting uncertainty in both user queries and model responses.

Human readers can efficiently comprehend scrambled words, a phenomenon known as Typoglycemia, primarily by relying on word form; if word form alone is insufficient, they further utilize contextual cues for interpretation. While advanced large language models (LLMs) exhibit similar abilities, the underlying mechanisms remain unclear. To investigate this, we conduct controlled experiments to analyze the roles of word form and contextual information in semantic reconstruction and examine LLM attention patterns. Specifically, we first propose SemRecScore, a reliable metric to quantify the degree of semantic reconstruction, and validate its effectiveness. Using this metric, we study how word form and contextual information influence LLMs' semantic reconstruction ability, identifying word form as the core factor in this process. Furthermore, we analyze how LLMs utilize word form and find that they rely on specialized attention heads to extract and process word form information, with this mechanism remaining stable across varying levels of word scrambling. This distinction between LLMs' fixed attention patterns primarily focused on word form and human readers' adaptive strategy in balancing word form and contextual information provides insights into enhancing LLM performance by incorporating human-like, context-aware mechanisms.

While holding great promise for improving and facilitating healthcare, large language models (LLMs) struggle to produce up-to-date responses on evolving topics due to outdated knowledge or hallucination. Retrieval-augmented generation (RAG) is a pivotal innovation that improves the accuracy and relevance of LLM responses by integrating LLMs with a search engine and external sources of knowledge. However, the quality of RAG responses can be largely impacted by the rank and density of key information in the retrieval results, such as the "lost-in-the-middle" problem. In this work, we aim to improve the robustness and reliability of the RAG workflow in the medical domain. Specifically, we propose a map-reduce strategy, BriefContext, to combat the "lost-in-the-middle" issue without modifying the model weights. We demonstrated the advantage of the workflow with various LLM backbones and on multiple QA datasets. This method promises to improve the safety and reliability of LLMs deployed in healthcare domains.

The integration of audio perception capabilities into Large Language Models (LLMs) has enabled significant advances in Audio-LLMs. Although application-focused developments, particularly in curating training data for specific capabilities e.g., audio reasoning, have progressed rapidly, the underlying mechanisms that govern efficient transfer of rich semantic representations from audio encoders to LLMs remain under-explored. We conceptualize effective audio-LLM interaction as the LLM's ability to proficiently probe the audio encoder representations to satisfy textual queries. This paper presents a systematic investigation on how architectural design choices can affect that. Beginning with a standard Pengi/LLaVA-style audio-LLM architecture, we propose and evaluate several modifications guided by hypotheses derived from mechanistic interpretability studies and LLM operational principles. Our experiments demonstrate that: (1) delaying audio integration until the LLM's initial layers establish textual context that enhances its ability to probe the audio representations for relevant information; (2) the LLM can proficiently probe audio representations exclusively through LLM layer's attention submodule, without requiring propagation to its Feed-Forward Network (FFN) submodule; (3) an efficiently integrated ensemble of diverse audio encoders provides richer, complementary representations, thereby broadening the LLM's capacity to probe a wider spectrum of audio information. All hypotheses are evaluated using an identical three-stage training curriculum on a dataset of 5.6 million audio-text pairs, ensuring controlled comparisons. Our final architecture, which incorporates all proposed modifications, achieves relative improvements from 10\% to 60\% over the baseline, validating our approach to optimizing cross-modal information transfer in audio-LLMs. Project page: https://ta012.github.io/PAL/

Surgical video-language pretraining (VLP) faces unique challenges due to the knowledge domain gap and the scarcity of multi-modal data. This study aims to bridge the gap by addressing issues regarding textual information loss in surgical lecture videos and the spatial-temporal challenges of surgical VLP. We propose a hierarchical knowledge augmentation approach and a novel Procedure-Encoded Surgical Knowledge-Augmented Video-Language Pretraining (PeskaVLP) framework to tackle these issues. The knowledge augmentation uses large language models (LLM) for refining and enriching surgical concepts, thus providing comprehensive language supervision and reducing the risk of overfitting. PeskaVLP combines language supervision with visual self-supervision, constructing hard negative samples and employing a Dynamic Time Warping (DTW) based loss function to effectively comprehend the cross-modal procedural alignment. Extensive experiments on multiple public surgical scene understanding and cross-modal retrieval datasets show that our proposed method significantly improves zero-shot transferring performance and offers a generalist visual representation for further advancements in surgical scene understanding.The code is available at https://github.com/CAMMA-public/SurgVLP

Retrieval-augmented generation (RAG) enhances large language models (LLMs) by incorporating external knowledge to generate a response within a context with improved accuracy and reduced hallucinations. However, multi-modal RAG systems face unique challenges: (i) the retrieval process may select irrelevant entries to user query (e.g., images, documents), and (ii) vision-language models or multi-modal language models like GPT-4o may hallucinate when processing these entries to generate RAG output. In this paper, we aim to address the first challenge, i.e, improving the selection of relevant context from the knowledge-base in retrieval phase of the multi-modal RAG. Specifically, we leverage the relevancy score (RS) measure designed in our previous work for evaluating the RAG performance to select more relevant entries in retrieval process. The retrieval based on embeddings, say CLIP-based embedding, and cosine similarity usually perform poorly particularly for multi-modal data. We show that by using a more advanced relevancy measure, one can enhance the retrieval process by selecting more relevant pieces from the knowledge-base and eliminate the irrelevant pieces from the context by adaptively selecting up-to-k entries instead of fixed number of entries. Our evaluation using COCO dataset demonstrates significant enhancement in selecting relevant context and accuracy of the generated response.

Recent label mix-based augmentation methods have shown their effectiveness in generalization despite their simplicity, and their favorable effects are often attributed to semantic-level augmentation. However, we found that they are vulnerable to highly skewed class distribution, because scarce data classes are rarely sampled for inter-class perturbation. We propose TextManiA, a text-driven manifold augmentation method that semantically enriches visual feature spaces, regardless of data distribution. TextManiA augments visual data with intra-class semantic perturbation by exploiting easy-to-understand visually mimetic words, i.e., attributes. To this end, we bridge between the text representation and a target visual feature space, and propose an efficient vector augmentation. To empirically support the validity of our design, we devise two visualization-based analyses and show the plausibility of the bridge between two different modality spaces. Our experiments demonstrate that TextManiA is powerful in scarce samples with class imbalance as well as even distribution. We also show compatibility with the label mix-based approaches in evenly distributed scarce data.

Self-Supervised Learning (SSL) has demonstrated promising results in 3D medical image analysis. However, the lack of high-level semantics in pre-training still heavily hinders the performance of downstream tasks. We observe that 3D medical images contain relatively consistent contextual position information, i.e., consistent geometric relations between different organs, which leads to a potential way for us to learn consistent semantic representations in pre-training. In this paper, we propose a simple-yet-effective Volume Contrast (VoCo) framework to leverage the contextual position priors for pre-training. Specifically, we first generate a group of base crops from different regions while enforcing feature discrepancy among them, where we employ them as class assignments of different regions. Then, we randomly crop sub-volumes and predict them belonging to which class (located at which region) by contrasting their similarity to different base crops, which can be seen as predicting contextual positions of different sub-volumes. Through this pretext task, VoCo implicitly encodes the contextual position priors into model representations without the guidance of annotations, enabling us to effectively improve the performance of downstream tasks that require high-level semantics. Extensive experimental results on six downstream tasks demonstrate the superior effectiveness of VoCo. Code will be available at https://github.com/Luffy03/VoCo.

Diffusion models have become the mainstream architecture for text-to-image generation, achieving remarkable progress in visual quality and prompt controllability. However, current inference pipelines generally lack interpretable semantic supervision and correction mechanisms throughout the denoising process. Most existing approaches rely solely on post-hoc scoring of the final image, prompt filtering, or heuristic resampling strategies-making them ineffective in providing actionable guidance for correcting the generative trajectory. As a result, models often suffer from object confusion, spatial errors, inaccurate counts, and missing semantic elements, severely compromising prompt-image alignment and image quality. To tackle these challenges, we propose MLLM Semantic-Corrected Ping-Pong-Ahead Diffusion (PPAD), a novel framework that, for the first time, introduces a Multimodal Large Language Model (MLLM) as a semantic observer during inference. PPAD performs real-time analysis on intermediate generations, identifies latent semantic inconsistencies, and translates feedback into controllable signals that actively guide the remaining denoising steps. The framework supports both inference-only and training-enhanced settings, and performs semantic correction at only extremely few diffusion steps, offering strong generality and scalability. Extensive experiments demonstrate PPAD's significant improvements.

Despite the potential of Large Language Models (LLMs) in medicine, they may generate responses lacking supporting evidence or based on hallucinated evidence. While Retrieval Augment Generation (RAG) is popular to address this issue, few studies implemented and evaluated RAG in downstream domain-specific applications. We developed a RAG pipeline with 70,000 ophthalmology-specific documents that retrieve relevant documents to augment LLMs during inference time. In a case study on long-form consumer health questions, we systematically evaluated the responses including over 500 references of LLMs with and without RAG on 100 questions with 10 healthcare professionals. The evaluation focuses on factuality of evidence, selection and ranking of evidence, attribution of evidence, and answer accuracy and completeness. LLMs without RAG provided 252 references in total. Of which, 45.3% hallucinated, 34.1% consisted of minor errors, and 20.6% were correct. In contrast, LLMs with RAG significantly improved accuracy (54.5% being correct) and reduced error rates (18.8% with minor hallucinations and 26.7% with errors). 62.5% of the top 10 documents retrieved by RAG were selected as the top references in the LLM response, with an average ranking of 4.9. The use of RAG also improved evidence attribution (increasing from 1.85 to 2.49 on a 5-point scale, P<0.001), albeit with slight decreases in accuracy (from 3.52 to 3.23, P=0.03) and completeness (from 3.47 to 3.27, P=0.17). The results demonstrate that LLMs frequently exhibited hallucinated and erroneous evidence in the responses, raising concerns for downstream applications in the medical domain. RAG substantially reduced the proportion of such evidence but encountered challenges.

Multimodal large language models (MLLMs) have made significant strides by integrating visual and textual modalities. A critical factor in training MLLMs is the quality of image-text pairs within multimodal pretraining datasets. However, de facto filter-based data quality enhancement paradigms often discard a substantial portion of high-quality image data due to inadequate semantic alignment between images and texts, leading to inefficiencies in data utilization and scalability. In this paper, we propose the Adaptive Image-Text Quality Enhancer (AITQE), a model that dynamically assesses and enhances the quality of image-text pairs. AITQE employs a text rewriting mechanism for low-quality pairs and incorporates a negative sample learning strategy to improve evaluative capabilities by integrating deliberately selected low-quality samples during training. Unlike prior approaches that significantly alter text distributions, our method minimally adjusts text to preserve data volume while enhancing quality. Experimental results demonstrate that AITQE surpasses existing methods on various benchmark, effectively leveraging raw data and scaling efficiently with increasing data volumes. We hope our work will inspire future works. The code and model are available at: https://github.com/hanhuang22/AITQE.

The proliferation of Large Language Models (LLMs) in medicine has enabled impressive capabilities, yet a critical gap remains in their ability to perform systematic, transparent, and verifiable reasoning, a cornerstone of clinical practice. This has catalyzed a shift from single-step answer generation to the development of LLMs explicitly designed for medical reasoning. This paper provides the first systematic review of this emerging field. We propose a taxonomy of reasoning enhancement techniques, categorized into training-time strategies (e.g., supervised fine-tuning, reinforcement learning) and test-time mechanisms (e.g., prompt engineering, multi-agent systems). We analyze how these techniques are applied across different data modalities (text, image, code) and in key clinical applications such as diagnosis, education, and treatment planning. Furthermore, we survey the evolution of evaluation benchmarks from simple accuracy metrics to sophisticated assessments of reasoning quality and visual interpretability. Based on an analysis of 60 seminal studies from 2022-2025, we conclude by identifying critical challenges, including the faithfulness-plausibility gap and the need for native multimodal reasoning, and outlining future directions toward building efficient, robust, and sociotechnically responsible medical AI.

Recent advancements in text-to-image generative models have demonstrated a remarkable ability to capture a deep semantic understanding of images. In this work, we leverage this semantic knowledge to transfer the visual appearance between objects that share similar semantics but may differ significantly in shape. To achieve this, we build upon the self-attention layers of these generative models and introduce a cross-image attention mechanism that implicitly establishes semantic correspondences across images. Specifically, given a pair of images -- one depicting the target structure and the other specifying the desired appearance -- our cross-image attention combines the queries corresponding to the structure image with the keys and values of the appearance image. This operation, when applied during the denoising process, leverages the established semantic correspondences to generate an image combining the desired structure and appearance. In addition, to improve the output image quality, we harness three mechanisms that either manipulate the noisy latent codes or the model's internal representations throughout the denoising process. Importantly, our approach is zero-shot, requiring no optimization or training. Experiments show that our method is effective across a wide range of object categories and is robust to variations in shape, size, and viewpoint between the two input images.

Deep learning has enabled the development of highly robust foundation models for various pathological tasks across diverse diseases and patient cohorts. Among these models, vision-language pre-training, which leverages large-scale paired data to align pathology image and text embedding spaces, and provides a novel zero-shot paradigm for downstream tasks. However, existing models have been primarily data-driven and lack the incorporation of domain-specific knowledge, which limits their performance in cancer diagnosis, especially for rare tumor subtypes. To address this limitation, we establish a Knowledge-enhanced Pathology (KEEP) foundation model that harnesses disease knowledge to facilitate vision-language pre-training. Specifically, we first construct a disease knowledge graph (KG) that covers 11,454 human diseases with 139,143 disease attributes, including synonyms, definitions, and hypernym relations. We then systematically reorganize the millions of publicly available noisy pathology image-text pairs, into 143K well-structured semantic groups linked through the hierarchical relations of the disease KG. To derive more nuanced image and text representations, we propose a novel knowledge-enhanced vision-language pre-training approach that integrates disease knowledge into the alignment within hierarchical semantic groups instead of unstructured image-text pairs. Validated on 18 diverse benchmarks with more than 14,000 whole slide images (WSIs), KEEP achieves state-of-the-art performance in zero-shot cancer diagnostic tasks. Notably, for cancer detection, KEEP demonstrates an average sensitivity of 89.8% at a specificity of 95.0% across 7 cancer types. For cancer subtyping, KEEP achieves a median balanced accuracy of 0.456 in subtyping 30 rare brain cancers, indicating strong generalizability for diagnosing rare tumors.

Multimodal Large Language Model (MLLMs) leverages Large Language Models as a cognitive framework for diverse visual-language tasks. Recent efforts have been made to equip MLLMs with visual perceiving and grounding capabilities. However, there still remains a gap in providing fine-grained pixel-level perceptions and extending interactions beyond text-specific inputs. In this work, we propose {AnyRef}, a general MLLM model that can generate pixel-wise object perceptions and natural language descriptions from multi-modality references, such as texts, boxes, images, or audio. This innovation empowers users with greater flexibility to engage with the model beyond textual and regional prompts, without modality-specific designs. Through our proposed refocusing mechanism, the generated grounding output is guided to better focus on the referenced object, implicitly incorporating additional pixel-level supervision. This simple modification utilizes attention scores generated during the inference of LLM, eliminating the need for extra computations while exhibiting performance enhancements in both grounding masks and referring expressions. With only publicly available training data, our model achieves state-of-the-art results across multiple benchmarks, including diverse modality referring segmentation and region-level referring expression generation.

Medical vision-and-language pre-training (Med-VLP) has received considerable attention owing to its applicability to extracting generic vision-and-language representations from medical images and texts. Most existing methods mainly contain three elements: uni-modal encoders (i.e., a vision encoder and a language encoder), a multi-modal fusion module, and pretext tasks, with few studies considering the importance of medical domain expert knowledge and explicitly exploiting such knowledge to facilitate Med-VLP. Although there exist knowledge-enhanced vision-and-language pre-training (VLP) methods in the general domain, most require off-the-shelf toolkits (e.g., object detectors and scene graph parsers), which are unavailable in the medical domain. In this paper, we propose a systematic and effective approach to enhance Med-VLP by structured medical knowledge from three perspectives. First, considering knowledge can be regarded as the intermediate medium between vision and language, we align the representations of the vision encoder and the language encoder through knowledge. Second, we inject knowledge into the multi-modal fusion model to enable the model to perform reasoning using knowledge as the supplementation of the input image and text. Third, we guide the model to put emphasis on the most critical information in images and texts by designing knowledge-induced pretext tasks. To perform a comprehensive evaluation and facilitate further research, we construct a medical vision-and-language benchmark including three tasks. Experimental results illustrate the effectiveness of our approach, where state-of-the-art performance is achieved on all downstream tasks. Further analyses explore the effects of different components of our approach and various settings of pre-training.

Over the past decade, predictive modeling of neural responses in the primate visual system has advanced significantly, largely driven by various DNN approaches. These include models optimized directly for visual recognition, cross-modal alignment through contrastive objectives, neural response prediction from scratch, and large language model embeddings.Likewise, different readout mechanisms, ranging from fully linear to spatial-feature factorized methods have been explored for mapping network activations to neural responses. Despite the diversity of these approaches, it remains unclear which method performs best across different visual regions. In this study, we systematically compare these approaches for modeling the human visual system and investigate alternative strategies to improve response predictions. Our findings reveal that for early to mid-level visual areas, response-optimized models with visual inputs offer superior prediction accuracy, while for higher visual regions, embeddings from LLMs based on detailed contextual descriptions of images and task-optimized models pretrained on large vision datasets provide the best fit. Through comparative analysis of these modeling approaches, we identified three distinct regions in the visual cortex: one sensitive primarily to perceptual features of the input that are not captured by linguistic descriptions, another attuned to fine-grained visual details representing semantic information, and a third responsive to abstract, global meanings aligned with linguistic content. We also highlight the critical role of readout mechanisms, proposing a novel scheme that modulates receptive fields and feature maps based on semantic content, resulting in an accuracy boost of 3-23% over existing SOTAs for all models and brain regions. Together, these findings offer key insights into building more precise models of the visual system.

Large language models (LLMs) have shown promise in medical question answering but often struggle with hallucinations and shallow reasoning, particularly in tasks requiring nuanced clinical understanding. Retrieval-augmented generation (RAG) offers a practical and privacy-preserving way to enhance LLMs with external medical knowledge. However, most existing approaches rely on surface-level semantic retrieval and lack the structured reasoning needed for clinical decision support. We introduce MedCoT-RAG, a domain-specific framework that combines causal-aware document retrieval with structured chain-of-thought prompting tailored to medical workflows. This design enables models to retrieve evidence aligned with diagnostic logic and generate step-by-step causal reasoning reflective of real-world clinical practice. Experiments on three diverse medical QA benchmarks show that MedCoT-RAG outperforms strong baselines by up to 10.3% over vanilla RAG and 6.4% over advanced domain-adapted methods, improving accuracy, interpretability, and consistency in complex medical tasks.

Radiologic diagnostic errors-under-reading errors, inattentional blindness, and communication failures-remain prevalent in clinical practice. These issues often stem from missed localized abnormalities, limited global context, and variability in report language. These challenges are amplified in 3D imaging, where clinicians must examine hundreds of slices per scan. Addressing them requires systems with precise localized detection, global volume-level reasoning, and semantically consistent natural language reporting. However, existing 3D vision-language models are unable to meet all three needs jointly, lacking local-global understanding for spatial reasoning and struggling with the variability and noise of uncurated radiology reports. We present MedVista3D, a multi-scale semantic-enriched vision-language pretraining framework for 3D CT analysis. To enable joint disease detection and holistic interpretation, MedVista3D performs local and global image-text alignment for fine-grained representation learning within full-volume context. To address report variability, we apply language model rewrites and introduce a Radiology Semantic Matching Bank for semantics-aware alignment. MedVista3D achieves state-of-the-art performance on zero-shot disease classification, report retrieval, and medical visual question answering, while transferring well to organ segmentation and prognosis prediction. Code and datasets will be released.

Despite the remarkable ability of large vision-language models (LVLMs) in image comprehension, these models frequently generate plausible yet factually incorrect responses, a phenomenon known as hallucination.Recently, in large language models (LLMs), augmenting LLMs by retrieving information from external knowledge resources has been proven as a promising solution to mitigate hallucinations.However, the retrieval augmentation in LVLM significantly lags behind the widespread applications of LVLM. Moreover, when transferred to augmenting LVLMs, sometimes the hallucination degree of the model is even exacerbated.Motivated by the research gap and counter-intuitive phenomenon, we introduce a novel framework, the Active Retrieval-Augmented large vision-language model (ARA), specifically designed to address hallucinations by incorporating three critical dimensions: (i) dissecting the retrieval targets based on the inherent hierarchical structures of images. (ii) pinpointing the most effective retrieval methods and filtering out the reliable retrieval results. (iii) timing the retrieval process to coincide with episodes of low certainty, while circumventing unnecessary retrieval during periods of high certainty. To assess the capability of our proposed ARA model in reducing hallucination, we employ three widely used LVLM models (LLaVA-1.5, Qwen-VL, and mPLUG-Owl2) across four benchmarks. Our empirical observations suggest that by utilizing fitting retrieval mechanisms and timing the retrieval judiciously, we can effectively mitigate the hallucination problem. We hope that this study can provide deeper insights into how to adapt the retrieval augmentation to LVLMs for reducing hallucinations with more effective retrieval and minimal retrieval occurrences.

A long standing goal in neuroscience has been to elucidate the functional organization of the brain. Within higher visual cortex, functional accounts have remained relatively coarse, focusing on regions of interest (ROIs) and taking the form of selectivity for broad categories such as faces, places, bodies, food, or words. Because the identification of such ROIs has typically relied on manually assembled stimulus sets consisting of isolated objects in non-ecological contexts, exploring functional organization without robust a priori hypotheses has been challenging. To overcome these limitations, we introduce a data-driven approach in which we synthesize images predicted to activate a given brain region using paired natural images and fMRI recordings, bypassing the need for category-specific stimuli. Our approach -- Brain Diffusion for Visual Exploration ("BrainDiVE") -- builds on recent generative methods by combining large-scale diffusion models with brain-guided image synthesis. Validating our method, we demonstrate the ability to synthesize preferred images with appropriate semantic specificity for well-characterized category-selective ROIs. We then show that BrainDiVE can characterize differences between ROIs selective for the same high-level category. Finally we identify novel functional subdivisions within these ROIs, validated with behavioral data. These results advance our understanding of the fine-grained functional organization of human visual cortex, and provide well-specified constraints for further examination of cortical organization using hypothesis-driven methods.

We introduce Medal S, a medical segmentation foundation model that supports native-resolution spatial and textual prompts within an end-to-end trainable framework. Unlike text-only methods lacking spatial awareness, Medal S achieves channel-wise alignment between volumetric prompts and text embeddings, mitigating inaccuracies from resolution mismatches. By preserving full 3D context, it efficiently processes multiple native-resolution masks in parallel, enhancing multi-class segmentation performance. A lightweight 3D convolutional module enables precise voxel-space refinement guided by both prompt types, supporting up to 243 classes across CT, MRI, PET, ultrasound, and microscopy modalities in the BiomedSegFM dataset. Medal S offers two prompting modes: a text-only mode, where model predictions serve as spatial prompts for self-refinement without human input, and a hybrid mode, incorporating manual annotations for enhanced flexibility. For 24-class segmentation, parallel spatial prompting reduces inference time by more than 90% compared to sequential prompting. We propose dynamic resampling to address target-patch ratio imbalance, extending SAT and nnU-Net for data augmentation. Furthermore, we develop optimized text preprocessing, a two-stage inference strategy, and post-processing techniques to improve memory efficiency, precision, and inference speed. On the five-modality average on the validation set, Medal S outperforms SAT with a DSC of 75.44 (vs. 69.83), NSD of 77.34 (vs. 71.06), F1 of 38.24 (vs. 24.88), and DSC TP of 65.46 (vs. 46.97). Medal S achieves excellent performance by harmonizing spatial precision with semantic textual guidance, demonstrating superior efficiency and accuracy in multi-class medical segmentation tasks compared to sequential prompt-based approaches. Medal S will be publicly available at https://github.com/yinghemedical/Medal-S.

Due to the lack of paired samples and the low signal-to-noise ratio of functional MRI (fMRI) signals, reconstructing perceived natural images or decoding their semantic contents from fMRI data are challenging tasks. In this work, we propose, for the first time, a task-agnostic fMRI-based brain decoding model, BrainCLIP, which leverages CLIP's cross-modal generalization ability to bridge the modality gap between brain activity, image, and text. Our experiments demonstrate that CLIP can act as a pivot for generic brain decoding tasks, including zero-shot visual categories decoding, fMRI-image/text matching, and fMRI-to-image generation. Specifically, BrainCLIP aims to train a mapping network that transforms fMRI patterns into a well-aligned CLIP embedding space by combining visual and textual supervision. Our experiments show that this combination can boost the decoding model's performance on certain tasks like fMRI-text matching and fMRI-to-image generation. On the zero-shot visual category decoding task, BrainCLIP achieves significantly better performance than BraVL, a recently proposed multi-modal method specifically designed for this task. BrainCLIP can also reconstruct visual stimuli with high semantic fidelity and establishes a new state-of-the-art for fMRI-based natural image reconstruction in terms of high-level semantic features.

Large Vision-Language Models (LVLMs) have shown remarkable performance on many visual-language tasks. However, these models still suffer from multimodal hallucination, which means the generation of objects or content that violates the images. Many existing work detects hallucination by directly judging whether an object exists in an image, overlooking the association between the object and semantics. To address this issue, we propose Hierarchical Feedback Learning with Vision-enhanced Penalty Decoding (HELPD). This framework incorporates hallucination feedback at both object and sentence semantic levels. Remarkably, even with a marginal degree of training, this approach can alleviate over 15% of hallucination. Simultaneously, HELPD penalizes the output logits according to the image attention window to avoid being overly affected by generated text. HELPD can be seamlessly integrated with any LVLMs. Our experiments demonstrate that the proposed framework yields favorable results across multiple hallucination benchmarks. It effectively mitigates hallucination for different LVLMs and concurrently improves their text generation quality.

Natural language could play an important role in developing generalist surgical models by providing a broad source of supervision from raw texts. This flexible form of supervision can enable the model's transferability across datasets and tasks as natural language can be used to reference learned visual concepts or describe new ones. In this work, we present HecVL, a novel hierarchical video-language pretraining approach for building a generalist surgical model. Specifically, we construct a hierarchical video-text paired dataset by pairing the surgical lecture video with three hierarchical levels of texts: at clip-level, atomic actions using transcribed audio texts; at phase-level, conceptual text summaries; and at video-level, overall abstract text of the surgical procedure. Then, we propose a novel fine-to-coarse contrastive learning framework that learns separate embedding spaces for the three video-text hierarchies using a single model. By disentangling embedding spaces of different hierarchical levels, the learned multi-modal representations encode short-term and long-term surgical concepts in the same model. Thanks to the injected textual semantics, we demonstrate that the HecVL approach can enable zero-shot surgical phase recognition without any human annotation. Furthermore, we show that the same HecVL model for surgical phase recognition can be transferred across different surgical procedures and medical centers. The code is available at https://github.com/CAMMA-public/SurgVLP

Recent studies of the emergent capabilities of transformer-based Natural Language Understanding (NLU) models have indicated that they have an understanding of lexical and compositional semantics. We provide evidence that suggests these claims should be taken with a grain of salt: we find that state-of-the-art Natural Language Inference (NLI) models are sensitive towards minor semantics preserving surface-form variations, which lead to sizable inconsistent model decisions during inference. Notably, this behaviour differs from valid and in-depth comprehension of compositional semantics, however does neither emerge when evaluating model accuracy on standard benchmarks nor when probing for syntactic, monotonic, and logically robust reasoning. We propose a novel framework to measure the extent of semantic sensitivity. To this end, we evaluate NLI models on adversarially generated examples containing minor semantics-preserving surface-form input noise. This is achieved using conditional text generation, with the explicit condition that the NLI model predicts the relationship between the original and adversarial inputs as a symmetric equivalence entailment. We systematically study the effects of the phenomenon across NLI models for in- and out-of- domain settings. Our experiments show that semantic sensitivity causes performance degradations of 12.92% and 23.71% average over in- and out-of- domain settings, respectively. We further perform ablation studies, analysing this phenomenon across models, datasets, and variations in inference and show that semantic sensitivity can lead to major inconsistency within model predictions.

Retrieval-augmented generation (RAG) improves large language models (LLMs) by using external knowledge to guide response generation, reducing hallucinations. However, RAG, particularly multi-modal RAG, can introduce new hallucination sources: (i) the retrieval process may select irrelevant pieces (e.g., documents, images) as raw context from the database, and (ii) retrieved images are processed into text-based context via vision-language models (VLMs) or directly used by multi-modal language models (MLLMs) like GPT-4o, which may hallucinate. To address this, we propose a novel framework to evaluate the reliability of multi-modal RAG using two performance measures: (i) the relevancy score (RS), assessing the relevance of retrieved entries to the query, and (ii) the correctness score (CS), evaluating the accuracy of the generated response. We train RS and CS models using a ChatGPT-derived database and human evaluator samples. Results show that both models achieve ~88% accuracy on test data. Additionally, we construct a 5000-sample human-annotated database evaluating the relevancy of retrieved pieces and the correctness of response statements. Our RS model aligns with human preferences 20% more often than CLIP in retrieval, and our CS model matches human preferences ~91% of the time. Finally, we assess various RAG systems' selection and generation performances using RS and CS.

Multimodal models trained on large natural image-text pair datasets have exhibited astounding abilities in generating high-quality images. Medical imaging data is fundamentally different to natural images, and the language used to succinctly capture relevant details in medical data uses a different, narrow but semantically rich, domain-specific vocabulary. Not surprisingly, multi-modal models trained on natural image-text pairs do not tend to generalize well to the medical domain. Developing generative imaging models faithfully representing medical concepts while providing compositional diversity could mitigate the existing paucity of high-quality, annotated medical imaging datasets. In this work, we develop a strategy to overcome the large natural-medical distributional shift by adapting a pre-trained latent diffusion model on a corpus of publicly available chest x-rays (CXR) and their corresponding radiology (text) reports. We investigate the model's ability to generate high-fidelity, diverse synthetic CXR conditioned on text prompts. We assess the model outputs quantitatively using image quality metrics, and evaluate image quality and text-image alignment by human domain experts. We present evidence that the resulting model (RoentGen) is able to create visually convincing, diverse synthetic CXR images, and that the output can be controlled to a new extent by using free-form text prompts including radiology-specific language. Fine-tuning this model on a fixed training set and using it as a data augmentation method, we measure a 5% improvement of a classifier trained jointly on synthetic and real images, and a 3% improvement when trained on a larger but purely synthetic training set. Finally, we observe that this fine-tuning distills in-domain knowledge in the text-encoder and can improve its representation capabilities of certain diseases like pneumothorax by 25%.

Advancements in Large Language Models (LLMs) and their increasing use in medical question-answering necessitate rigorous evaluation of their reliability. A critical challenge lies in hallucination, where models generate plausible yet factually incorrect outputs. In the medical domain, this poses serious risks to patient safety and clinical decision-making. To address this, we introduce MedHallu, the first benchmark specifically designed for medical hallucination detection. MedHallu comprises 10,000 high-quality question-answer pairs derived from PubMedQA, with hallucinated answers systematically generated through a controlled pipeline. Our experiments show that state-of-the-art LLMs, including GPT-4o, Llama-3.1, and the medically fine-tuned UltraMedical, struggle with this binary hallucination detection task, with the best model achieving an F1 score as low as 0.625 for detecting "hard" category hallucinations. Using bidirectional entailment clustering, we show that harder-to-detect hallucinations are semantically closer to ground truth. Through experiments, we also show incorporating domain-specific knowledge and introducing a "not sure" category as one of the answer categories improves the precision and F1 scores by up to 38% relative to baselines.

Objectives: We aim to dynamically retrieve informative demonstrations, enhancing in-context learning in multimodal large language models (MLLMs) for disease classification. Methods: We propose a Retrieval-Augmented In-Context Learning (RAICL) framework, which integrates retrieval-augmented generation (RAG) and in-context learning (ICL) to adaptively select demonstrations with similar disease patterns, enabling more effective ICL in MLLMs. Specifically, RAICL examines embeddings from diverse encoders, including ResNet, BERT, BioBERT, and ClinicalBERT, to retrieve appropriate demonstrations, and constructs conversational prompts optimized for ICL. We evaluated the framework on two real-world multi-modal datasets (TCGA and IU Chest X-ray), assessing its performance across multiple MLLMs (Qwen, Llava, Gemma), embedding strategies, similarity metrics, and varying numbers of demonstrations. Results: RAICL consistently improved classification performance. Accuracy increased from 0.7854 to 0.8368 on TCGA and from 0.7924 to 0.8658 on IU Chest X-ray. Multi-modal inputs outperformed single-modal ones, with text-only inputs being stronger than images alone. The richness of information embedded in each modality will determine which embedding model can be used to get better results. Few-shot experiments showed that increasing the number of retrieved examples further enhanced performance. Across different similarity metrics, Euclidean distance achieved the highest accuracy while cosine similarity yielded better macro-F1 scores. RAICL demonstrated consistent improvements across various MLLMs, confirming its robustness and versatility. Conclusions: RAICL provides an efficient and scalable approach to enhance in-context learning in MLLMs for multimodal disease classification.

Information retrieval (IR) is essential in biomedical knowledge acquisition and clinical decision support. While recent progress has shown that language model encoders perform better semantic retrieval, training such models requires abundant query-article annotations that are difficult to obtain in biomedicine. As a result, most biomedical IR systems only conduct lexical matching. In response, we introduce BioCPT, a first-of-its-kind Contrastively Pre-trained Transformer model for zero-shot biomedical IR. To train BioCPT, we collected an unprecedented scale of 255 million user click logs from PubMed. With such data, we use contrastive learning to train a pair of closely-integrated retriever and re-ranker. Experimental results show that BioCPT sets new state-of-the-art performance on five biomedical IR tasks, outperforming various baselines including much larger models such as GPT-3-sized cpt-text-XL. In addition, BioCPT also generates better biomedical article and sentence representations for semantic evaluations. As such, BioCPT can be readily applied to various real-world biomedical IR tasks. BioCPT API and code are publicly available at https://github.com/ncbi/BioCPT.

This paper describes the results of SemEval 2023 task 7 -- Multi-Evidence Natural Language Inference for Clinical Trial Data (NLI4CT) -- consisting of 2 tasks, a Natural Language Inference (NLI) task, and an evidence selection task on clinical trial data. The proposed challenges require multi-hop biomedical and numerical reasoning, which are of significant importance to the development of systems capable of large-scale interpretation and retrieval of medical evidence, to provide personalized evidence-based care. Task 1, the entailment task, received 643 submissions from 40 participants, and Task 2, the evidence selection task, received 364 submissions from 23 participants. The tasks are challenging, with the majority of submitted systems failing to significantly outperform the majority class baseline on the entailment task, and we observe significantly better performance on the evidence selection task than on the entailment task. Increasing the number of model parameters leads to a direct increase in performance, far more significant than the effect of biomedical pre-training. Future works could explore the limitations of large models for generalization and numerical inference, and investigate methods to augment clinical datasets to allow for more rigorous testing and to facilitate fine-tuning. We envisage that the dataset, models, and results of this task will be useful to the biomedical NLI and evidence retrieval communities. The dataset, competition leaderboard, and website are publicly available.

Decoding non-invasive brain recordings is pivotal for advancing our understanding of human cognition but faces challenges due to individual differences and complex neural signal representations. Traditional methods often require customized models and extensive trials, lacking interpretability in visual reconstruction tasks. Our framework integrates 3D brain structures with visual semantics using a Vision Transformer 3D. This unified feature extractor efficiently aligns fMRI features with multiple levels of visual embeddings, eliminating the need for subject-specific models and allowing extraction from single-trial data. The extractor consolidates multi-level visual features into one network, simplifying integration with Large Language Models (LLMs). Additionally, we have enhanced the fMRI dataset with diverse fMRI-image-related textual data to support multimodal large model development. Integrating with LLMs enhances decoding capabilities, enabling tasks such as brain captioning, complex reasoning, concept localization, and visual reconstruction. Our approach demonstrates superior performance across these tasks, precisely identifying language-based concepts within brain signals, enhancing interpretability, and providing deeper insights into neural processes. These advances significantly broaden the applicability of non-invasive brain decoding in neuroscience and human-computer interaction, setting the stage for advanced brain-computer interfaces and cognitive models.

We propose semantic entropy probes (SEPs), a cheap and reliable method for uncertainty quantification in Large Language Models (LLMs). Hallucinations, which are plausible-sounding but factually incorrect and arbitrary model generations, present a major challenge to the practical adoption of LLMs. Recent work by Farquhar et al. (2024) proposes semantic entropy (SE), which can detect hallucinations by estimating uncertainty in the space semantic meaning for a set of model generations. However, the 5-to-10-fold increase in computation cost associated with SE computation hinders practical adoption. To address this, we propose SEPs, which directly approximate SE from the hidden states of a single generation. SEPs are simple to train and do not require sampling multiple model generations at test time, reducing the overhead of semantic uncertainty quantification to almost zero. We show that SEPs retain high performance for hallucination detection and generalize better to out-of-distribution data than previous probing methods that directly predict model accuracy. Our results across models and tasks suggest that model hidden states capture SE, and our ablation studies give further insights into the token positions and model layers for which this is the case.

Understanding the hidden mechanisms behind human's visual perception is a fundamental question in neuroscience. To that end, investigating into the neural responses of human mind activities, such as functional Magnetic Resonance Imaging (fMRI), has been a significant research vehicle. However, analyzing fMRI signals is challenging, costly, daunting, and demanding for professional training. Despite remarkable progress in fMRI analysis, existing approaches are limited to generating 2D images and far away from being biologically meaningful and practically useful. Under this insight, we propose to generate visually plausible and functionally more comprehensive 3D outputs decoded from brain signals, enabling more sophisticated modeling of fMRI data. Conceptually, we reformulate this task as a {\em fMRI conditioned 3D object generation} problem. We design a novel 3D object representation learning method, Brain3D, that takes as input the fMRI data of a subject who was presented with a 2D image, and yields as output the corresponding 3D object images. The key capabilities of this model include tackling the noises with high-level semantic signals and a two-stage architecture design for progressive high-level information integration. Extensive experiments validate the superior capability of our model over previous state-of-the-art 3D object generation methods. Importantly, we show that our model captures the distinct functionalities of each region of human vision system as well as their intricate interplay relationships, aligning remarkably with the established discoveries in neuroscience. Further, preliminary evaluations indicate that Brain3D can successfully identify the disordered brain regions in simulated scenarios, such as V1, V2, V3, V4, and the medial temporal lobe (MTL) within the human visual system. Our data and code will be available at https://brain-3d.github.io/.

Recent advancements in text-guided image editing have achieved notable success by leveraging natural language prompts for fine-grained semantic control. However, certain editing semantics are challenging to specify precisely using textual descriptions alone. A practical alternative involves learning editing semantics from paired source-target examples. Existing exemplar-based editing methods still rely on text prompts describing the change within paired examples or learning implicit text-based editing instructions. In this paper, we introduce PairEdit, a novel visual editing method designed to effectively learn complex editing semantics from a limited number of image pairs or even a single image pair, without using any textual guidance. We propose a target noise prediction that explicitly models semantic variations within paired images through a guidance direction term. Moreover, we introduce a content-preserving noise schedule to facilitate more effective semantic learning. We also propose optimizing distinct LoRAs to disentangle the learning of semantic variations from content. Extensive qualitative and quantitative evaluations demonstrate that PairEdit successfully learns intricate semantics while significantly improving content consistency compared to baseline methods. Code will be available at https://github.com/xudonmao/PairEdit.

The alignment of vision-language representations endows current Vision-Language Models (VLMs) with strong multi-modal reasoning capabilities. However, the interpretability of the alignment component remains uninvestigated due to the difficulty in mapping the semantics of multi-modal representations into a unified concept set. To address this problem, we propose VL-SAE, a sparse autoencoder that encodes vision-language representations into its hidden activations. Each neuron in its hidden layer correlates to a concept represented by semantically similar images and texts, thereby interpreting these representations with a unified concept set. To establish the neuron-concept correlation, we encourage semantically similar representations to exhibit consistent neuron activations during self-supervised training. First, to measure the semantic similarity of multi-modal representations, we perform their alignment in an explicit form based on cosine similarity. Second, we construct the VL-SAE with a distance-based encoder and two modality-specific decoders to ensure the activation consistency of semantically similar representations. Experiments across multiple VLMs (e.g., CLIP, LLaVA) demonstrate the superior capability of VL-SAE in interpreting and enhancing the vision-language alignment. For interpretation, the alignment between vision and language representations can be understood by comparing their semantics with concepts. For enhancement, the alignment can be strengthened by aligning vision-language representations at the concept level, contributing to performance improvements in downstream tasks, including zero-shot image classification and hallucination elimination. Codes are available at https://github.com/ssfgunner/VL-SAE.

Retrieval augmented generation (RAG) has shown great power in improving Large Language Models (LLMs). However, most existing RAG-based LLMs are dedicated to retrieving single modality information, mainly text; while for many real-world problems, such as healthcare, information relevant to queries can manifest in various modalities such as knowledge graph, text (clinical notes), and complex molecular structure. Thus, being able to retrieve relevant multi-modality domain-specific information, and reason and synthesize diverse knowledge to generate an accurate response is important. To address the gap, we present BioMol-MQA, a new question-answering (QA) dataset on polypharmacy, which is composed of two parts (i) a multimodal knowledge graph (KG) with text and molecular structure for information retrieval; and (ii) challenging questions that designed to test LLM capabilities in retrieving and reasoning over multimodal KG to answer questions. Our benchmarks indicate that existing LLMs struggle to answer these questions and do well only when given the necessary background data, signaling the necessity for strong RAG frameworks.

In this study, we investigate the potential of Large Language Models to complement biomedical knowledge graphs in the training of semantic models for the biomedical and clinical domains. Drawing on the wealth of the UMLS knowledge graph and harnessing cutting-edge Large Language Models, we propose a new state-of-the-art approach for obtaining high-fidelity representations of biomedical concepts and sentences, consisting of three steps: an improved contrastive learning phase, a novel self-distillation phase, and a weight averaging phase. Through rigorous evaluations via the extensive BioLORD testing suite and diverse downstream tasks, we demonstrate consistent and substantial performance improvements over the previous state of the art (e.g. +2pts on MedSTS, +2.5pts on MedNLI-S, +6.1pts on EHR-Rel-B). Besides our new state-of-the-art biomedical model for English, we also distill and release a multilingual model compatible with 50+ languages and finetuned on 7 European languages. Many clinical pipelines can benefit from our latest models. Our new multilingual model enables a range of languages to benefit from our advancements in biomedical semantic representation learning, opening a new avenue for bioinformatics researchers around the world. As a result, we hope to see BioLORD-2023 becoming a precious tool for future biomedical applications.

Large Language Models (LLMs) often produce fluent yet factually incorrect statements-a phenomenon known as hallucination-posing serious risks in high-stakes domains. We present Layer-wise Semantic Dynamics (LSD), a geometric framework for hallucination detection that analyzes the evolution of hidden-state semantics across transformer layers. Unlike prior methods that rely on multiple sampling passes or external verification sources, LSD operates intrinsically within the model's representational space. Using margin-based contrastive learning, LSD aligns hidden activations with ground-truth embeddings derived from a factual encoder, revealing a distinct separation in semantic trajectories: factual responses preserve stable alignment, while hallucinations exhibit pronounced semantic drift across depth. Evaluated on the TruthfulQA and synthetic factual-hallucination datasets, LSD achieves an F1-score of 0.92, AUROC of 0.96, and clustering accuracy of 0.89, outperforming SelfCheckGPT and Semantic Entropy baselines while requiring only a single forward pass. This efficiency yields a 5-20x speedup over sampling-based methods without sacrificing precision or interpretability. LSD offers a scalable, model-agnostic mechanism for real-time hallucination monitoring and provides new insights into the geometry of factual consistency within large language models.

Although Vision Language Models (VLMs) have shown strong generalization in medical imaging, pathology presents unique challenges due to ultra-high resolution, complex tissue structures, and nuanced clinical semantics. These factors make pathology VLMs prone to hallucinations, i.e., generating outputs inconsistent with visual evidence, which undermines clinical trust. Existing RAG approaches in this domain largely depend on text-based knowledge bases, limiting their ability to leverage diagnostic visual cues. To address this, we propose Patho-AgenticRAG, a multimodal RAG framework with a database built on page-level embeddings from authoritative pathology textbooks. Unlike traditional text-only retrieval systems, it supports joint text-image search, enabling direct retrieval of textbook pages that contain both the queried text and relevant visual cues, thus avoiding the loss of critical image-based information. Patho-AgenticRAG also supports reasoning, task decomposition, and multi-turn search interactions, improving accuracy in complex diagnostic scenarios. Experiments show that Patho-AgenticRAG significantly outperforms existing multimodal models in complex pathology tasks like multiple-choice diagnosis and visual question answering. Our project is available at the Patho-AgenticRAG repository: https://github.com/Wenchuan-Zhang/Patho-AgenticRAG.

Drug repurposing plays a critical role in accelerating treatment discovery, especially for complex and rare diseases. Biomedical knowledge graphs (KGs), which encode rich clinical associations, have been widely adopted to support this task. However, existing methods largely overlook common-sense biomedical concept knowledge in real-world labs, such as mechanistic priors indicating that certain drugs are fundamentally incompatible with specific treatments. To address this gap, we propose LLaDR, a Large Language Model-assisted framework for Drug Repurposing, which improves the representation of biomedical concepts within KGs. Specifically, we extract semantically enriched treatment-related textual representations of biomedical entities from large language models (LLMs) and use them to fine-tune knowledge graph embedding (KGE) models. By injecting treatment-relevant knowledge into KGE, LLaDR largely improves the representation of biomedical concepts, enhancing semantic understanding of under-studied or complex indications. Experiments based on benchmarks demonstrate that LLaDR achieves state-of-the-art performance across different scenarios, with case studies on Alzheimer's disease further confirming its robustness and effectiveness. Code is available at https://github.com/xiaomingaaa/LLaDR.

People perceive the world with multiple senses (e.g., through hearing sounds, reading words and seeing objects). However, most existing AI systems only process an individual modality. This paper presents an approach that excels at handling multiple modalities of information with a single model. In our "{SkillNet}" model, different parts of the parameters are specialized for processing different modalities. Unlike traditional dense models that always activate all the model parameters, our model sparsely activates parts of the parameters whose skills are relevant to the task. Such model design enables SkillNet to learn skills in a more interpretable way. We develop our model for five modalities including text, image, sound, video and code. Results show that, SkillNet performs comparably to five modality-specific fine-tuned models. Moreover, our model supports self-supervised pretraining with the same sparsely activated way, resulting in better initialized parameters for different modalities. We find that pretraining significantly improves the performance of SkillNet on five modalities, on par with or even better than baselines with modality-specific pretraining. On the task of Chinese text-to-image retrieval, our final system achieves higher accuracy than existing leading systems including Wukong{ViT-B} and Wenlan 2.0 while using less number of activated parameters.

The recent emergence of Medical Large Vision Language Models (Med-LVLMs) has enhanced medical diagnosis. However, current Med-LVLMs frequently encounter factual issues, often generating responses that do not align with established medical facts. Retrieval-Augmented Generation (RAG), which utilizes external knowledge, can improve the factual accuracy of these models but introduces two major challenges. First, limited retrieved contexts might not cover all necessary information, while excessive retrieval can introduce irrelevant and inaccurate references, interfering with the model's generation. Second, in cases where the model originally responds correctly, applying RAG can lead to an over-reliance on retrieved contexts, resulting in incorrect answers. To address these issues, we propose RULE, which consists of two components. First, we introduce a provably effective strategy for controlling factuality risk through the calibrated selection of the number of retrieved contexts. Second, based on samples where over-reliance on retrieved contexts led to errors, we curate a preference dataset to fine-tune the model, balancing its dependence on inherent knowledge and retrieved contexts for generation. We demonstrate the effectiveness of RULE on three medical VQA datasets, achieving an average improvement of 20.8% in factual accuracy. We publicly release our benchmark and code in https://github.com/richard-peng-xia/RULE.

Although Visual-Language Models (VLMs) have shown impressive capabilities in tasks like visual question answering and image captioning, they still struggle with hallucinations. Analysis of attention distribution in these models shows that VLMs tend to processing textual tokens rather than visual tokens. This imbalance of attention distribution causes VLMs to favor textual knowledge in the case of multimodal knowledge conflicts, resulting in differences from the image information. In this paper, we propose Re-Balancing Contrastive Decoding (RBD) method, which employs textual and visual branches to recalibrate attention distribution in VLMs. Specifically, the textual branch injects image noise to stimulate the model's dependency on text, thereby reducing textual bias. Concurrently, the visual branch focuses on the selection of significant tokens, refining the attention mechanism to highlight the primary subject. This dual-branch strategy enables the RBD method to diminish textual bias while enhancing visual information. Experimental results demonstrate that our method, RBD, outperforms the existing methods by the CHAIR and POPE metrics, mitigate hallucinations without reducing the model's general capabilities.

Visual neural decoding seeks to reconstruct or infer perceived visual stimuli from brain activity patterns, providing critical insights into human cognition and enabling transformative applications in brain-computer interfaces and artificial intelligence. Current approaches, however, remain constrained by the scarcity of high-quality stimulus-brain response pairs and the inherent semantic mismatch between neural representations and visual content. Inspired by perceptual variability and co-adaptive strategy of the biological systems, we propose a novel self-supervised architecture, named NeuroBridge, which integrates Cognitive Prior Augmentation (CPA) with Shared Semantic Projector (SSP) to promote effective cross-modality alignment. Specifically, CPA simulates perceptual variability by applying asymmetric, modality-specific transformations to both EEG signals and images, enhancing semantic diversity. Unlike previous approaches, SSP establishes a bidirectional alignment process through a co-adaptive strategy, which mutually aligns features from two modalities into a shared semantic space for effective cross-modal learning. NeuroBridge surpasses previous state-of-the-art methods under both intra-subject and inter-subject settings. In the intra-subject scenario, it achieves the improvements of 12.3% in top-1 accuracy and 10.2% in top-5 accuracy, reaching 63.2% and 89.9% respectively on a 200-way zero-shot retrieval task. Extensive experiments demonstrate the effectiveness, robustness, and scalability of the proposed framework for neural visual decoding.

Large language models (LLMs) are transforming the landscape of medicine, yet two fundamental challenges persist: keeping up with rapidly evolving medical knowledge and providing verifiable, evidence-grounded reasoning. Retrieval-augmented generation (RAG) has been widely adopted to address these limitations by supplementing model outputs with retrieved evidence. However, whether RAG reliably achieves these goals remains unclear. Here, we present the most comprehensive expert evaluation of RAG in medicine to date. Eighteen medical experts contributed a total of 80,502 annotations, assessing 800 model outputs generated by GPT-4o and Llama-3.1-8B across 200 real-world patient and USMLE-style queries. We systematically decomposed the RAG pipeline into three components: (i) evidence retrieval (relevance of retrieved passages), (ii) evidence selection (accuracy of evidence usage), and (iii) response generation (factuality and completeness of outputs). Contrary to expectation, standard RAG often degraded performance: only 22% of top-16 passages were relevant, evidence selection remained weak (precision 41-43%, recall 27-49%), and factuality and completeness dropped by up to 6% and 5%, respectively, compared with non-RAG variants. Retrieval and evidence selection remain key failure points for the model, contributing to the overall performance drop. We further show that simple yet effective strategies, including evidence filtering and query reformulation, substantially mitigate these issues, improving performance on MedMCQA and MedXpertQA by up to 12% and 8.2%, respectively. These findings call for re-examining RAG's role in medicine and highlight the importance of stage-aware evaluation and deliberate system design for reliable medical LLM applications.

Textual Inversion (TI) is an efficient approach to text-to-image personalization but often fails on complex prompts. We trace these failures to embedding norm inflation: learned tokens drift to out-of-distribution magnitudes, degrading prompt conditioning in pre-norm Transformers. Empirically, we show semantics are primarily encoded by direction in CLIP token space, while inflated norms harm contextualization; theoretically, we analyze how large magnitudes attenuate positional information and hinder residual updates in pre-norm blocks. We propose Directional Textual Inversion (DTI), which fixes the embedding magnitude to an in-distribution scale and optimizes only direction on the unit hypersphere via Riemannian SGD. We cast direction learning as MAP with a von Mises-Fisher prior, yielding a constant-direction prior gradient that is simple and efficient to incorporate. Across personalization tasks, DTI improves text fidelity over TI and TI-variants while maintaining subject similarity. Crucially, DTI's hyperspherical parameterization enables smooth, semantically coherent interpolation between learned concepts (slerp), a capability that is absent in standard TI. Our findings suggest that direction-only optimization is a robust and scalable path for prompt-faithful personalization.

Prior work has analyzed the robustness of visual encoders to image transformations and corruptions, particularly in cases where such alterations are not seen during training. When this occurs, they introduce a form of distribution shift at test time, often leading to performance degradation. The primary focus has been on severe corruptions that, when applied aggressively, distort useful signals necessary for accurate semantic predictions. We take a different perspective by analyzing parameters of the image acquisition process and transformations that may be subtle or even imperceptible to the human eye. We find that such parameters are systematically encoded in the learned visual representations and can be easily recovered. More strikingly, their presence can have a profound impact, either positively or negatively, on semantic predictions. This effect depends on whether there is a strong correlation or anti-correlation between semantic labels and these acquisition-based or processing-based labels. Our code and data are available at: https://github.com/ryan-caesar-ramos/visual-encoder-traces

Multimodal Large Language Models (MLLMs) have achieved impressive advances, yet object hallucination remains a persistent challenge. Existing methods, based on the flawed assumption that omission and fabrication hallucinations share a common cause, often reduce omissions only to trigger more fabrications. In this work, we overturn this view by demonstrating that omission hallucinations arise from insufficient confidence when mapping perceived visual features to linguistic expressions, whereas fabrication hallucinations result from spurious associations within the cross-modal representation space due to statistical biases in the training corpus. Building on findings from visual attention intervention experiments, we propose the Visual-Semantic Attention Potential Field, a conceptual framework that reveals how the model constructs visual evidence to infer the presence or absence of objects. Leveraging this insight, we introduce Visual Potential Field Calibration (VPFC), a plug-and-play hallucination mitigation method that effectively reduces omission hallucinations without introducing additional fabrication hallucinations. Our findings reveal a critical oversight in current object hallucination research and chart new directions for developing more robust and balanced hallucination mitigation strategies.

Medical Dialogue Generation serves a critical role in telemedicine by facilitating the dissemination of medical expertise to patients. Existing studies focus on incorporating textual representations, which have limited their ability to represent the semantics of text, such as ignoring important medical entities. To enhance the model's understanding of the textual semantics and the medical knowledge including entities and relations, we introduce the use of Abstract Meaning Representations (AMR) to construct graphical representations that delineate the roles of language constituents and medical entities within the dialogues. In this paper, We propose a novel framework that models dialogues between patients and healthcare professionals using AMR graphs, where the neural networks incorporate textual and graphical knowledge with a dual attention mechanism. Experimental results show that our framework outperforms strong baseline models in medical dialogue generation, demonstrating the effectiveness of AMR graphs in enhancing the representations of medical knowledge and logical relationships. Furthermore, to support future research in this domain, we provide the corresponding source code at https://github.com/Bernard-Yang/MedDiaAMR.

Large Language Models (LLMs) require efficient knowledge editing (KE) to update factual information, yet existing methods exhibit significant performance decay in multi-hop factual recall. This failure is particularly acute when edits involve intermediate implicit subjects within reasoning chains. Through causal analysis, we reveal that this limitation stems from an oversight of how chained knowledge is dynamically represented and utilized at the neuron level. We discover that during multi hop reasoning, implicit subjects function as query neurons, which sequentially activate corresponding value neurons across transformer layers to accumulate information toward the final answer, a dynamic prior KE work has overlooked. Guided by this insight, we propose ACE: Attribution-Controlled Knowledge Editing for Multi-hop Factual Recall, a framework that leverages neuron-level attribution to identify and edit these critical query-value (Q-V) pathways. ACE provides a mechanistically grounded solution for multi-hop KE, empirically outperforming state-of-the-art methods by 9.44% on GPT-J and 37.46% on Qwen3-8B. Our analysis further reveals more fine-grained activation patterns in Qwen3 and demonstrates that the semantic interpretability of value neurons is orchestrated by query-driven accumulation. These findings establish a new pathway for advancing KE capabilities based on the principled understanding of internal reasoning mechanisms.

This study presents Latent Diffusion Autoencoder (LDAE), a novel encoder-decoder diffusion-based framework for efficient and meaningful unsupervised learning in medical imaging, focusing on Alzheimer disease (AD) using brain MR from the ADNI database as a case study. Unlike conventional diffusion autoencoders operating in image space, LDAE applies the diffusion process in a compressed latent representation, improving computational efficiency and making 3D medical imaging representation learning tractable. To validate the proposed approach, we explore two key hypotheses: (i) LDAE effectively captures meaningful semantic representations on 3D brain MR associated with AD and ageing, and (ii) LDAE achieves high-quality image generation and reconstruction while being computationally efficient. Experimental results support both hypotheses: (i) linear-probe evaluations demonstrate promising diagnostic performance for AD (ROC-AUC: 90%, ACC: 84%) and age prediction (MAE: 4.1 years, RMSE: 5.2 years); (ii) the learned semantic representations enable attribute manipulation, yielding anatomically plausible modifications; (iii) semantic interpolation experiments show strong reconstruction of missing scans, with SSIM of 0.969 (MSE: 0.0019) for a 6-month gap. Even for longer gaps (24 months), the model maintains robust performance (SSIM > 0.93, MSE < 0.004), indicating an ability to capture temporal progression trends; (iv) compared to conventional diffusion autoencoders, LDAE significantly increases inference throughput (20x faster) while also enhancing reconstruction quality. These findings position LDAE as a promising framework for scalable medical imaging applications, with the potential to serve as a foundation model for medical image analysis. Code available at https://github.com/GabrieleLozupone/LDAE

We propose a novel Generalized Zero-Shot learning (GZSL) method that is agnostic to both unseen images and unseen semantic vectors during training. Prior works in this context propose to map high-dimensional visual features to the semantic domain, we believe contributes to the semantic gap. To bridge the gap, we propose a novel low-dimensional embedding of visual instances that is "visually semantic." Analogous to semantic data that quantifies the existence of an attribute in the presented instance, components of our visual embedding quantifies existence of a prototypical part-type in the presented instance. In parallel, as a thought experiment, we quantify the impact of noisy semantic data by utilizing a novel visual oracle to visually supervise a learner. These factors, namely semantic noise, visual-semantic gap and label noise lead us to propose a new graphical model for inference with pairwise interactions between label, semantic data, and inputs. We tabulate results on a number of benchmark datasets demonstrating significant improvement in accuracy over state-of-the-art under both semantic and visual supervision.

Recent advances such as Chain-of-Thought prompting have significantly improved large language models (LLMs) in zero-shot medical reasoning. However, prompting-based methods often remain shallow and unstable, while fine-tuned medical LLMs suffer from poor generalization under distribution shifts and limited adaptability to unseen clinical scenarios. To address these limitations, we present TAGS, a test-time framework that combines a broadly capable generalist with a domain-specific specialist to offer complementary perspectives without any model fine-tuning or parameter updates. To support this generalist-specialist reasoning process, we introduce two auxiliary modules: a hierarchical retrieval mechanism that provides multi-scale exemplars by selecting examples based on both semantic and rationale-level similarity, and a reliability scorer that evaluates reasoning consistency to guide final answer aggregation. TAGS achieves strong performance across nine MedQA benchmarks, boosting GPT-4o accuracy by 13.8%, DeepSeek-R1 by 16.8%, and improving a vanilla 7B model from 14.1% to 23.9%. These results surpass several fine-tuned medical LLMs, without any parameter updates. The code will be available at https://github.com/JianghaoWu/TAGS.

Multimodal language models (MLMs) show promise for clinical decision support and diagnostic reasoning, raising the prospect of end-to-end automated medical image interpretation. However, clinicians are highly selective in adopting AI tools; a model that makes errors on seemingly simple perception tasks such as determining image orientation or identifying whether a CT scan is contrast-enhance are unlikely to be adopted for clinical tasks. We introduce Medblink, a benchmark designed to probe these models for such perceptual abilities. Medblink spans eight clinically meaningful tasks across multiple imaging modalities and anatomical regions, totaling 1,429 multiple-choice questions over 1,605 images. We evaluate 19 state-of-the-art MLMs, including general purpose (GPT4o, Claude 3.5 Sonnet) and domain specific (Med Flamingo, LLaVA Med, RadFM) models. While human annotators achieve 96.4% accuracy, the best-performing model reaches only 65%. These results show that current MLMs frequently fail at routine perceptual checks, suggesting the need to strengthen their visual grounding to support clinical adoption. Data is available on our project page.

The dynamic nature of information necessitates continuously updating large vision-language models (LVLMs). While recent knowledge editing techniques hint at promising directions, they often focus on editing a single modality (vision or language) in isolation. This prevalent practice neglects the inherent multimodality of LVLMs and the continuous nature of knowledge updates, potentially leading to suboptimal editing outcomes when considering the interplay between modalities and the need for ongoing knowledge refinement. To address these limitations, we propose MemEIC, a novel method for Continual and Compositional Knowledge Editing (CCKE) in LVLMs. MemEIC enables compositional editing of both visual and textual knowledge sequentially. Our approach employs a hybrid external-internal editor featuring a dual external memory for cross-modal evidence retrieval and dual LoRA adapters that facilitate disentangled parameter updates for each modality. A key component is a brain-inspired knowledge connector, activated selectively for compositional reasoning, that integrates information across different modalities. Experiments demonstrate that MemEIC significantly improves performance on complex multimodal questions and effectively preserves prior edits, setting a new benchmark for CCKE in LVLMs.

Biomedical literature often uses complex language and inaccessible professional terminologies. That is why simplification plays an important role in improving public health literacy. Applying Natural Language Processing (NLP) models to automate such tasks allows for quick and direct accessibility for lay readers. In this work, we investigate the ability of state-of-the-art large language models (LLMs) on the task of biomedical abstract simplification, using the publicly available dataset for plain language adaptation of biomedical abstracts (PLABA). The methods applied include domain fine-tuning and prompt-based learning (PBL) on: 1) Encoder-decoder models (T5, SciFive, and BART), 2) Decoder-only GPT models (GPT-3.5 and GPT-4) from OpenAI and BioGPT, and 3) Control-token mechanisms on BART-based models. We used a range of automatic evaluation metrics, including BLEU, ROUGE, SARI, and BERTscore, and also conducted human evaluations. BART-Large with Control Token (BART-L-w-CT) mechanisms reported the highest SARI score of 46.54 and T5-base reported the highest BERTscore 72.62. In human evaluation, BART-L-w-CTs achieved a better simplicity score over T5-Base (2.9 vs. 2.2), while T5-Base achieved a better meaning preservation score over BART-L-w-CTs (3.1 vs. 2.6). We also categorised the system outputs with examples, hoping this will shed some light for future research on this task. Our code, fine-tuned models, and data splits are available at https://github.com/HECTA-UoM/PLABA-MU

Traditional image editing typically relies on manual prompting, making it labor-intensive and inaccessible to individuals with limited motor control or language abilities. Leveraging recent advances in brain-computer interfaces (BCIs) and generative models, we propose LoongX, a hands-free image editing approach driven by multimodal neurophysiological signals. LoongX utilizes state-of-the-art diffusion models trained on a comprehensive dataset of 23,928 image editing pairs, each paired with synchronized electroencephalography (EEG), functional near-infrared spectroscopy (fNIRS), photoplethysmography (PPG), and head motion signals that capture user intent. To effectively address the heterogeneity of these signals, LoongX integrates two key modules. The cross-scale state space (CS3) module encodes informative modality-specific features. The dynamic gated fusion (DGF) module further aggregates these features into a unified latent space, which is then aligned with edit semantics via fine-tuning on a diffusion transformer (DiT). Additionally, we pre-train the encoders using contrastive learning to align cognitive states with semantic intentions from embedded natural language. Extensive experiments demonstrate that LoongX achieves performance comparable to text-driven methods (CLIP-I: 0.6605 vs. 0.6558; DINO: 0.4812 vs. 0.4636) and outperforms them when neural signals are combined with speech (CLIP-T: 0.2588 vs. 0.2549). These results highlight the promise of neural-driven generative models in enabling accessible, intuitive image editing and open new directions for cognitive-driven creative technologies. Datasets and code will be released to support future work and foster progress in this emerging area.

Retrieval-Augmented Generation (RAG) models are designed to incorporate external knowledge, reducing hallucinations caused by insufficient parametric (internal) knowledge. However, even with accurate and relevant retrieved content, RAG models can still produce hallucinations by generating outputs that conflict with the retrieved information. Detecting such hallucinations requires disentangling how Large Language Models (LLMs) utilize external and parametric knowledge. Current detection methods often focus on one of these mechanisms or without decoupling their intertwined effects, making accurate detection difficult. In this paper, we investigate the internal mechanisms behind hallucinations in RAG scenarios. We discover hallucinations occur when the Knowledge FFNs in LLMs overemphasize parametric knowledge in the residual stream, while Copying Heads fail to effectively retain or integrate external knowledge from retrieved content. Based on these findings, we propose ReDeEP, a novel method that detects hallucinations by decoupling LLM's utilization of external context and parametric knowledge. Our experiments show that ReDeEP significantly improves RAG hallucination detection accuracy. Additionally, we introduce AARF, which mitigates hallucinations by modulating the contributions of Knowledge FFNs and Copying Heads.

Self-supervised learning (SSL) has recently achieved promising performance for 3D medical image analysis tasks. Most current methods follow existing SSL paradigm originally designed for photographic or natural images, which cannot explicitly and thoroughly exploit the intrinsic similar anatomical structures across varying medical images. This may in fact degrade the quality of learned deep representations by maximizing the similarity among features containing spatial misalignment information and different anatomical semantics. In this work, we propose a new self-supervised learning framework, namely Alice, that explicitly fulfills Anatomical invariance modeling and semantic alignment via elaborately combining discriminative and generative objectives. Alice introduces a new contrastive learning strategy which encourages the similarity between views that are diversely mined but with consistent high-level semantics, in order to learn invariant anatomical features. Moreover, we design a conditional anatomical feature alignment module to complement corrupted embeddings with globally matched semantics and inter-patch topology information, conditioned by the distribution of local image content, which permits to create better contrastive pairs. Our extensive quantitative experiments on three 3D medical image analysis tasks demonstrate and validate the performance superiority of Alice, surpassing the previous best SSL counterpart methods and showing promising ability for united representation learning. Codes are available at https://github.com/alibaba-damo-academy/alice.

Despite the remarkable capabilities of Large Language Models (LLMs) in various NLP tasks, they remain vulnerable to hallucinations due to their limited parametric knowledge and lack of domain-specific expertise. Retrieval-Augmented Generation (RAG) addresses this challenge by incorporating external document retrieval to augment the knowledge base of LLMs. In this approach, RAG retrieves document chunks from an external corpus in response to a query, which are then used as context for the downstream language model to generate an answer. However, these retrieved knowledge sources often include irrelevant or erroneous information, undermining the effectiveness of RAG in downstream tasks. To overcome this limitation, we introduce a compact, efficient, and pluggable module designed to refine external knowledge sources before feeding them to the generator. The module reconstructs retrieved content by extracting the most relevant and supportive information and reorganising it into a concise, query-specific format. Through a three-stage training paradigm - comprising supervised fine-tuning, contrastive multi-task learning, and reinforcement learning-based alignment - it prioritises critical knowledge and aligns it with the generator's preferences. This method enables LLMs to produce outputs that are more accurate, reliable, and contextually appropriate.

Slot Filling (SF) is one of the sub-tasks of Spoken Language Understanding (SLU) which aims to extract semantic constituents from a given natural language utterance. It is formulated as a sequence labeling task. Recently, it has been shown that contextual information is vital for this task. However, existing models employ contextual information in a restricted manner, e.g., using self-attention. Such methods fail to distinguish the effects of the context on the word representation and the word label. To address this issue, in this paper, we propose a novel method to incorporate the contextual information in two different levels, i.e., representation level and task-specific (i.e., label) level. Our extensive experiments on three benchmark datasets on SF show the effectiveness of our model leading to new state-of-the-art results on all three benchmark datasets for the task of SF.

Modern language models can process inputs across diverse languages and modalities. We hypothesize that models acquire this capability through learning a shared representation space across heterogeneous data types (e.g., different languages and modalities), which places semantically similar inputs near one another, even if they are from different modalities/languages. We term this the semantic hub hypothesis, following the hub-and-spoke model from neuroscience (Patterson et al., 2007) which posits that semantic knowledge in the human brain is organized through a transmodal semantic "hub" which integrates information from various modality-specific "spokes" regions. We first show that model representations for semantically equivalent inputs in different languages are similar in the intermediate layers, and that this space can be interpreted using the model's dominant pretraining language via the logit lens. This tendency extends to other data types, including arithmetic expressions, code, and visual/audio inputs. Interventions in the shared representation space in one data type also predictably affect model outputs in other data types, suggesting that this shared representations space is not simply a vestigial byproduct of large-scale training on broad data, but something that is actively utilized by the model during input processing.

Large Language Models (LLMs) demonstrate remarkable versatility in various NLP tasks but encounter distinct challenges in biomedical due to the complexities of language and data scarcity. This paper investigates LLMs application in the biomedical domain by exploring strategies to enhance their performance for the NER task. Our study reveals the importance of meticulously designed prompts in the biomedical. Strategic selection of in-context examples yields a marked improvement, offering ~15-20\% increase in F1 score across all benchmark datasets for biomedical few-shot NER. Additionally, our results indicate that integrating external biomedical knowledge via prompting strategies can enhance the proficiency of general-purpose LLMs to meet the specialized needs of biomedical NER. Leveraging a medical knowledge base, our proposed method, DiRAG, inspired by Retrieval-Augmented Generation (RAG), can boost the zero-shot F1 score of LLMs for biomedical NER. Code is released at https://github.com/masoud-monajati/LLM_Bio_NER

In order to thrive in hostile and ever-changing natural environments, mammalian brains evolved to store large amounts of knowledge about the world and continually integrate new information while avoiding catastrophic forgetting. Despite the impressive accomplishments, large language models (LLMs), even with retrieval-augmented generation (RAG), still struggle to efficiently and effectively integrate a large amount of new experiences after pre-training. In this work, we introduce HippoRAG, a novel retrieval framework inspired by the hippocampal indexing theory of human long-term memory to enable deeper and more efficient knowledge integration over new experiences. HippoRAG synergistically orchestrates LLMs, knowledge graphs, and the Personalized PageRank algorithm to mimic the different roles of neocortex and hippocampus in human memory. We compare HippoRAG with existing RAG methods on multi-hop question answering and show that our method outperforms the state-of-the-art methods remarkably, by up to 20%. Single-step retrieval with HippoRAG achieves comparable or better performance than iterative retrieval like IRCoT while being 10-30 times cheaper and 6-13 times faster, and integrating HippoRAG into IRCoT brings further substantial gains. Finally, we show that our method can tackle new types of scenarios that are out of reach of existing methods. Code and data are available at https://github.com/OSU-NLP-Group/HippoRAG.

Several recent works seek to develop foundation models specifically for medical applications, adapting general-purpose large language models (LLMs) and vision-language models (VLMs) via continued pretraining on publicly available biomedical corpora. These works typically claim that such domain-adaptive pretraining (DAPT) improves performance on downstream medical tasks, such as answering medical licensing exam questions. In this paper, we compare ten public "medical" LLMs and two VLMs against their corresponding base models, arriving at a different conclusion: all medical VLMs and nearly all medical LLMs fail to consistently improve over their base models in the zero-/few-shot prompting and supervised fine-tuning regimes for medical question-answering (QA). For instance, across all tasks and model pairs we consider in the 3-shot setting, medical LLMs only outperform their base models in 22.7% of cases, reach a (statistical) tie in 36.8% of cases, and are significantly worse than their base models in the remaining 40.5% of cases. Our conclusions are based on (i) comparing each medical model head-to-head, directly against the corresponding base model; (ii) optimizing the prompts for each model separately in zero-/few-shot prompting; and (iii) accounting for statistical uncertainty in comparisons. While these basic practices are not consistently adopted in the literature, our ablations show that they substantially impact conclusions. Meanwhile, we find that after fine-tuning on specific QA tasks, medical LLMs can show performance improvements, but the benefits do not carry over to tasks based on clinical notes. Our findings suggest that state-of-the-art general-domain models may already exhibit strong medical knowledge and reasoning capabilities, and offer recommendations to strengthen the conclusions of future studies.

Humans have a natural ability to perform semantic associations with the surrounding objects in the environment. This allows them to create a mental map of the environment, allowing them to navigate on-demand when given linguistic instructions. A natural goal in Vision Language Navigation (VLN) research is to impart autonomous agents with similar capabilities. Recent works take a step towards this goal by creating a semantic spatial map representation of the environment without any labeled data. However, their representations are limited for practical applicability as they do not distinguish between different instances of the same object. In this work, we address this limitation by integrating instance-level information into spatial map representation using a community detection algorithm and utilizing word ontology learned by large language models (LLMs) to perform open-set semantic associations in the mapping representation. The resulting map representation improves the navigation performance by two-fold (233%) on realistic language commands with instance-specific descriptions compared to the baseline. We validate the practicality and effectiveness of our approach through extensive qualitative and quantitative experiments.

Large language models (LLMs) have shown promise for generative and knowledge-intensive tasks including question-answering (QA) tasks. However, the practical deployment still faces challenges, notably the issue of "hallucination", where models generate plausible-sounding but unfaithful or nonsensical information. This issue becomes particularly critical in the medical domain due to the uncommon professional concepts and potential social risks involved. This paper analyses the phenomenon of hallucination in medical generative QA systems using widely adopted LLMs and datasets. Our investigation centers on the identification and comprehension of common problematic answers, with a specific emphasis on hallucination. To tackle this challenge, we present an interactive self-reflection methodology that incorporates knowledge acquisition and answer generation. Through this feedback process, our approach steadily enhances the factuality, consistency, and entailment of the generated answers. Consequently, we harness the interactivity and multitasking ability of LLMs and produce progressively more precise and accurate answers. Experimental results on both automatic and human evaluation demonstrate the superiority of our approach in hallucination reduction compared to baselines.

Pretrained generative models have opened new frontiers in brain decoding by enabling the synthesis of realistic texts and images from non-invasive brain recordings. However, the reliability of such outputs remains questionable--whether they truly reflect semantic activation in the brain, or are merely hallucinated by the powerful generative models. In this paper, we focus on EEG-to-text decoding and address its hallucination issue through the lens of posterior collapse. Acknowledging the underlying mismatch in information capacity between EEG and text, we reframe the decoding task as semantic summarization of core meanings rather than previously verbatim reconstruction of stimulus texts. To this end, we propose the Generative Language Inspection Model (GLIM), which emphasizes learning informative and interpretable EEG representations to improve semantic grounding under heterogeneous and small-scale data conditions. Experiments on the public ZuCo dataset demonstrate that GLIM consistently generates fluent, EEG-grounded sentences without teacher forcing. Moreover, it supports more robust evaluation beyond text similarity, through EEG-text retrieval and zero-shot semantic classification across sentiment categories, relation types, and corpus topics. Together, our architecture and evaluation protocols lay the foundation for reliable and scalable benchmarking in generative brain decoding.

We address prevailing challenges of the brain-powered research, departing from the observation that the literature hardly recover accurate spatial information and require subject-specific models. To address these challenges, we propose UMBRAE, a unified multimodal decoding of brain signals. First, to extract instance-level conceptual and spatial details from neural signals, we introduce an efficient universal brain encoder for multimodal-brain alignment and recover object descriptions at multiple levels of granularity from subsequent multimodal large language model (MLLM). Second, we introduce a cross-subject training strategy mapping subject-specific features to a common feature space. This allows a model to be trained on multiple subjects without extra resources, even yielding superior results compared to subject-specific models. Further, we demonstrate this supports weakly-supervised adaptation to new subjects, with only a fraction of the total training data. Experiments demonstrate that UMBRAE not only achieves superior results in the newly introduced tasks but also outperforms methods in well established tasks. To assess our method, we construct and share with the community a comprehensive brain understanding benchmark BrainHub. Our code and benchmark are available at https://weihaox.github.io/UMBRAE.

Memes, combining text and images, frequently use metaphors to convey persuasive messages, shaping public opinion. Motivated by this, our team engaged in SemEval-2024 Task 4, a hierarchical multi-label classification task designed to identify rhetorical and psychological persuasion techniques embedded within memes. To tackle this problem, we introduced a caption generation step to assess the modality gap and the impact of additional semantic information from images, which improved our result. Our best model utilizes GPT-4 generated captions alongside meme text to fine-tune RoBERTa as the text encoder and CLIP as the image encoder. It outperforms the baseline by a large margin in all 12 subtasks. In particular, it ranked in top-3 across all languages in Subtask 2a, and top-4 in Subtask 2b, demonstrating quantitatively strong performance. The improvement achieved by the introduced intermediate step is likely attributable to the metaphorical essence of images that challenges visual encoders. This highlights the potential for improving abstract visual semantics encoding.

The ability to acquire latent semantics is one of the key properties that determines the performance of language models. One convenient approach to invoke this ability is to prepend metadata (e.g. URLs, domains, and styles) at the beginning of texts in the pre-training data, making it easier for the model to access latent semantics before observing the entire text. Previous studies have reported that this technique actually improves the performance of trained models in downstream tasks; however, this improvement has been observed only in specific downstream tasks, without consistent enhancement in average next-token prediction loss. To understand this phenomenon, we closely investigate how prepending metadata during pre-training affects model performance by examining its behavior using artificial data. Interestingly, we found that this approach produces both positive and negative effects on the downstream tasks. We demonstrate that the effectiveness of the approach depends on whether latent semantics can be inferred from the downstream task's prompt. Specifically, through investigations using data generated by probabilistic context-free grammars, we show that training with metadata helps improve model's performance when the given context is long enough to infer the latent semantics. In contrast, the technique negatively impacts performance when the context lacks the necessary information to make an accurate posterior inference.

Semantic representation and inference is essential for Natural Language Processing (NLP). The state of the art for semantic representation and inference is deep learning, and particularly Recurrent Neural Networks (RNNs), Convolutional Neural Networks (CNNs), and transformer Self-Attention models. This thesis investigates the use of deep learning for novel semantic representation and inference, and makes contributions in the following three areas: creating training data, improving semantic representations and extending inference learning. In terms of creating training data, we contribute the largest publicly available dataset of real-life factual claims for the purpose of automatic claim verification (MultiFC), and we present a novel inference model composed of multi-scale CNNs with different kernel sizes that learn from external sources to infer fact checking labels. In terms of improving semantic representations, we contribute a novel model that captures non-compositional semantic indicators. By definition, the meaning of a non-compositional phrase cannot be inferred from the individual meanings of its composing words (e.g., hot dog). Motivated by this, we operationalize the compositionality of a phrase contextually by enriching the phrase representation with external word embeddings and knowledge graphs. Finally, in terms of inference learning, we propose a series of novel deep learning architectures that improve inference by using syntactic dependencies, by ensembling role guided attention heads, incorporating gating layers, and concatenating multiple heads in novel and effective ways. This thesis consists of seven publications (five published and two under review).

In contrastive self-supervised learning, the common way to learn discriminative representation is to pull different augmented "views" of the same image closer while pushing all other images further apart, which has been proven to be effective. However, it is unavoidable to construct undesirable views containing different semantic concepts during the augmentation procedure. It would damage the semantic consistency of representation to pull these augmentations closer in the feature space indiscriminately. In this study, we introduce feature-level augmentation and propose a novel semantics-consistent feature search (SCFS) method to mitigate this negative effect. The main idea of SCFS is to adaptively search semantics-consistent features to enhance the contrast between semantics-consistent regions in different augmentations. Thus, the trained model can learn to focus on meaningful object regions, improving the semantic representation ability. Extensive experiments conducted on different datasets and tasks demonstrate that SCFS effectively improves the performance of self-supervised learning and achieves state-of-the-art performance on different downstream tasks.

Decoding continuous language from neural signals remains a significant challenge in the intersection of neuroscience and artificial intelligence. We introduce Neuro2Semantic, a novel framework that reconstructs the semantic content of perceived speech from intracranial EEG (iEEG) recordings. Our approach consists of two phases: first, an LSTM-based adapter aligns neural signals with pre-trained text embeddings; second, a corrector module generates continuous, natural text directly from these aligned embeddings. This flexible method overcomes the limitations of previous decoding approaches and enables unconstrained text generation. Neuro2Semantic achieves strong performance with as little as 30 minutes of neural data, outperforming a recent state-of-the-art method in low-data settings. These results highlight the potential for practical applications in brain-computer interfaces and neural decoding technologies.

We introduce Latent Meaning Cells, a deep latent variable model which learns contextualized representations of words by combining local lexical context and metadata. Metadata can refer to granular context, such as section type, or to more global context, such as unique document ids. Reliance on metadata for contextualized representation learning is apropos in the clinical domain where text is semi-structured and expresses high variation in topics. We evaluate the LMC model on the task of zero-shot clinical acronym expansion across three datasets. The LMC significantly outperforms a diverse set of baselines at a fraction of the pre-training cost and learns clinically coherent representations. We demonstrate that not only is metadata itself very helpful for the task, but that the LMC inference algorithm provides an additional large benefit.

Understanding how the brain represents visual information is a fundamental challenge in neuroscience and artificial intelligence. While AI-driven decoding of neural data has provided insights into the human visual system, integrating multimodal neuroimaging signals, such as EEG, MEG, and fMRI, remains a critical hurdle due to their inherent spatiotemporal misalignment. Current approaches often analyze these modalities in isolation, limiting a holistic view of neural representation. In this study, we introduce BrainFLORA, a unified framework for integrating cross-modal neuroimaging data to construct a shared neural representation. Our approach leverages multimodal large language models (MLLMs) augmented with modality-specific adapters and task decoders, achieving state-of-the-art performance in joint-subject visual retrieval task and has the potential to extend multitasking. Combining neuroimaging analysis methods, we further reveal how visual concept representations align across neural modalities and with real world object perception. We demonstrate that the brain's structured visual concept representations exhibit an implicit mapping to physical-world stimuli, bridging neuroscience and machine learning from different modalities of neural imaging. Beyond methodological advancements, BrainFLORA offers novel implications for cognitive neuroscience and brain-computer interfaces (BCIs). Our code is available at https://github.com/ncclab-sustech/BrainFLORA.