Daily Papers

We present a new probing dataset named PROST: Physical Reasoning about Objects Through Space and Time. This dataset contains 18,736 multiple-choice questions made from 14 manually curated templates, covering 10 physical reasoning concepts. All questions are designed to probe both causal and masked language models in a zero-shot setting. We conduct an extensive analysis which demonstrates that state-of-the-art pretrained models are inadequate at physical reasoning: they are influenced by the order in which answer options are presented to them, they struggle when the superlative in a question is inverted (e.g., most <-> least), and increasing the amount of pretraining data and parameters only yields minimal improvements. These results provide support for the hypothesis that current pretrained models' ability to reason about physical interactions is inherently limited by a lack of real world experience. By highlighting these limitations, we hope to motivate the development of models with a human-like understanding of the physical world.

Prostate cancer, a growing global health concern, necessitates precise diagnostic tools, with Magnetic Resonance Imaging (MRI) offering high-resolution soft tissue imaging that significantly enhances diagnostic accuracy. Recent advancements in explainable AI and representation learning have significantly improved prostate cancer diagnosis by enabling automated and precise lesion classification. However, existing explainable AI methods, particularly those based on frameworks like generative adversarial networks (GANs), are predominantly developed for natural image generation, and their application to medical imaging often leads to suboptimal performance due to the unique characteristics and complexity of medical image. To address these challenges, our paper introduces three key contributions. First, we propose ProjectedEx, a generative framework that provides interpretable, multi-attribute explanations, effectively linking medical image features to classifier decisions. Second, we enhance the encoder module by incorporating feature pyramids, which enables multiscale feedback to refine the latent space and improves the quality of generated explanations. Additionally, we conduct comprehensive experiments on both the generator and classifier, demonstrating the clinical relevance and effectiveness of ProjectedEx in enhancing interpretability and supporting the adoption of AI in medical settings. Code will be released at https://github.com/Richardqiyi/ProjectedEx

Prosthetic legs play a pivotal role in clinical rehabilitation, allowing individuals with lower-limb amputations the ability to regain mobility and improve their quality of life. Gait analysis is fundamental for optimizing prosthesis design and alignment, directly impacting the mobility and life quality of individuals with lower-limb amputations. Vision-based machine learning (ML) methods offer a scalable and non-invasive solution to gait analysis, but face challenges in correctly detecting and analyzing prosthesis, due to their unique appearances and new movement patterns. In this paper, we aim to bridge this gap by introducing a multi-purpose dataset, namely ProGait, to support multiple vision tasks including Video Object Segmentation, 2D Human Pose Estimation, and Gait Analysis (GA). ProGait provides 412 video clips from four above-knee amputees when testing multiple newly-fitted prosthetic legs through walking trials, and depicts the presence, contours, poses, and gait patterns of human subjects with transfemoral prosthetic legs. Alongside the dataset itself, we also present benchmark tasks and fine-tuned baseline models to illustrate the practical application and performance of the ProGait dataset. We compared our baseline models against pre-trained vision models, demonstrating improved generalizability when applying the ProGait dataset for prosthesis-specific tasks. Our code is available at https://github.com/pittisl/ProGait and dataset at https://huggingface.co/datasets/ericyxy98/ProGait.

Surgical triplet detection has emerged as a pivotal task in surgical video analysis, with significant implications for performance assessment and the training of novice surgeons. However, existing datasets such as CholecT50 exhibit critical limitations: they lack precise spatial bounding box annotations, provide inconsistent and clinically ungrounded temporal labels, and rely on a single data source, which limits model generalizability.To address these shortcomings, we introduce ProstaTD, a large-scale, multi-institutional dataset for surgical triplet detection, developed from the technically demanding domain of robot-assisted prostatectomy. ProstaTD offers clinically defined temporal boundaries and high-precision bounding box annotations for each structured triplet action. The dataset comprises 60,529 video frames and 165,567 annotated triplet instances, collected from 21 surgeries performed across multiple institutions, reflecting a broad range of surgical practices and intraoperative conditions. The annotation process was conducted under rigorous medical supervision and involved more than 50 contributors, including practicing surgeons and medically trained annotators, through multiple iterative phases of labeling and verification. ProstaTD is the largest and most diverse surgical triplet dataset to date, providing a robust foundation for fair benchmarking, the development of reliable surgical AI systems, and scalable tools for procedural training.

Accurate prostate cancer diagnosis remains challenging. Even when using MRI, radiologists exhibit low specificity and significant inter-observer variability, leading to potential delays or inaccuracies in identifying clinically significant cancers. This leads to numerous unnecessary biopsies and risks of missing clinically significant cancers. Here we present prostate vision contrastive network (ProViCNet), prostate organ-specific vision foundation models for Magnetic Resonance Imaging (MRI) and Trans-Rectal Ultrasound imaging (TRUS) for comprehensive cancer detection. ProViCNet was trained and validated using 4,401 patients across six institutions, as a prostate cancer detection model on radiology images relying on patch-level contrastive learning guided by biopsy confirmed radiologist annotations. ProViCNet demonstrated consistent performance across multiple internal and external validation cohorts with area under the receiver operating curve values ranging from 0.875 to 0.966, significantly outperforming radiologists in the reader study (0.907 versus 0.805, p<0.001) for mpMRI, while achieving 0.670 to 0.740 for TRUS. We also integrated ProViCNet with standard PSA to develop a virtual screening test, and we showed that we can maintain the high sensitivity for detecting clinically significant cancers while more than doubling specificity from 15% to 38% (p<0.001), thereby substantially reducing unnecessary biopsies. These findings highlight that ProViCNet's potential for enhancing prostate cancer diagnosis accuracy and reduce unnecessary biopsies, thereby optimizing diagnostic pathways.

A transhumeral prosthesis restores missing anatomical segments below the shoulder, including the hand. Active prostheses utilize real-valued, continuous sensor data to recognize patient target poses, or goals, and proactively move the artificial limb. Previous studies have examined how well the data collected in stationary poses, without considering the time steps, can help discriminate the goals. In this case study paper, we focus on using time series data from surface electromyography electrodes and kinematic sensors to sequentially recognize patients' goals. Our approach involves transforming the data into discrete events and training an existing process mining-based goal recognition system. Results from data collected in a virtual reality setting with ten subjects demonstrate the effectiveness of our proposed goal recognition approach, which achieves significantly better precision and recall than the state-of-the-art machine learning techniques and is less confident when wrong, which is beneficial when approximating smoother movements of prostheses.

Deep neural networks have introduced significant advancements in the field of machine learning-based analysis of digital pathology images including prostate tissue images. With the help of transfer learning, classification and segmentation performance of neural network models have been further increased. However, due to the absence of large, extensively annotated, publicly available prostate histopathology datasets, several previous studies employ datasets from well-studied computer vision tasks such as ImageNet dataset. In this work, we propose a transfer learning scheme from breast histopathology images to improve prostate cancer detection performance. We validate our approach on annotated prostate whole slide images by using a publicly available breast histopathology dataset as pre-training. We show that the proposed cross-cancer approach outperforms transfer learning from ImageNet dataset.

Multiparametric magnetic resonance imaging (mpMRI) has demonstrated promising results in prostate cancer (PCa) detection using deep convolutional neural networks (CNNs). Recently, transformers have achieved competitive performance compared to CNNs in computer vision. Large-scale transformers need abundant annotated data for training, which are difficult to obtain in medical imaging. Self-supervised learning can effectively leverage unlabeled data to extract useful semantic representations without annotation and its associated costs. This can improve model performance on downstream tasks with limited labelled data and increase generalizability. We introduce a novel end-to-end Cross-Shaped windows (CSwin) transformer UNet model, CSwin UNet, to detect clinically significant prostate cancer (csPCa) in prostate bi-parametric MR imaging (bpMRI) and demonstrate the effectiveness of our proposed self-supervised pre-training framework. Using a large prostate bpMRI dataset with 1500 patients, we first pre-train CSwin transformer using multi-task self-supervised learning to improve data-efficiency and network generalizability. We then finetuned using lesion annotations to perform csPCa detection. Five-fold cross validation shows that self-supervised CSwin UNet achieves 0.888 AUC and 0.545 Average Precision (AP), significantly outperforming four state-of-the-art models (Swin UNETR, DynUNet, Attention UNet, UNet). Using a separate bpMRI dataset with 158 patients, we evaluated our model robustness to external hold-out data. Self-supervised CSwin UNet achieves 0.79 AUC and 0.45 AP, still outperforming all other comparable methods and demonstrating generalization to a dataset shift.

The PI-CAI (Prostate Imaging: Cancer AI) challenge led to expert-level diagnostic algorithms for clinically significant prostate cancer detection. The algorithms receive biparametric MRI scans as input, which consist of T2-weighted and diffusion-weighted scans. These scans can be misaligned due to multiple factors in the scanning process. Image registration can alleviate this issue by predicting the deformation between the sequences. We investigate the effect of image registration on the diagnostic performance of AI-based prostate cancer diagnosis. First, the image registration algorithm, developed in MeVisLab, is analyzed using a dataset with paired lesion annotations. Second, the effect on diagnosis is evaluated by comparing case-level cancer diagnosis performance between using the original dataset, rigidly aligned diffusion-weighted scans, or deformably aligned diffusion-weighted scans. Rigid registration showed no improvement. Deformable registration demonstrated a substantial improvement in lesion overlap (+10% median Dice score) and a positive yet non-significant improvement in diagnostic performance (+0.3% AUROC, p=0.18). Our investigation shows that a substantial improvement in lesion alignment does not directly lead to a significant improvement in diagnostic performance. Qualitative analysis indicated that jointly developing image registration methods and diagnostic AI algorithms could enhance diagnostic accuracy and patient outcomes.

TRPM4 is overexpressed in prostate cancer (PCa) associated with metastasis or recurrence. There is paucity of information pertaining to TRPM4 characterization and functions at single-cell level in PCa. In this study, generalized additive model (GAM) was utilized to model the relationship between TRPM4 and genes shortlisted using Spearman-Kendall dual-filter in aggressive PCa and benign prostate (BP) control cells derived from scRNA-seq dataset. Seven ribosomal genes (RPL10, RPL27, RPL28, RPS2, RPS8, RPS12, and RPS26; averaged into Ribo as the gene set), passed the dual-filter specifically in PCa cells. GAM modeling of TRPM4-Ribo significantly outperformed TRPM4 modeling with alternative cancer gene sets (GSK-3B, mTOR, NF-KB, PI3K/AKT, and Wnt). Cell explanatory power (CEP) classification was devised and verified by cross-validation to identify individual PCa cells most well-predicted by the model. CEP classification binarized PCa cells into top-ranked explanatory power (TREP; more well-predicted by the model) and non-TREP cells. In TRPM4-Ribo GAM plots, distribution pattern of TREP cells shifted at an inflection point (IP) i.e., the specific TRPM4 expression value that further binarized the plot into pre-IP (TRPM4 values below IP) and post-IP (TRPM4 values above IP) regions, producing a quadrant of TREP versus non-TREP cells for each PCa patient. Gene Ontology (GO) enrichment analysis showed that pre-IP TREP cells enriched for immune-related GOs, while post-IP TREP cells enriched for ribosomal, translation, and cell adhesion GOs. In conclusion, the CEP-IP framework based on pairwise genes produces quadrants of cancer cell subpopulations, enabling the identification of distinctive biology with potential therapeutic implications.

Recent advancements in control of prosthetic hands have focused on increasing autonomy through the use of cameras and other sensory inputs. These systems aim to reduce the cognitive load on the user by automatically controlling certain degrees of freedom. In robotics, imitation learning has emerged as a promising approach for learning grasping and complex manipulation tasks while simplifying data collection. Its application to the control of prosthetic hands remains, however, largely unexplored. Bridging this gap could enhance dexterity restoration and enable prosthetic devices to operate in more unconstrained scenarios, where tasks are learned from demonstrations rather than relying on manually annotated sequences. To this end, we present HannesImitationPolicy, an imitation learning-based method to control the Hannes prosthetic hand, enabling object grasping in unstructured environments. Moreover, we introduce the HannesImitationDataset comprising grasping demonstrations in table, shelf, and human-to-prosthesis handover scenarios. We leverage such data to train a single diffusion policy and deploy it on the prosthetic hand to predict the wrist orientation and hand closure for grasping. Experimental evaluation demonstrates successful grasps across diverse objects and conditions. Finally, we show that the policy outperforms a segmentation-based visual servo controller in unstructured scenarios. Additional material is provided on our project page: https://hsp-iit.github.io/HannesImitation

The detailed images produced by Magnetic Resonance Imaging (MRI) provide life-critical information for the diagnosis and treatment of prostate cancer. To provide standardized acquisition, interpretation and usage of the complex MRI images, the PI-RADS v2 guideline was proposed. An automated segmentation following the guideline facilitates consistent and precise lesion detection, staging and treatment. The guideline recommends a division of the prostate into four zones, PZ (peripheral zone), TZ (transition zone), DPU (distal prostatic urethra) and AFS (anterior fibromuscular stroma). Not every zone shares a boundary with the others and is present in every slice. Further, the representations captured by a single model might not suffice for all zones. This motivated us to design a dual-branch convolutional neural network (CNN), where each branch captures the representations of the connected zones separately. Further, the representations from different branches act complementary to each other at the second stage of training, where they are fine-tuned through an unsupervised loss. The loss penalises the difference in predictions from the two branches for the same class. We also incorporate multi-task learning in our framework to further improve the segmentation accuracy. The proposed approach improves the segmentation accuracy of the baseline (mean absolute symmetric distance) by 7.56%, 11.00%, 58.43% and 19.67% for PZ, TZ, DPU and AFS zones respectively.

Histology review is often used as the `gold standard' for disease diagnosis. Computer aided diagnosis tools can potentially help improve current pathology workflows by reducing examination time and interobserver variability. Previous work in cancer grading has focused mainly on classifying pre-defined regions of interest (ROIs), or relied on large amounts of fine-grained labels. In this paper, we propose a two-stage attention-based multiple instance learning model for slide-level cancer grading and weakly-supervised ROI detection and demonstrate its use in prostate cancer. Compared with existing Gleason classification models, our model goes a step further by utilizing visualized saliency maps to select informative tiles for fine-grained grade classification. The model was primarily developed on a large-scale whole slide dataset consisting of 3,521 prostate biopsy slides with only slide-level labels from 718 patients. The model achieved state-of-the-art performance for prostate cancer grading with an accuracy of 85.11\% for classifying benign, low-grade (Gleason grade 3+3 or 3+4), and high-grade (Gleason grade 4+3 or higher) slides on an independent test set.

The recent introduction of synthetic correlated diffusion (CDI^s) imaging has demonstrated significant potential in the realm of clinical decision support for prostate cancer (PCa). CDI^s is a new form of magnetic resonance imaging (MRI) designed to characterize tissue characteristics through the joint correlation of diffusion signal attenuation across different Brownian motion sensitivities. Despite the performance improvement, the CDI^s data for PCa has not been previously made publicly available. In our commitment to advance research efforts for PCa, we introduce Cancer-Net PCa-Data, an open-source benchmark dataset of volumetric CDI^s imaging data of PCa patients. Cancer-Net PCa-Data consists of CDI^s volumetric images from a patient cohort of 200 patient cases, along with full annotations (gland masks, tumor masks, and PCa diagnosis for each tumor). We also analyze the demographic and label region diversity of Cancer-Net PCa-Data for potential biases. Cancer-Net PCa-Data is the first-ever public dataset of CDI^s imaging data for PCa, and is a part of the global open-source initiative dedicated to advancement in machine learning and imaging research to aid clinicians in the global fight against cancer.

In this paper, we propose to regularize ill-posed inverse problems using a deep hierarchical variational autoencoder (HVAE) as an image prior. The proposed method synthesizes the advantages of i) denoiser-based Plug \& Play approaches and ii) generative model based approaches to inverse problems. First, we exploit VAE properties to design an efficient algorithm that benefits from convergence guarantees of Plug-and-Play (PnP) methods. Second, our approach is not restricted to specialized datasets and the proposed PnP-HVAE model is able to solve image restoration problems on natural images of any size. Our experiments show that the proposed PnP-HVAE method is competitive with both SOTA denoiser-based PnP approaches, and other SOTA restoration methods based on generative models.

Shadows in videos are difficult to detect because of the large shadow deformation between frames. In this work, we argue that accounting for shadow deformation is essential when designing a video shadow detection method. To this end, we introduce the shadow deformation attention trajectory (SODA), a new type of video self-attention module, specially designed to handle the large shadow deformations in videos. Moreover, we present a new shadow contrastive learning mechanism (SCOTCH) which aims at guiding the network to learn a unified shadow representation from massive positive shadow pairs across different videos. We demonstrate empirically the effectiveness of our two contributions in an ablation study. Furthermore, we show that SCOTCH and SODA significantly outperforms existing techniques for video shadow detection. Code is available at the project page: https://lihaoliu-cambridge.github.io/scotch_and_soda/

In SPARQL, the query forms SELECT and CONSTRUCT have been the subject of several studies, both theoretical and practical. However, the composition of such queries and their interweaving when forming involved nested queries has not yet received much interest in the literature. We mainly tackle the problem of composing such queries. For this purpose, we introduce a language close to SPARQL where queries can be nested at will, involving either CONSTRUCT or SELECT query forms and provide a formal semantics for it. This semantics is based on a uniform interpretation of queries. This uniformity is due to an extension of the notion of RDF graphs to include isolated items such as variables. As a key feature of this work, we show how classical SELECT queries can be easily encoded as a particular case of CONSTRUCT queries.

Language model alignment has become a critical step in training modern generative language models. The goal of alignment is to finetune a reference model such that the win rate of a sample from the aligned model over a sample from the reference model is high, subject to a KL divergence constraint. Today, we are increasingly using inference-time algorithms (e.g., Best-of-N, controlled decoding, tree search) to decode from language models rather than standard sampling. However, the alignment objective does not capture such inference-time decoding procedures. We show that the existing alignment framework is sub-optimal in view of such inference-time methods. We then modify the alignment objective and propose a framework for inference-aware alignment (IAPO). We prove that for any inference-time decoding algorithm, the optimal solution that optimizes the inference-time win rate of the aligned policy against the reference policy is the solution to the typical RLHF problem with a transformation of the reward. This motivates us to provide the KL-regularized calibrate-and-transform RL (CTRL) algorithm to solve this problem, which involves a reward calibration step and a KL-regularized reward maximization step with a transformation of the calibrated reward. We particularize our study to two important inference-time strategies: best-of-N sampling and best-of-N jailbreaking, where N responses are sampled from the model and the one with the highest or lowest reward is selected. We propose specific transformations for these strategies and demonstrate that our framework offers significant improvements over existing state-of-the-art methods for language model alignment. Empirically, we outperform baselines that are designed without taking inference-time decoding into consideration by 8-12% and 4-9% on inference-time win rates over the Anthropic helpfulness and harmlessness dialog benchmark datasets.

In this report, we introduce the Gemini 2.X model family: Gemini 2.5 Pro and Gemini 2.5 Flash, as well as our earlier Gemini 2.0 Flash and Flash-Lite models. Gemini 2.5 Pro is our most capable model yet, achieving SoTA performance on frontier coding and reasoning benchmarks. In addition to its incredible coding and reasoning skills, Gemini 2.5 Pro is a thinking model that excels at multimodal understanding and it is now able to process up to 3 hours of video content. Its unique combination of long context, multimodal and reasoning capabilities can be combined to unlock new agentic workflows. Gemini 2.5 Flash provides excellent reasoning abilities at a fraction of the compute and latency requirements and Gemini 2.0 Flash and Flash-Lite provide high performance at low latency and cost. Taken together, the Gemini 2.X model generation spans the full Pareto frontier of model capability vs cost, allowing users to explore the boundaries of what is possible with complex agentic problem solving.

This report introduces a new family of multimodal models, Gemini, that exhibit remarkable capabilities across image, audio, video, and text understanding. The Gemini family consists of Ultra, Pro, and Nano sizes, suitable for applications ranging from complex reasoning tasks to on-device memory-constrained use-cases. Evaluation on a broad range of benchmarks shows that our most-capable Gemini Ultra model advances the state of the art in 30 of 32 of these benchmarks - notably being the first model to achieve human-expert performance on the well-studied exam benchmark MMLU, and improving the state of the art in every one of the 20 multimodal benchmarks we examined. We believe that the new capabilities of Gemini models in cross-modal reasoning and language understanding will enable a wide variety of use cases and we discuss our approach toward deploying them responsibly to users.