Daily Papers

Enterprises often own large collections of structured data in the form of large databases or an enterprise data lake. Such data collections come with limited metadata and strict access policies that could limit access to the data contents and, therefore, limit the application of classic retrieval and analysis solutions. As a result, there is a need for solutions that can effectively utilize the available metadata. In this paper, we study the problem of matching table metadata to a business glossary containing data labels and descriptions. The resulting matching enables the use of an available or curated business glossary for retrieval and analysis without or before requesting access to the data contents. One solution to this problem is to use manually-defined rules or similarity measures on column names and glossary descriptions (or their vector embeddings) to find the closest match. However, such approaches need to be tuned through manual labeling and cannot handle many business glossaries that contain a combination of simple as well as complex and long descriptions. In this work, we leverage the power of large language models (LLMs) to design generic matching methods that do not require manual tuning and can identify complex relations between column names and glossaries. We propose methods that utilize LLMs in two ways: a) by generating additional context for column names that can aid with matching b) by using LLMs to directly infer if there is a relation between column names and glossary descriptions. Our preliminary experimental results show the effectiveness of our proposed methods.

Tabular representation learning has recently gained a lot of attention. However, existing approaches only learn a representation from a single table, and thus ignore the potential to learn from the full structure of relational databases, including neighboring tables that can contain important information for a contextualized representation. Moreover, current models are significantly limited in scale, which prevents that they learn from large databases. In this paper, we thus introduce our vision of relational representation learning, that can not only learn from the full relational structure, but also can scale to larger database sizes that are commonly found in real-world. Moreover, we also discuss opportunities and challenges we see along the way to enable this vision and present initial very promising results. Overall, we argue that this direction can lead to foundation models for relational databases that are today only available for text and images.

While most conversational agents are grounded on either free-text or structured knowledge, many knowledge corpora consist of hybrid sources. This paper presents the first conversational agent that supports the full generality of hybrid data access for large knowledge corpora, through a language we developed called SUQL (Structured and Unstructured Query Language). Specifically, SUQL extends SQL with free-text primitives (summary and answer), so information retrieval can be composed with structured data accesses arbitrarily in a formal, succinct, precise, and interpretable notation. With SUQL, we propose the first semantic parser, an LLM with in-context learning, that can handle hybrid data sources. Our in-context learning-based approach, when applied to the HybridQA dataset, comes within 8.9% exact match and 7.1% F1 of the SOTA, which was trained on 62K data samples. More significantly, unlike previous approaches, our technique is applicable to large databases and free-text corpora. We introduce a dataset consisting of crowdsourced questions and conversations on Yelp, a large, real restaurant knowledge base with structured and unstructured data. We show that our few-shot conversational agent based on SUQL finds an entity satisfying all user requirements 90.3% of the time, compared to 63.4% for a baseline based on linearization.

Intelligently extracting and linking complex scientific information from unstructured text is a challenging endeavor particularly for those inexperienced with natural language processing. Here, we present a simple sequence-to-sequence approach to joint named entity recognition and relation extraction for complex hierarchical information in scientific text. The approach leverages a pre-trained large language model (LLM), GPT-3, that is fine-tuned on approximately 500 pairs of prompts (inputs) and completions (outputs). Information is extracted either from single sentences or across sentences in abstracts/passages, and the output can be returned as simple English sentences or a more structured format, such as a list of JSON objects. We demonstrate that LLMs trained in this way are capable of accurately extracting useful records of complex scientific knowledge for three representative tasks in materials chemistry: linking dopants with their host materials, cataloging metal-organic frameworks, and general chemistry/phase/morphology/application information extraction. This approach represents a simple, accessible, and highly-flexible route to obtaining large databases of structured knowledge extracted from unstructured text. An online demo is available at http://www.matscholar.com/info-extraction.

Detection and recognition of a licence plate is important when automating weighbridge services. While many large databases are available for Latin and Chinese alphanumeric license plates, data for Indian License Plates is inadequate. In particular, databases of Indian commercial truck license plates are inadequate, despite the fact that commercial vehicle license plate recognition plays a profound role in terms of logistics management and weighbridge automation. Moreover, models to recognise license plates are not effectively able to generalise to such data due to its challenging nature, and due to the abundant frequency of handwritten license plates, leading to the usage of diverse font styles. Thus, a database and effective models to recognise and detect such license plates are crucial. This paper provides a database on commercial truck license plates, and using state-of-the-art models in real-time object Detection: You Only Look Once Version 7, and SceneText Recognition: Permuted Autoregressive Sequence Models, our method outperforms the other cited references where the maximum accuracy obtained was less than 90%, while we have achieved 95.82% accuracy in our algorithm implementation on the presented challenging license plate dataset. Index Terms- Automatic License Plate Recognition, character recognition, license plate detection, vision transformer.

Recent research in representation learning utilizes large databases of proteins or molecules to acquire knowledge of drug and protein structures through unsupervised learning techniques. These pre-trained representations have proven to significantly enhance the accuracy of subsequent tasks, such as predicting the affinity between drugs and target proteins. In this study, we demonstrate that by incorporating knowledge graphs from diverse sources and modalities into the sequences or SMILES representation, we can further enrich the representation and achieve state-of-the-art results on established benchmark datasets. We provide preprocessed and integrated data obtained from 7 public sources, which encompass over 30M triples. Additionally, we make available the pre-trained models based on this data, along with the reported outcomes of their performance on three widely-used benchmark datasets for drug-target binding affinity prediction found in the Therapeutic Data Commons (TDC) benchmarks. Additionally, we make the source code for training models on benchmark datasets publicly available. Our objective in releasing these pre-trained models, accompanied by clean data for model pretraining and benchmark results, is to encourage research in knowledge-enhanced representation learning.

Existing Text-to-SQL generators require the entire schema to be encoded with the user text. This is expensive or impractical for large databases with tens of thousands of columns. Standard dense retrieval techniques are inadequate for schema subsetting of a large structured database, where the correct semantics of retrieval demands that we rank sets of schema elements rather than individual elements. In response, we propose a two-stage process for effective coverage during retrieval. First, we instruct an LLM to hallucinate a minimal DB schema deemed adequate to answer the query. We use the hallucinated schema to retrieve a subset of the actual schema, by composing the results from multiple dense retrievals. Remarkably, hallucination x2013 generally considered a nuisance x2013 turns out to be actually useful as a bridging mechanism. Since no existing benchmarks exist for schema subsetting on large databases, we introduce three benchmarks. Two semi-synthetic datasets are derived from the union of schemas in two well-known datasets, SPIDER and BIRD, resulting in 4502 and 798 schema elements respectively. A real-life benchmark called SocialDB is sourced from an actual large data warehouse comprising 17844 schema elements. We show that our method1 leads to significantly higher recall than SOTA retrieval-based augmentation methods.

Image copy detection and retrieval from large databases leverage two components. First, a neural network maps an image to a vector representation, that is relatively robust to various transformations of the image. Second, an efficient but approximate similarity search algorithm trades scalability (size and speed) against quality of the search, thereby introducing a source of error. This paper improves the robustness of image copy detection with active indexing, that optimizes the interplay of these two components. We reduce the quantization loss of a given image representation by making imperceptible changes to the image before its release. The loss is back-propagated through the deep neural network back to the image, under perceptual constraints. These modifications make the image more retrievable. Our experiments show that the retrieval and copy detection of activated images is significantly improved. For instance, activation improves by +40% the Recall1@1 on various image transformations, and for several popular indexing structures based on product quantization and locality sensitivity hashing.

This work addresses the problem of speech separation in the Spanish Language using pre-trained deep learning models. As with many speech processing tasks, large databases in other languages different from English are scarce. Therefore this work explores different training strategies using the Conv-TasNet model as a benchmark. A scale-invariant signal distortion ratio (SI-SDR) metric value of 9.9 dB was achieved for the best training strategy. Then, experimentally, we identified an inverse relationship between the speakers' similarity and the model's performance, so an improved ConvTasNet architecture was proposed. The enhanced Conv-TasNet model uses pre-trained speech embeddings to add a between-speakers cosine similarity term in the cost function, yielding an SI-SDR of 10.6 dB. Lastly, final experiments regarding real-time deployment show some drawbacks in the speakers' channel synchronization due to the need to process small speech segments where only one of the speakers appears.

The objectives of this work are cross-modal text-audio and audio-text retrieval, in which the goal is to retrieve the audio content from a pool of candidates that best matches a given written description and vice versa. Text-audio retrieval enables users to search large databases through an intuitive interface: they simply issue free-form natural language descriptions of the sound they would like to hear. To study the tasks of text-audio and audio-text retrieval, which have received limited attention in the existing literature, we introduce three challenging new benchmarks. We first construct text-audio and audio-text retrieval benchmarks from the AudioCaps and Clotho audio captioning datasets. Additionally, we introduce the SoundDescs benchmark, which consists of paired audio and natural language descriptions for a diverse collection of sounds that are complementary to those found in AudioCaps and Clotho. We employ these three benchmarks to establish baselines for cross-modal text-audio and audio-text retrieval, where we demonstrate the benefits of pre-training on diverse audio tasks. We hope that our benchmarks will inspire further research into audio retrieval with free-form text queries. Code, audio features for all datasets used, and the SoundDescs dataset are publicly available at https://github.com/akoepke/audio-retrieval-benchmark.

Retrieving and extracting knowledge from extensive research documents and large databases presents significant challenges for researchers, students, and professionals in today's information-rich era. Existing retrieval systems, which rely on general-purpose Large Language Models (LLMs), often fail to provide accurate responses to domain-specific inquiries. Additionally, the high cost of pretraining or fine-tuning LLMs for specific domains limits their widespread adoption. To address these limitations, we propose a novel methodology that combines the generative capabilities of LLMs with the fast and accurate retrieval capabilities of vector databases. This advanced retrieval system can efficiently handle both tabular and non-tabular data, understand natural language user queries, and retrieve relevant information without fine-tuning. The developed model, Generative Text Retrieval (GTR), is adaptable to both unstructured and structured data with minor refinement. GTR was evaluated on both manually annotated and public datasets, achieving over 90% accuracy and delivering truthful outputs in 87% of cases. Our model achieved state-of-the-art performance with a Rouge-L F1 score of 0.98 on the MSMARCO dataset. The refined model, Generative Tabular Text Retrieval (GTR-T), demonstrated its efficiency in large database querying, achieving an Execution Accuracy (EX) of 0.82 and an Exact-Set-Match (EM) accuracy of 0.60 on the Spider dataset, using an open-source LLM. These efforts leverage Generative AI and In-Context Learning to enhance human-text interaction and make advanced AI capabilities more accessible. By integrating robust retrieval systems with powerful LLMs, our approach aims to democratize access to sophisticated AI tools, improving the efficiency, accuracy, and scalability of AI-driven information retrieval and database querying.

This paper aims to investigate representation learning for large scale visual place recognition, which consists of determining the location depicted in a query image by referring to a database of reference images. This is a challenging task due to the large-scale environmental changes that can occur over time (i.e., weather, illumination, season, traffic, occlusion). Progress is currently challenged by the lack of large databases with accurate ground truth. To address this challenge, we introduce GSV-Cities, a new image dataset providing the widest geographic coverage to date with highly accurate ground truth, covering more than 40 cities across all continents over a 14-year period. We subsequently explore the full potential of recent advances in deep metric learning to train networks specifically for place recognition, and evaluate how different loss functions influence performance. In addition, we show that performance of existing methods substantially improves when trained on GSV-Cities. Finally, we introduce a new fully convolutional aggregation layer that outperforms existing techniques, including GeM, NetVLAD and CosPlace, and establish a new state-of-the-art on large-scale benchmarks, such as Pittsburgh, Mapillary-SLS, SPED and Nordland. The dataset and code are available for research purposes at https://github.com/amaralibey/gsv-cities.

The aim of a Content-Based Image Retrieval (CBIR) system, also known as Query by Image Content (QBIC), is to help users to retrieve relevant images based on their contents. CBIR technologies provide a method to find images in large databases by using unique descriptors from a trained image. The image descriptors include texture, color, intensity and shape of the object inside an image. Several feature-extraction techniques viz., Average RGB, Color Moments, Co-occurrence, Local Color Histogram, Global Color Histogram and Geometric Moment have been critically compared in this paper. However, individually these techniques result in poor performance. So, combinations of these techniques have also been evaluated and results for the most efficient combination of techniques have been presented and optimized for each class of image query. We also propose an improvement in image retrieval performance by introducing the idea of Query modification through image cropping. It enables the user to identify a region of interest and modify the initial query to refine and personalize the image retrieval results.

We investigate the mathematical capabilities of ChatGPT by testing it on publicly available datasets, as well as hand-crafted ones, and measuring its performance against other models trained on a mathematical corpus, such as Minerva. We also test whether ChatGPT can be a useful assistant to professional mathematicians by emulating various use cases that come up in the daily professional activities of mathematicians (question answering, theorem searching). In contrast to formal mathematics, where large databases of formal proofs are available (e.g., the Lean Mathematical Library), current datasets of natural-language mathematics, used to benchmark language models, only cover elementary mathematics. We address this issue by introducing a new dataset: GHOSTS. It is the first natural-language dataset made and curated by working researchers in mathematics that (1) aims to cover graduate-level mathematics and (2) provides a holistic overview of the mathematical capabilities of language models. We benchmark ChatGPT on GHOSTS and evaluate performance against fine-grained criteria. We make this new dataset publicly available to assist a community-driven comparison of ChatGPT with (future) large language models in terms of advanced mathematical comprehension. We conclude that contrary to many positive reports in the media (a potential case of selection bias), ChatGPT's mathematical abilities are significantly below those of an average mathematics graduate student. Our results show that ChatGPT often understands the question but fails to provide correct solutions. Hence, if your goal is to use it to pass a university exam, you would be better off copying from your average peer!

Multi-document summarization (MDS) is a difficult task in Natural Language Processing, aiming to summarize information from several documents. However, the source documents are often insufficient to obtain a qualitative summary. We propose a retriever-guided model combined with non-parametric memory for summary generation. This model retrieves relevant candidates from a database and then generates the summary considering the candidates with a copy mechanism and the source documents. The retriever is implemented with Approximate Nearest Neighbor Search (ANN) to search large databases. Our method is evaluated on the MultiXScience dataset which includes scientific articles. Finally, we discuss our results and possible directions for future work.

The ability to understand visual concepts and replicate and compose these concepts from images is a central goal for computer vision. Recent advances in text-to-image (T2I) models have lead to high definition and realistic image quality generation by learning from large databases of images and their descriptions. However, the evaluation of T2I models has focused on photorealism and limited qualitative measures of visual understanding. To quantify the ability of T2I models in learning and synthesizing novel visual concepts, we introduce ConceptBed, a large-scale dataset that consists of 284 unique visual concepts, 5K unique concept compositions, and 33K composite text prompts. Along with the dataset, we propose an evaluation metric, Concept Confidence Deviation (CCD), that uses the confidence of oracle concept classifiers to measure the alignment between concepts generated by T2I generators and concepts contained in ground truth images. We evaluate visual concepts that are either objects, attributes, or styles, and also evaluate four dimensions of compositionality: counting, attributes, relations, and actions. Our human study shows that CCD is highly correlated with human understanding of concepts. Our results point to a trade-off between learning the concepts and preserving the compositionality which existing approaches struggle to overcome.

There has recently been growing interest in conversational agents with long-term memory which has led to the rapid development of language models that use retrieval-augmented generation (RAG). Until recently, most work on RAG has focused on information retrieval from large databases of texts, like Wikipedia, rather than information from long-form conversations. In this paper, we argue that effective retrieval from long-form conversational data faces two unique problems compared to static database retrieval: 1) time/event-based queries, which requires the model to retrieve information about previous conversations based on time or the order of a conversational event (e.g., the third conversation on Tuesday), and 2) ambiguous queries that require surrounding conversational context to understand. To better develop RAG-based agents that can deal with these challenges, we generate a new dataset of ambiguous and time-based questions that build upon a recent dataset of long-form, simulated conversations, and demonstrate that standard RAG based approaches handle such questions poorly. We then develop a novel retrieval model which combines chained-of-table search methods, standard vector-database retrieval, and a prompting method to disambiguate queries, and demonstrate that this approach substantially improves over current methods at solving these tasks. We believe that this new dataset and more advanced RAG agent can act as a key benchmark and stepping stone towards effective memory augmented conversational agents that can be used in a wide variety of AI applications.

Crossword puzzles are one of the most popular word games, played in different languages all across the world, where riddle style can vary significantly from one country to another. Automated crossword resolution is challenging, and typical solvers rely on large databases of previously solved crosswords. In this work, we extend WebCrow 2.0, an automatic crossword solver, to French, making it the first program for crossword solving in the French language. To cope with the lack of a large repository of clue-answer crossword data, WebCrow 2.0 exploits multiple modules, called experts, that retrieve candidate answers from heterogeneous resources, such as the web, knowledge graphs, and linguistic rules. We compared WebCrow's performance against humans in two different challenges. Despite the limited amount of past crosswords, French WebCrow was competitive, actually outperforming humans in terms of speed and accuracy, thus proving its capabilities to generalize to new languages.

While significant progress has been made on the text-to-SQL task, recent solutions repeatedly encode the same database schema for every question, resulting in unnecessary high inference cost and often overlooking crucial database knowledge. To address these issues, we propose You Only Read Once (YORO), a novel paradigm that directly internalizes database knowledge into the parametric knowledge of a text-to-SQL model during training and eliminates the need for schema encoding during inference. YORO significantly reduces the input token length by 66%-98%. Despite its shorter inputs, our empirical results demonstrate YORO's competitive performances with traditional systems on three benchmarks as well as its significant outperformance on large databases. Furthermore, YORO excels in handling questions with challenging value retrievals such as abbreviation.

We develop a multi-step workflow for the discovery of conventional superconductors, starting with a Bardeen Cooper Schrieffer inspired pre-screening of 1736 materials with high Debye temperature and electronic density of states. Next, we perform electron-phonon coupling calculations for 1058 of them to establish a large and systematic database of BCS superconducting properties. Using the McMillan-Allen-Dynes formula, we identify 105 dynamically stable materials with transition temperatures, Tc>5 K. Additionally, we analyze trends in our dataset and individual materials including MoN, VC, VTe, KB6, Ru3NbC, V3Pt, ScN, LaN2, RuO2, and TaC. We demonstrate that deep-learning(DL) models can predict superconductor properties faster than direct first principles computations. Notably, we find that by predicting the Eliashberg function as an intermediate quantity, we can improve model performance versus a direct DL prediction of Tc. We apply the trained models on the crystallographic open database and pre-screen candidates for further DFT calculations.

The task of converting natural language queries into SQL queries is intricate, necessitating a blend of precise techniques for an accurate translation. The DIN-SQL (Decomposed-In-Context SQL) methodology represents a significant development in this domain. This paper introduces DFIN (Decomposed Focused-In-Context), an innovative extension of DIN-SQL that enhances Text-to-SQL conversion by addressing schema linking errors, which are a major source of inaccuracies. DFIN uniquely alternates between prompting techniques and Retrieval-Augmented Generation (RAG), adapting to the size and complexity of the database schema. A preprocessing phase embeds database definitions and leverages annotated files, akin to those in the BIRD dataset, facilitating the runtime retrieval of pertinent schema information. This strategy significantly reduces the token count for schema linking prompts, enabling the use of a standard GPT-4 model over its larger context variant, thus handling large-scale databases more effectively and economically. Our evaluation on the BIRD dataset, a challenging real-world benchmark, demonstrates that DFIN not only scales efficiently but also improves accuracy, achieving a score of 51.69. This improvement surpasses DIN-SQL method (the current third-place), which is the highest-ranked model employing in-context learning rather than fine-tuning, previously scoring 50.72. The advancement of DFIN underscores the evolving capabilities of in-context learning methodologies combined with advanced language models, offering a promising avenue for future research in complex Text-to-SQL conversion tasks.

Schema linking is a critical bottleneck in applying existing Text-to-SQL models to real-world, large-scale, multi-database environments. Through error analysis, we identify two major challenges in schema linking: (1) Database Retrieval: accurately selecting the target database from a large schema pool, while effectively filtering out irrelevant ones; and (2) Schema Item Grounding: precisely identifying the relevant tables and columns within complex and often redundant schemas for SQL generation. Based on these, we introduce LinkAlign, a novel framework tailored for large-scale databases with thousands of fields. LinkAlign comprises three key steps: multi-round semantic enhanced retrieval and irrelevant information isolation for Challenge 1, and schema extraction enhancement for Challenge 2. Each stage supports both Agent and Pipeline execution modes, enabling balancing efficiency and performance via modular design. To enable more realistic evaluation, we construct AmbiDB, a synthetic dataset designed to reflect the ambiguity of real-world schema linking. Experiments on widely-used Text-to-SQL benchmarks demonstrate that LinkAlign consistently outperforms existing baselines on all schema linking metrics. Notably, it improves the overall Text-to-SQL pipeline and achieves a new state-of-the-art score of 33.09% on the Spider 2.0-Lite benchmark using only open-source LLMs, ranking first on the leaderboard at the time of submission. The codes are available at https://github.com/Satissss/LinkAlign

By leveraging the retrieval of information from external knowledge databases, Large Language Models (LLMs) exhibit enhanced capabilities for accomplishing many knowledge-intensive tasks. However, due to the inherent flaws of current retrieval systems, there might exist irrelevant information within those retrieving top-ranked passages. In this work, we present a comprehensive investigation into the robustness of LLMs to different types of irrelevant information under various conditions. We initially introduce a framework to construct high-quality irrelevant information that ranges from semantically unrelated, partially related, and related to questions. Furthermore, our analysis demonstrates that the constructed irrelevant information not only scores highly on similarity metrics, being highly retrieved by existing systems, but also bears semantic connections to the context. Our investigation reveals that current LLMs still face challenges in discriminating highly semantically related information and can be easily distracted by these irrelevant yet misleading contents. Besides, we also find that current solutions for handling irrelevant information have limitations in improving the robustness of LLMs to such distractions. Resources are available at https://github.com/Di-viner/LLM-Robustness-to-Irrelevant-Information.

The size, diversity, and quality of pretraining datasets critically determine the generalization ability of foundation models. Despite their growing importance in chemoinformatics, the effectiveness of molecular representation learning has been hindered by limitations in existing small molecule datasets. To address this gap, we present MolPILE, large-scale, diverse, and rigorously curated collection of 222 million compounds, constructed from 6 large-scale databases using an automated curation pipeline. We present a comprehensive analysis of current pretraining datasets, highlighting considerable shortcomings for training ML models, and demonstrate how retraining existing models on MolPILE yields improvements in generalization performance. This work provides a standardized resource for model training, addressing the pressing need for an ImageNet-like dataset in molecular chemistry.

Generative models, such as DALL-E, Midjourney, and Stable Diffusion, have societal implications that extend beyond the field of computer science. These models require large image databases like LAION-2B, which contain two billion images. At this scale, manual inspection is difficult and automated analysis is challenging. In addition, recent studies show that duplicated images pose copyright problems for models trained on LAION2B, which hinders its usability. This paper proposes an algorithmic chain that runs with modest compute, that compresses CLIP features to enable efficient duplicate detection, even for vast image volumes. Our approach demonstrates that roughly 700 million images, or about 30\%, of LAION-2B's images are likely duplicated. Our method also provides the histograms of duplication on this dataset, which we use to reveal more examples of verbatim copies by Stable Diffusion and further justify the approach. The current version of the de-duplicated set will be distributed online.

Retrieval-Augmented Generation (RAG) often relies on large vector databases and cross-encoders tuned for large-scale corpora, which can be excessive for small, domain-specific collections. We present MODE (Mixture of Document Experts), a lightweight alternative that replaces fine-grained nearest-neighbor search with cluster-and-route retrieval. Documents are embedded, grouped into semantically coherent clusters, and represented by cached centroids. At query time, we route to the top centroid(s) and retrieve context only within those clusters, eliminating external vector-database infrastructure and reranking while keeping latency low. On HotpotQA and SQuAD corpora with 100-500 chunks, MODE matches or exceeds a dense-retrieval baseline in answer quality while reducing end-to-end retrieval time. Ablations show that cluster granularity and multi-cluster routing control the recall/precision trade-off, and that tighter clusters improve downstream accuracy. MODE offers a practical recipe for small and medium corpora where simplicity, speed, and topical focus matter.

We present MindEye, a novel fMRI-to-image approach to retrieve and reconstruct viewed images from brain activity. Our model comprises two parallel submodules that are specialized for retrieval (using contrastive learning) and reconstruction (using a diffusion prior). MindEye can map fMRI brain activity to any high dimensional multimodal latent space, like CLIP image space, enabling image reconstruction using generative models that accept embeddings from this latent space. We comprehensively compare our approach with other existing methods, using both qualitative side-by-side comparisons and quantitative evaluations, and show that MindEye achieves state-of-the-art performance in both reconstruction and retrieval tasks. In particular, MindEye can retrieve the exact original image even among highly similar candidates indicating that its brain embeddings retain fine-grained image-specific information. This allows us to accurately retrieve images even from large-scale databases like LAION-5B. We demonstrate through ablations that MindEye's performance improvements over previous methods result from specialized submodules for retrieval and reconstruction, improved training techniques, and training models with orders of magnitude more parameters. Furthermore, we show that MindEye can better preserve low-level image features in the reconstructions by using img2img, with outputs from a separate autoencoder. All code is available on GitHub.

To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a clonal family. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic in silico experiments and designs stronger and more stable binders in in vitro wet lab experiments.

Cross-modal drone navigation remains a challenging task in robotics, requiring efficient retrieval of relevant images from large-scale databases based on natural language descriptions. The RoboSense 2025 Track 4 challenge addresses this challenge, focusing on robust, natural language-guided cross-view image retrieval across multiple platforms (drones, satellites, and ground cameras). Current baseline methods, while effective for initial retrieval, often struggle to achieve fine-grained semantic matching between text queries and visual content, especially in complex aerial scenes. To address this challenge, we propose a two-stage retrieval refinement method: Caption-Guided Retrieval System (CGRS) that enhances the baseline coarse ranking through intelligent reranking. Our method first leverages a baseline model to obtain an initial coarse ranking of the top 20 most relevant images for each query. We then use Vision-Language-Model (VLM) to generate detailed captions for these candidate images, capturing rich semantic descriptions of their visual content. These generated captions are then used in a multimodal similarity computation framework to perform fine-grained reranking of the original text query, effectively building a semantic bridge between the visual content and natural language descriptions. Our approach significantly improves upon the baseline, achieving a consistent 5\% improvement across all key metrics (Recall@1, Recall@5, and Recall@10). Our approach win TOP-2 in the challenge, demonstrating the practical value of our semantic refinement strategy in real-world robotic navigation scenarios.

Recent advances in text-to-image synthesis have been enabled by exploiting a combination of language and vision through foundation models. These models are pre-trained on tremendous amounts of text-image pairs sourced from the World Wide Web or other large-scale databases. As the demand for high-quality image generation shifts towards ensuring content alignment between text and image, novel evaluation metrics have been developed with the aim of mimicking human judgments. Thus, researchers have started to collect datasets with increasingly complex annotations to study the compositionality of vision-language models and their incorporation as a quality measure of compositional alignment between text and image contents. In this work, we provide a comprehensive overview of existing text-to-image evaluation metrics and propose a new taxonomy for categorizing these metrics. We also review frequently adopted text-image benchmark datasets before discussing techniques to optimize text-to-image synthesis models towards quality and human preferences. Ultimately, we derive guidelines for improving text-to-image evaluation and discuss the open challenges and current limitations.

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or the use of deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against state of the art deep learning models. We also demonstrate the use of C3PO to classify out-of-distribution examples taken from metabolomics repositories and natural product databases. We also demonstrate the potential use of our approach to find systematic classification errors in existing chemical databases, and show how an ensemble artificial intelligence approach combining generated ontologies, automated literature search, and multimodal vision models can be used to pinpoint potential errors requiring expert validation

In this paper we propose an efficient data-driven solution to self-localization within a floorplan. Floorplan data is readily available, long-term persistent and inherently robust to changes in the visual appearance. Our method does not require retraining per map and location or demand a large database of images of the area of interest. We propose a novel probabilistic model consisting of an observation and a novel temporal filtering module. Operating internally with an efficient ray-based representation, the observation module consists of a single and a multiview module to predict horizontal depth from images and fuses their results to benefit from advantages offered by either methodology. Our method operates on conventional consumer hardware and overcomes a common limitation of competing methods that often demand upright images. Our full system meets real-time requirements, while outperforming the state-of-the-art by a significant margin.

We propose a method for the weakly supervised detection of objects in paintings. At training time, only image-level annotations are needed. This, combined with the efficiency of our multiple-instance learning method, enables one to learn new classes on-the-fly from globally annotated databases, avoiding the tedious task of manually marking objects. We show on several databases that dropping the instance-level annotations only yields mild performance losses. We also introduce a new database, IconArt, on which we perform detection experiments on classes that could not be learned on photographs, such as Jesus Child or Saint Sebastian. To the best of our knowledge, these are the first experiments dealing with the automatic (and in our case weakly supervised) detection of iconographic elements in paintings. We believe that such a method is of great benefit for helping art historians to explore large digital databases.

Recent advancements in Large Language Models (LLMs) have empowered LLM agents to autonomously collect world information, over which to conduct reasoning to solve complex problems. Given this capability, increasing interests have been put into employing LLM agents for predicting international events, which can influence decision-making and shape policy development on an international scale. Despite such a growing interest, there is a lack of a rigorous benchmark of LLM agents' forecasting capability and reliability. To address this gap, we introduce MIRAI, a novel benchmark designed to systematically evaluate LLM agents as temporal forecasters in the context of international events. Our benchmark features an agentic environment with tools for accessing an extensive database of historical, structured events and textual news articles. We refine the GDELT event database with careful cleaning and parsing to curate a series of relational prediction tasks with varying forecasting horizons, assessing LLM agents' abilities from short-term to long-term forecasting. We further implement APIs to enable LLM agents to utilize different tools via a code-based interface. In summary, MIRAI comprehensively evaluates the agents' capabilities in three dimensions: 1) autonomously source and integrate critical information from large global databases; 2) write codes using domain-specific APIs and libraries for tool-use; and 3) jointly reason over historical knowledge from diverse formats and time to accurately predict future events. Through comprehensive benchmarking, we aim to establish a reliable framework for assessing the capabilities of LLM agents in forecasting international events, thereby contributing to the development of more accurate and trustworthy models for international relation analysis.

The creation of manufacturable and editable 3D shapes through Computer-Aided Design (CAD) remains a highly manual and time-consuming task, hampered by the complex topology of boundary representations of 3D solids and unintuitive design tools. While most work in the 3D shape generation literature focuses on representations like meshes, voxels, or point clouds, practical engineering applications demand the modifiability and manufacturability of CAD models and the ability for multi-modal conditional CAD model generation. This paper introduces GenCAD, a generative model that employs autoregressive transformers with a contrastive learning framework and latent diffusion models to transform image inputs into parametric CAD command sequences, resulting in editable 3D shape representations. Extensive evaluations demonstrate that GenCAD significantly outperforms existing state-of-the-art methods in terms of the unconditional and conditional generations of CAD models. Additionally, the contrastive learning framework of GenCAD facilitates the retrieval of CAD models using image queries from large CAD databases, which is a critical challenge within the CAD community. Our results provide a significant step forward in highlighting the potential of generative models to expedite the entire design-to-production pipeline and seamlessly integrate different design modalities.

We introduce a novel problem, i.e., the localization of an input image within a multi-modal reference map represented by a database of 3D scene graphs. These graphs comprise multiple modalities, including object-level point clouds, images, attributes, and relationships between objects, offering a lightweight and efficient alternative to conventional methods that rely on extensive image databases. Given the available modalities, the proposed method SceneGraphLoc learns a fixed-sized embedding for each node (i.e., representing an object instance) in the scene graph, enabling effective matching with the objects visible in the input query image. This strategy significantly outperforms other cross-modal methods, even without incorporating images into the map embeddings. When images are leveraged, SceneGraphLoc achieves performance close to that of state-of-the-art techniques depending on large image databases, while requiring three orders-of-magnitude less storage and operating orders-of-magnitude faster. The code will be made public.

Despite decades of clinical research, sepsis remains a global public health crisis with high mortality, and morbidity. Currently, when sepsis is detected and the underlying pathogen is identified, organ damage may have already progressed to irreversible stages. Effective sepsis management is therefore highly time-sensitive. By systematically analysing trends in the plethora of clinical data available in the intensive care unit (ICU), an early prediction of sepsis could lead to earlier pathogen identification, resistance testing, and effective antibiotic and supportive treatment, and thereby become a life-saving measure. Here, we developed and validated a machine learning (ML) system for the prediction of sepsis in the ICU. Our analysis represents the largest multi-national, multi-centre in-ICU study for sepsis prediction using ML to date. Our dataset contains 156,309 unique ICU admissions, which represent a refined and harmonised subset of five large ICU databases originating from three countries. Using the international consensus definition Sepsis-3, we derived hourly-resolved sepsis label annotations, amounting to 26,734 (17.1%) septic stays. We compared our approach, a deep self-attention model, to several clinical baselines as well as ML baselines and performed an extensive internal and external validation within and across databases. On average, our model was able to predict sepsis with an AUROC of 0.847 pm 0.050 (internal out-of sample validation) and 0.761 pm 0.052 (external validation). For a harmonised prevalence of 17%, at 80% recall our model detects septic patients with 39% precision 3.7 hours in advance.

Activity and property prediction models are the central workhorses in drug discovery and materials sciences, but currently they have to be trained or fine-tuned for new tasks. Without training or fine-tuning, scientific language models could be used for such low-data tasks through their announced zero- and few-shot capabilities. However, their predictive quality at activity prediction is lacking. In this work, we envision a novel type of activity prediction model that is able to adapt to new prediction tasks at inference time, via understanding textual information describing the task. To this end, we propose a new architecture with separate modules for chemical and natural language inputs, and a contrastive pre-training objective on data from large biochemical databases. In extensive experiments, we show that our method CLAMP yields improved predictive performance on few-shot learning benchmarks and zero-shot problems in drug discovery. We attribute the advances of our method to the modularized architecture and to our pre-training objective.

Understanding the relationships between protein sequence, structure and function is a long-standing biological challenge with manifold implications from drug design to our understanding of evolution. Recently, protein language models have emerged as the preferred method for this challenge, thanks to their ability to harness large sequence databases. Yet, their reliance on expansive sequence data and parameter sets limits their flexibility and practicality in real-world scenarios. Concurrently, the recent surge in computationally predicted protein structures unlocks new opportunities in protein representation learning. While promising, the computational burden carried by such complex data still hinders widely-adopted practical applications. To address these limitations, we introduce a novel framework that enhances protein language models by integrating protein structural data. Drawing from recent advances in graph transformers, our approach refines the self-attention mechanisms of pretrained language transformers by integrating structural information with structure extractor modules. This refined model, termed Protein Structure Transformer (PST), is further pretrained on a small protein structure database, using the same masked language modeling objective as traditional protein language models. Empirical evaluations of PST demonstrate its superior parameter efficiency relative to protein language models, despite being pretrained on a dataset comprising only 542K structures. Notably, PST consistently outperforms the state-of-the-art foundation model for protein sequences, ESM-2, setting a new benchmark in protein function prediction. Our findings underscore the potential of integrating structural information into protein language models, paving the way for more effective and efficient protein modeling Code and pretrained models are available at https://github.com/BorgwardtLab/PST.

Database administrators (DBAs) play an important role in managing, maintaining and optimizing database systems. However, it is hard and tedious for DBAs to manage a large number of databases and give timely response (waiting for hours is intolerable in many online cases). In addition, existing empirical methods only support limited diagnosis scenarios, which are also labor-intensive to update the diagnosis rules for database version updates. Recently large language models (LLMs) have shown great potential in various fields. Thus, we propose D-Bot, an LLM-based database diagnosis system that can automatically acquire knowledge from diagnosis documents, and generate reasonable and well-founded diagnosis report (i.e., identifying the root causes and solutions) within acceptable time (e.g., under 10 minutes compared to hours by a DBA). The techniques in D-Bot include (i) offline knowledge extraction from documents, (ii) automatic prompt generation (e.g., knowledge matching, tool retrieval), (iii) root cause analysis using tree search algorithm, and (iv) collaborative mechanism for complex anomalies with multiple root causes. We verify D-Bot on real benchmarks (including 539 anomalies of six typical applications), and the results show that D-Bot can effectively analyze the root causes of unseen anomalies and significantly outperforms traditional methods and vanilla models like GPT-4.

Text-Video Retrieval aims to find the most relevant text (or video) candidate given a video (or text) query from large-scale online databases. Recent work leverages multi-modal large language models (MLLMs) to improve retrieval, especially for long or complex query-candidate pairs. However, we observe that the naive application of MLLMs, i.e., retrieval based on candidate likelihood, introduces candidate prior bias, favoring candidates with inherently higher priors over those more relevant to the query. To this end, we propose a novel retrieval framework, Bidirectional Likelihood Estimation with MLLM (BLiM), which leverages both query and candidate likelihoods by training the model to generate text from a given video as well as video features from a given text. Furthermore, we introduce Candidate Prior Normalization (CPN), a simple yet effective training-free score calibration module designed to mitigate candidate prior bias in candidate likelihood. On four Text-Video Retrieval benchmarks, our BLiM equipped with CPN outperforms previous state-of-the-art models by 6.4 R@1 on average, effectively alleviating candidate prior bias and emphasizing query-candidate relevance. Our in-depth analysis across various multi-modal tasks beyond retrieval highlights the broad applicability of CPN which enhances visual understanding by reducing reliance on textual priors. Code is available at https://github.com/mlvlab/BLiM.

Vector databases manage large collections of embedding vectors. As AI applications are growing rapidly, so are the number of embeddings that need to be stored and indexed. The Faiss library is dedicated to vector similarity search, a core functionality of vector databases. Faiss is a toolkit of indexing methods and related primitives used to search, cluster, compress and transform vectors. This paper first describes the tradeoff space of vector search, then the design principles of Faiss in terms of structure, approach to optimization and interfacing. We benchmark key features of the library and discuss a few selected applications to highlight its broad applicability.

Large-scale image databases remain largely biased towards objects and activities encountered in a select few cultures. This absence of culturally-diverse images, which we refer to as the hidden tail, limits the applicability of pre-trained neural networks and inadvertently excludes researchers from under-represented regions. To begin remedying this issue, we curate Turath-150K, a database of images of the Arab world that reflect objects, activities, and scenarios commonly found there. In the process, we introduce three benchmark databases, Turath Standard, Art, and UNESCO, specialised subsets of the Turath dataset. After demonstrating the limitations of existing networks pre-trained on ImageNet when deployed on such benchmarks, we train and evaluate several networks on the task of image classification. As a consequence of Turath, we hope to engage machine learning researchers in under-represented regions, and to inspire the release of additional culture-focused databases. The database can be accessed here: danikiyasseh.github.io/Turath.

Large-scale image databases such as ImageNet have significantly advanced image classification and other visual recognition tasks. However much of these datasets are constructed only for single-label and coarse object-level classification. For real-world applications, multiple labels and fine-grained categories are often needed, yet very few such datasets exist publicly, especially those of large-scale and high quality. In this work, we contribute to the community a new dataset called iMaterialist Fashion Attribute (iFashion-Attribute) to address this problem in the fashion domain. The dataset is constructed from over one million fashion images with a label space that includes 8 groups of 228 fine-grained attributes in total. Each image is annotated by experts with multiple, high-quality fashion attributes. The result is the first known million-scale multi-label and fine-grained image dataset. We conduct extensive experiments and provide baseline results with modern deep Convolutional Neural Networks (CNNs). Additionally, we demonstrate models pre-trained on iFashion-Attribute achieve superior transfer learning performance on fashion related tasks compared with pre-training from ImageNet or other fashion datasets. Data is available at: https://github.com/visipedia/imat_fashion_comp

The free access to large-scale public databases, together with the fast progress of deep learning techniques, in particular Generative Adversarial Networks, have led to the generation of very realistic fake content with its corresponding implications towards society in this era of fake news. This survey provides a thorough review of techniques for manipulating face images including DeepFake methods, and methods to detect such manipulations. In particular, four types of facial manipulation are reviewed: i) entire face synthesis, ii) identity swap (DeepFakes), iii) attribute manipulation, and iv) expression swap. For each manipulation group, we provide details regarding manipulation techniques, existing public databases, and key benchmarks for technology evaluation of fake detection methods, including a summary of results from those evaluations. Among all the aspects discussed in the survey, we pay special attention to the latest generation of DeepFakes, highlighting its improvements and challenges for fake detection. In addition to the survey information, we also discuss open issues and future trends that should be considered to advance in the field.

The availability of large-scale facial databases, together with the remarkable progresses of deep learning technologies, in particular Generative Adversarial Networks (GANs), have led to the generation of extremely realistic fake facial content, raising obvious concerns about the potential for misuse. Such concerns have fostered the research on manipulation detection methods that, contrary to humans, have already achieved astonishing results in various scenarios. In this study, we focus on the synthesis of entire facial images, which is a specific type of facial manipulation. The main contributions of this study are four-fold: i) a novel strategy to remove GAN "fingerprints" from synthetic fake images based on autoencoders is described, in order to spoof facial manipulation detection systems while keeping the visual quality of the resulting images; ii) an in-depth analysis of the recent literature in facial manipulation detection; iii) a complete experimental assessment of this type of facial manipulation, considering the state-of-the-art fake detection systems (based on holistic deep networks, steganalysis, and local artifacts), remarking how challenging is this task in unconstrained scenarios; and finally iv) we announce a novel public database, named iFakeFaceDB, yielding from the application of our proposed GAN-fingerprint Removal approach (GANprintR) to already very realistic synthetic fake images. The results obtained in our empirical evaluation show that additional efforts are required to develop robust facial manipulation detection systems against unseen conditions and spoof techniques, such as the one proposed in this study.

Biomedical researchers increasingly rely on large-scale structured databases for complex analytical tasks. However, current text-to-SQL systems often struggle to map qualitative scientific questions into executable SQL, particularly when implicit domain reasoning is required. We introduce BiomedSQL, the first benchmark explicitly designed to evaluate scientific reasoning in text-to-SQL generation over a real-world biomedical knowledge base. BiomedSQL comprises 68,000 question/SQL query/answer triples grounded in a harmonized BigQuery knowledge base that integrates gene-disease associations, causal inference from omics data, and drug approval records. Each question requires models to infer domain-specific criteria, such as genome-wide significance thresholds, effect directionality, or trial phase filtering, rather than rely on syntactic translation alone. We evaluate a range of open- and closed-source LLMs across prompting strategies and interaction paradigms. Our results reveal a substantial performance gap: GPT-o3-mini achieves 59.0% execution accuracy, while our custom multi-step agent, BMSQL, reaches 62.6%, both well below the expert baseline of 90.0%. BiomedSQL provides a new foundation for advancing text-to-SQL systems capable of supporting scientific discovery through robust reasoning over structured biomedical knowledge bases. Our dataset is publicly available at https://huggingface.co/datasets/NIH-CARD/BiomedSQL, and our code is open-source at https://github.com/NIH-CARD/biomedsql.

Much research has been done on user-generated textual passwords. Surprisingly, semantic information in such passwords remain underinvestigated, with passwords created by English- and/or Chinese-speaking users being more studied with limited semantics. This paper fills this gap by proposing a general framework based on semantically enhanced PCFG (probabilistic context-free grammars) named SE#PCFG. It allowed us to consider 43 types of semantic information, the richest set considered so far, for semantic password analysis. Applying SE#PCFG to 17 large leaked password databases of user speaking four languages (English, Chinese, German and French), we demonstrate its usefulness and report a wide range of new insights about password semantics at different levels such as cross-website password correlations. Furthermore, based on SE#PCFG and a new systematic smoothing method, we proposed the Semantically Enhanced Password Cracking Architecture (SEPCA). To compare the performance of SEPCA against three state-of-the-art (SOTA) benchmarks in terms of the password coverage rate: two other PCFG variants and FLA. Our experimental results showed that SEPCA outperformed all the three benchmarks consistently and significantly across 52 test cases, by up to 21.53%, 52.55% and 7.86%, respectively, at the user level (with duplicate passwords). At the level of unique passwords, SEPCA also beats the three benchmarks by up to 33.32%, 86.19% and 10.46%, respectively. The results demonstrated the power of SEPCA as a new password cracking framework.

Latent heat thermal energy storage (LHTES) systems are compelling candidates for energy storage, primarily owing to their high storage density. Improving their performance is crucial for developing the next-generation efficient and cost effective devices. Topology optimization (TO) has emerged as a powerful computational tool to design LHTES systems by optimally distributing a high-conductivity material (HCM) and a phase change material (PCM). However, conventional TO typically limits to optimizing the geometry for a fixed, pre-selected materials. This approach does not leverage the large and expanding databases of novel materials. Consequently, the co-design of material and geometry for LHTES remains a challenge and unexplored. To address this limitation, we present an automated design framework for the concurrent optimization of material choice and topology. A key challenge is the discrete nature of material selection, which is incompatible with the gradient-based methods used for TO. We overcome this by using a data-driven variational autoencoder (VAE) to project discrete material databases for both the HCM and PCM onto continuous and differentiable latent spaces. These continuous material representations are integrated into an end-to-end differentiable, transient nonlinear finite-element solver that accounts for phase change. We demonstrate this framework on a problem aimed at maximizing the discharged energy within a specified time, subject to cost constraints. The effectiveness of the proposed method is validated through several illustrative examples.

We present a physics-based humanoid controller that achieves high-fidelity motion imitation and fault-tolerant behavior in the presence of noisy input (e.g. pose estimates from video or generated from language) and unexpected falls. Our controller scales up to learning ten thousand motion clips without using any external stabilizing forces and learns to naturally recover from fail-state. Given reference motion, our controller can perpetually control simulated avatars without requiring resets. At its core, we propose the progressive multiplicative control policy (PMCP), which dynamically allocates new network capacity to learn harder and harder motion sequences. PMCP allows efficient scaling for learning from large-scale motion databases and adding new tasks, such as fail-state recovery, without catastrophic forgetting. We demonstrate the effectiveness of our controller by using it to imitate noisy poses from video-based pose estimators and language-based motion generators in a live and real-time multi-person avatar use case.

Deep face recognition has achieved great success due to large-scale training databases and rapidly developing loss functions. The existing algorithms devote to realizing an ideal idea: minimizing the intra-class distance and maximizing the inter-class distance. However, they may neglect that there are also low quality training images which should not be optimized in this strict way. Considering the imperfection of training databases, we propose that intra-class and inter-class objectives can be optimized in a moderate way to mitigate overfitting problem, and further propose a novel loss function, named sigmoid-constrained hypersphere loss (SFace). Specifically, SFace imposes intra-class and inter-class constraints on a hypersphere manifold, which are controlled by two sigmoid gradient re-scale functions respectively. The sigmoid curves precisely re-scale the intra-class and inter-class gradients so that training samples can be optimized to some degree. Therefore, SFace can make a better balance between decreasing the intra-class distances for clean examples and preventing overfitting to the label noise, and contributes more robust deep face recognition models. Extensive experiments of models trained on CASIA-WebFace, VGGFace2, and MS-Celeb-1M databases, and evaluated on several face recognition benchmarks, such as LFW, MegaFace and IJB-C databases, have demonstrated the superiority of SFace.

Attribute detection is crucial for many computer vision tasks, as it enables systems to describe properties such as color, texture, and material. Current approaches often rely on labor-intensive annotation processes which are inherently limited: objects can be described at an arbitrary level of detail (e.g., color vs. color shades), leading to ambiguities when the annotators are not instructed carefully. Furthermore, they operate within a predefined set of attributes, reducing scalability and adaptability to unforeseen downstream applications. We present Compositional Caching (ComCa), a training-free method for open-vocabulary attribute detection that overcomes these constraints. ComCa requires only the list of target attributes and objects as input, using them to populate an auxiliary cache of images by leveraging web-scale databases and Large Language Models to determine attribute-object compatibility. To account for the compositional nature of attributes, cache images receive soft attribute labels. Those are aggregated at inference time based on the similarity between the input and cache images, refining the predictions of underlying Vision-Language Models (VLMs). Importantly, our approach is model-agnostic, compatible with various VLMs. Experiments on public datasets demonstrate that ComCa significantly outperforms zero-shot and cache-based baselines, competing with recent training-based methods, proving that a carefully designed training-free approach can successfully address open-vocabulary attribute detection.

Large Vision-Language Models (LVLMs) have made remarkable strides in multimodal tasks such as visual question answering, visual grounding, and complex reasoning. However, they remain limited by static training data, susceptibility to hallucinations, and inability to verify claims against up-to-date, external evidence, compromising their performance in dynamic real-world applications. Retrieval-Augmented Generation (RAG) offers a practical solution to mitigate these challenges by allowing the LVLMs to access large-scale knowledge databases via retrieval mechanisms, thereby grounding model outputs in factual, contextually relevant information. Here in this paper, we conduct the first systematic dissection of the multimodal RAG pipeline for LVLMs, explicitly investigating (1) the retrieval phase: on the modality configurations and retrieval strategies, (2) the re-ranking stage: on strategies to mitigate positional biases and improve the relevance of retrieved evidence, and (3) the generation phase: we further investigate how to best integrate retrieved candidates into the final generation process. Finally, we extend to explore a unified agentic framework that integrates re-ranking and generation through self-reflection, enabling LVLMs to select relevant evidence and suppress irrelevant context dynamically. Our full-stack exploration of RAG for LVLMs yields substantial insights, resulting in an average performance boost of 5% without any fine-tuning.

Textual passwords are still the most widely used user authentication mechanism. Due to the close connections between textual passwords and natural languages, advanced technologies in natural language processing (NLP) and machine learning (ML) could be used to model passwords for different purposes such as studying human password-creation behaviors and developing more advanced password cracking methods for informing better defence mechanisms. In this paper, we propose PassTSL (modeling human-created Passwords through Two-Stage Learning), inspired by the popular pretraining-finetuning framework in NLP and deep learning (DL). We report how different pretraining settings affected PassTSL and proved its effectiveness by applying it to six large leaked password databases. Experimental results showed that it outperforms five state-of-the-art (SOTA) password cracking methods on password guessing by a significant margin ranging from 4.11% to 64.69% at the maximum point. Based on PassTSL, we also implemented a password strength meter (PSM), and our experiments showed that it was able to estimate password strength more accurately, causing fewer unsafe errors (overestimating the password strength) than two other SOTA PSMs when they produce the same rate of safe errors (underestimating the password strength): a neural-network based method and zxcvbn. Furthermore, we explored multiple finetuning settings, and our evaluations showed that, even a small amount of additional training data, e.g., only 0.1% of the pretrained data, can lead to over 3% improvement in password guessing on average. We also proposed a heuristic approach to selecting finetuning passwords based on JS (Jensen-Shannon) divergence and experimental results validated its usefulness. In summary, our contributions demonstrate the potential and feasibility of applying advanced NLP and ML methods to password modeling and cracking.

Converting natural language queries into SQL queries is a crucial challenge in both industry and academia, aiming to increase access to databases and large-scale applications. This work examines how in-context learning and chain-of-thought can be utilized to develop a robust solution for text-to-SQL systems. We propose SQL-of-Thought: a multi-agent framework that decomposes the Text2SQL task into schema linking, subproblem identification, query plan generation, SQL generation, and a guided correction loop. Unlike prior systems that rely only on execution-based static correction, we introduce taxonomy-guided dynamic error modification informed by in-context learning. SQL-of-Thought achieves state-of-the-art results on the Spider dataset and its variants, combining guided error taxonomy with reasoning-based query planning.

Large Language Models (LLMs) excel in stand-alone code tasks like HumanEval and MBPP, but struggle with handling entire code repositories. This challenge has prompted research on enhancing LLM-codebase interaction at a repository scale. Current solutions rely on similarity-based retrieval or manual tools and APIs, each with notable drawbacks. Similarity-based retrieval often has low recall in complex tasks, while manual tools and APIs are typically task-specific and require expert knowledge, reducing their generalizability across diverse code tasks and real-world applications. To mitigate these limitations, we introduce \framework, a system that integrates LLM agents with graph database interfaces extracted from code repositories. By leveraging the structural properties of graph databases and the flexibility of the graph query language, \framework enables the LLM agent to construct and execute queries, allowing for precise, code structure-aware context retrieval and code navigation. We assess \framework using three benchmarks: CrossCodeEval, SWE-bench, and EvoCodeBench. Additionally, we develop five real-world coding applications. With a unified graph database schema, \framework demonstrates competitive performance and potential in both academic and real-world environments, showcasing its versatility and efficacy in software engineering. Our application demo: https://github.com/modelscope/modelscope-agent/tree/master/apps/codexgraph_agent.

Large Language Models (LLMs) have demonstrated their potential in hardware design tasks, such as Hardware Description Language (HDL) generation and debugging. Yet, their performance in real-world, repository-level HDL projects with thousands or even tens of thousands of code lines is hindered. To this end, we propose HDLxGraph, a novel framework that integrates Graph Retrieval Augmented Generation (Graph RAG) with LLMs, introducing HDL-specific graph representations by incorporating Abstract Syntax Trees (ASTs) and Data Flow Graphs (DFGs) to capture both code graph view and hardware graph view. HDLxGraph utilizes a dual-retrieval mechanism that not only mitigates the limited recall issues inherent in similarity-based semantic retrieval by incorporating structural information, but also enhances its extensibility to various real-world tasks by a task-specific retrieval finetuning. Additionally, to address the lack of comprehensive HDL search benchmarks, we introduce HDLSearch, a multi-granularity evaluation dataset derived from real-world repository-level projects. Experimental results demonstrate that HDLxGraph significantly improves average search accuracy, debugging efficiency and completion quality by 12.04%, 12.22% and 5.04% compared to similarity-based RAG, respectively. The code of HDLxGraph and collected HDLSearch benchmark are available at https://github.com/Nick-Zheng-Q/HDLxGraph.

This survey explores the synergistic potential of Large Language Models (LLMs) and Vector Databases (VecDBs), a burgeoning but rapidly evolving research area. With the proliferation of LLMs comes a host of challenges, including hallucinations, outdated knowledge, prohibitive commercial application costs, and memory issues. VecDBs emerge as a compelling solution to these issues by offering an efficient means to store, retrieve, and manage the high-dimensional vector representations intrinsic to LLM operations. Through this nuanced review, we delineate the foundational principles of LLMs and VecDBs and critically analyze their integration's impact on enhancing LLM functionalities. This discourse extends into a discussion on the speculative future developments in this domain, aiming to catalyze further research into optimizing the confluence of LLMs and VecDBs for advanced data handling and knowledge extraction capabilities.

Enterprise applications of Large Language Models (LLMs) hold promise for question answering on enterprise SQL databases. However, the extent to which LLMs can accurately respond to enterprise questions in such databases remains unclear, given the absence of suitable Text-to-SQL benchmarks tailored to enterprise settings. Additionally, the potential of Knowledge Graphs (KGs) to enhance LLM-based question answering by providing business context is not well understood. This study aims to evaluate the accuracy of LLM-powered question answering systems in the context of enterprise questions and SQL databases, while also exploring the role of knowledge graphs in improving accuracy. To achieve this, we introduce a benchmark comprising an enterprise SQL schema in the insurance domain, a range of enterprise queries encompassing reporting to metrics, and a contextual layer incorporating an ontology and mappings that define a knowledge graph. Our primary finding reveals that question answering using GPT-4, with zero-shot prompts directly on SQL databases, achieves an accuracy of 16%. Notably, this accuracy increases to 54% when questions are posed over a Knowledge Graph representation of the enterprise SQL database. Therefore, investing in Knowledge Graph provides higher accuracy for LLM powered question answering systems.

Large language models (LLMs) with memory are computationally universal. However, mainstream LLMs are not taking full advantage of memory, and the designs are heavily influenced by biological brains. Due to their approximate nature and proneness to the accumulation of errors, conventional neural memory mechanisms cannot support LLMs to simulate complex reasoning. In this paper, we seek inspiration from modern computer architectures to augment LLMs with symbolic memory for complex multi-hop reasoning. Such a symbolic memory framework is instantiated as an LLM and a set of SQL databases, where the LLM generates SQL instructions to manipulate the SQL databases. We validate the effectiveness of the proposed memory framework on a synthetic dataset requiring complex reasoning. The project website is available at https://chatdatabase.github.io/ .

Tabular data, ubiquitous and rich in informational value, is an increasing focus for deep representation learning, yet progress is hindered by studies centered on single tables or isolated databases, which limits model capabilities due to data scale. While collaborative learning approaches such as federated learning, transfer learning, split learning, and tabular foundation models aim to learn from multiple correlated databases, they are challenged by a scarcity of real-world interconnected tabular resources. Current data lakes and corpora largely consist of isolated databases lacking defined inter-database correlations. To overcome this, we introduce WikiDBGraph, a large-scale graph of 100,000 real-world tabular databases from WikiData, interconnected by 17 million edges and characterized by 13 node and 12 edge properties derived from its database schema and data distribution. WikiDBGraph's weighted edges identify both instance- and feature-overlapped databases. Experiments on these newly identified databases confirm that collaborative learning yields superior performance, thereby offering considerable promise for structured foundation model training while also exposing key challenges and future directions for learning from interconnected tabular data.

Relational databases often suffer from uninformative descriptors of table contents, such as ambiguous columns and hard-to-interpret values, impacting both human users and Text-to-SQL models. This paper explores the use of large language models (LLMs) to generate informative column descriptions as a semantic layer for relational databases. Using the BIRD-Bench development set, we created ColSQL, a dataset with gold-standard column descriptions generated and refined by LLMs and human annotators. We evaluated several instruction-tuned models, finding that GPT-4o and Command R+ excelled in generating high-quality descriptions. Additionally, we applied an LLM-as-a-judge to evaluate model performance. Although this method does not align well with human evaluations, we included it to explore its potential and to identify areas for improvement. More work is needed to improve the reliability of automatic evaluations for this task. We also find that detailed column descriptions significantly improve Text-to-SQL execution accuracy, especially when columns are uninformative. This study establishes LLMs as effective tools for generating detailed metadata, enhancing the usability of relational databases.

The development of successful artificial intelligence models for chest X-ray analysis relies on large, diverse datasets with high-quality annotations. While several databases of chest X-ray images have been released, most include disease diagnosis labels but lack detailed pixel-level anatomical segmentation labels. To address this gap, we introduce an extensive chest X-ray multi-center segmentation dataset with uniform and fine-grain anatomical annotations for images coming from six well-known publicly available databases: CANDID-PTX, ChestX-ray8, Chexpert, MIMIC-CXR-JPG, Padchest, and VinDr-CXR, resulting in 676,803 segmentation masks. Our methodology utilizes the HybridGNet model to ensure consistent and high-quality segmentations across all datasets. Rigorous validation, including expert physician evaluation and automatic quality control, was conducted to validate the resulting masks. Additionally, we provide individualized quality indices per mask and an overall quality estimation per dataset. This dataset serves as a valuable resource for the broader scientific community, streamlining the development and assessment of innovative methodologies in chest X-ray analysis. The CheXmask dataset is publicly available at: https://physionet.org/content/chexmask-cxr-segmentation-data/.

Recent advances in large language models (LLMs) have demonstrated remarkable potential in the field of natural language processing. Unfortunately, LLMs face significant security and ethical risks. Although techniques such as safety alignment are developed for defense, prior researches reveal the possibility of bypassing such defenses through well-designed jailbreak attacks. In this paper, we propose QueryAttack, a novel framework to examine the generalizability of safety alignment. By treating LLMs as knowledge databases, we translate malicious queries in natural language into structured non-natural query language to bypass the safety alignment mechanisms of LLMs. We conduct extensive experiments on mainstream LLMs, and the results show that QueryAttack not only can achieve high attack success rates (ASRs), but also can jailbreak various defense methods. Furthermore, we tailor a defense method against QueryAttack, which can reduce ASR by up to 64% on GPT-4-1106. Our code is available at https://github.com/horizonsinzqs/QueryAttack.

Several large-scale datasets (e.g., WikiSQL, Spider) for developing natural language interfaces to databases have recently been proposed. These datasets cover a wide breadth of domains but fall short on some essential domains, such as finance and accounting. Given that accounting databases are used worldwide, particularly by non-technical people, there is an imminent need to develop models that could help extract information from accounting databases via natural language queries. In this resource paper, we aim to fill this gap by proposing a new large-scale Text-to-SQL dataset for the accounting and financial domain: BookSQL. The dataset consists of 100k natural language queries-SQL pairs, and accounting databases of 1 million records. We experiment with and analyze existing state-of-the-art models (including GPT-4) for the Text-to-SQL task on BookSQL. We find significant performance gaps, thus pointing towards developing more focused models for this domain.

Large language models (LLMs) are increasingly used as personal agents, accessing sensitive user data such as calendars, emails, and medical records. Users currently face a trade-off: They can send private records, many of which are stored in remote databases, to powerful but untrusted LLM providers, increasing their exposure risk. Alternatively, they can run less powerful models locally on trusted devices. We bridge this gap. Our Socratic Chain-of-Thought Reasoning first sends a generic, non-private user query to a powerful, untrusted LLM, which generates a Chain-of-Thought (CoT) prompt and detailed sub-queries without accessing user data. Next, we embed these sub-queries and perform encrypted sub-second semantic search using our Homomorphically Encrypted Vector Database across one million entries of a single user's private data. This represents a realistic scale of personal documents, emails, and records accumulated over years of digital activity. Finally, we feed the CoT prompt and the decrypted records to a local language model and generate the final response. On the LoCoMo long-context QA benchmark, our hybrid framework, combining GPT-4o with a local Llama-3.2-1B model, outperforms using GPT-4o alone by up to 7.1 percentage points. This demonstrates a first step toward systems where tasks are decomposed and split between untrusted strong LLMs and weak local ones, preserving user privacy.

With the introduction of ChatGPT, Large Language Models (LLMs) have received enormous attention in healthcare. Despite their potential benefits, researchers have underscored various ethical implications. While individual instances have drawn much attention, the debate lacks a systematic overview of practical applications currently researched and ethical issues connected to them. Against this background, this work aims to map the ethical landscape surrounding the current stage of deployment of LLMs in medicine and healthcare. Electronic databases and preprint servers were queried using a comprehensive search strategy. Studies were screened and extracted following a modified rapid review approach. Methodological quality was assessed using a hybrid approach. For 53 records, a meta-aggregative synthesis was performed. Four fields of applications emerged and testify to a vivid exploration phase. Advantages of using LLMs are attributed to their capacity in data analysis, personalized information provisioning, support in decision-making, mitigating information loss and enhancing information accessibility. However, we also identifies recurrent ethical concerns connected to fairness, bias, non-maleficence, transparency, and privacy. A distinctive concern is the tendency to produce harmful misinformation or convincingly but inaccurate content. A recurrent plea for ethical guidance and human oversight is evident. Given the variety of use cases, it is suggested that the ethical guidance debate be reframed to focus on defining what constitutes acceptable human oversight across the spectrum of applications. This involves considering diverse settings, varying potentials for harm, and different acceptable thresholds for performance and certainty in healthcare. In addition, a critical inquiry is necessary to determine the extent to which the current experimental use of LLMs is necessary and justified.

The increasing volume of data stored in relational databases has led to the need for efficient querying and utilization of this data in various sectors. However, writing SQL queries requires specialized knowledge, which poses a challenge for non-professional users trying to access and query databases. Text-to-SQL parsing solves this issue by converting natural language queries into SQL queries, thus making database access more accessible for non-expert users. To take advantage of the recent developments in Large Language Models (LLMs), a range of new methods have emerged, with a primary focus on prompt engineering and fine-tuning. This survey provides a comprehensive overview of LLMs in text-to-SQL tasks, discussing benchmark datasets, prompt engineering, fine-tuning methods, and future research directions. We hope this review will enable readers to gain a broader understanding of the recent advances in this field and offer some insights into its future trajectory.

Text-to-SQL simplifies database interactions by enabling non-experts to convert their natural language (NL) questions into Structured Query Language (SQL) queries. While recent advances in large language models (LLMs) have improved the zero-shot text-to-SQL paradigm, existing methods face scalability challenges when dealing with massive, dynamically changing databases. This paper introduces DBCopilot, a framework that addresses these challenges by employing a compact and flexible copilot model for routing across massive databases. Specifically, DBCopilot decouples the text-to-SQL process into schema routing and SQL generation, leveraging a lightweight sequence-to-sequence neural network-based router to formulate database connections and navigate natural language questions through databases and tables. The routed schemas and questions are then fed into LLMs for efficient SQL generation. Furthermore, DBCopilot also introduced a reverse schema-to-question generation paradigm, which can learn and adapt the router over massive databases automatically without requiring manual intervention. Experimental results demonstrate that DBCopilot is a scalable and effective solution for real-world text-to-SQL tasks, providing a significant advancement in handling large-scale schemas.

The cross-domain text-to-SQL task aims to build a system that can parse user questions into SQL on complete unseen databases, and the single-domain text-to-SQL task evaluates the performance on identical databases. Both of these setups confront unavoidable difficulties in real-world applications. To this end, we introduce the cross-schema text-to-SQL task, where the databases of evaluation data are different from that in the training data but come from the same domain. Furthermore, we present CSS, a large-scale CrosS-Schema Chinese text-to-SQL dataset, to carry on corresponding studies. CSS originally consisted of 4,340 question/SQL pairs across 2 databases. In order to generalize models to different medical systems, we extend CSS and create 19 new databases along with 29,280 corresponding dataset examples. Moreover, CSS is also a large corpus for single-domain Chinese text-to-SQL studies. We present the data collection approach and a series of analyses of the data statistics. To show the potential and usefulness of CSS, benchmarking baselines have been conducted and reported. Our dataset is publicly available at https://huggingface.co/datasets/zhanghanchong/css.

Accelerating inference in Large Language Models (LLMs) is critical for real-time interactions, as they have been widely incorporated into real-world services. Speculative decoding, a fully algorithmic solution, has gained attention for improving inference speed by drafting and verifying tokens, thereby generating multiple tokens in a single forward pass. However, current drafting strategies usually require significant fine-tuning or have inconsistent performance across tasks. To address these challenges, we propose Hierarchy Drafting (HD), a novel lossless drafting approach that organizes various token sources into multiple databases in a hierarchical framework based on temporal locality. In the drafting step, HD sequentially accesses multiple databases to obtain draft tokens from the highest to the lowest locality, ensuring consistent acceleration across diverse tasks and minimizing drafting latency. Our experiments on Spec-Bench using LLMs with 7B and 13B parameters demonstrate that HD outperforms existing database drafting methods, achieving robust inference speedups across model sizes, tasks, and temperatures.

We present Spider, a large-scale, complex and cross-domain semantic parsing and text-to-SQL dataset annotated by 11 college students. It consists of 10,181 questions and 5,693 unique complex SQL queries on 200 databases with multiple tables, covering 138 different domains. We define a new complex and cross-domain semantic parsing and text-to-SQL task where different complex SQL queries and databases appear in train and test sets. In this way, the task requires the model to generalize well to both new SQL queries and new database schemas. Spider is distinct from most of the previous semantic parsing tasks because they all use a single database and the exact same programs in the train set and the test set. We experiment with various state-of-the-art models and the best model achieves only 12.4% exact matching accuracy on a database split setting. This shows that Spider presents a strong challenge for future research. Our dataset and task are publicly available at https://yale-lily.github.io/spider

We survey the large language model (LLM) serving area to understand the intricate dynamics between cost-efficiency and accuracy, which is magnified by the growing need for longer contextual understanding when deploying models at a massive scale. Our findings reveal that works in this space optimize along three distinct but conflicting goals: improving serving context length (C), improving serving accuracy (A), and improving serving performance (P). Drawing inspiration from the CAP theorem in databases, we propose a CAP principle for LLM serving, which suggests that any optimization can improve at most two of these three goals simultaneously. Our survey categorizes existing works within this framework. We find the definition and continuity of user-perceived measurement metrics are crucial in determining whether a goal has been met, akin to prior CAP databases in the wild. We recognize the CAP principle for LLM serving as a guiding principle, rather than a formal theorem, to inform designers of the inherent and dynamic trade-offs in serving models. As serving accuracy and performance have been extensively studied, this survey focuses on works that extend serving context length and address the resulting challenges.

Text-to-SQL translates natural language queries into Structured Query Language (SQL) commands, enabling users to interact with databases using natural language. Essentially, the text-to-SQL task is a text generation task, and its development is primarily dependent on changes in language models. Especially with the rapid development of Large Language Models (LLMs), the pattern of text-to-SQL has undergone significant changes. Existing survey work mainly focuses on rule-based and neural-based approaches, but it still lacks a survey of Text-to-SQL with LLMs. In this paper, we survey the large language model enhanced text-to-SQL generations, classifying them into prompt engineering, fine-tuning, pre-trained, and Agent groups according to training strategies. We also summarize datasets and evaluation metrics comprehensively. This survey could help people better understand the pattern, research status, and challenges of LLM-based text-to-SQL generations.

Large Language Models (LLMs) are constrained by outdated information and a tendency to generate incorrect data, commonly referred to as "hallucinations." Retrieval-Augmented Generation (RAG) addresses these limitations by combining the strengths of retrieval-based methods and generative models. This approach involves retrieving relevant information from a large, up-to-date dataset and using it to enhance the generation process, leading to more accurate and contextually appropriate responses. Despite its benefits, RAG introduces a new attack surface for LLMs, particularly because RAG databases are often sourced from public data, such as the web. In this paper, we propose to identify the vulnerabilities and attacks on retrieval parts (RAG database) and their indirect attacks on generative parts (LLMs). Specifically, we identify that poisoning several customized content passages could achieve a retrieval backdoor, where the retrieval works well for clean queries but always returns customized poisoned adversarial queries. Triggers and poisoned passages can be highly customized to implement various attacks. For example, a trigger could be a semantic group like "The Republican Party, Donald Trump, etc." Adversarial passages can be tailored to different contents, not only linked to the triggers but also used to indirectly attack generative LLMs without modifying them. These attacks can include denial-of-service attacks on RAG and semantic steering attacks on LLM generations conditioned by the triggers. Our experiments demonstrate that by just poisoning 10 adversarial passages can induce 98.2\% success rate to retrieve the adversarial passages. Then, these passages can increase the reject ratio of RAG-based GPT-4 from 0.01\% to 74.6\% or increase the rate of negative responses from 0.22\% to 72\% for targeted queries.

We propose AutoQA, a methodology and toolkit to generate semantic parsers that answer questions on databases, with no manual effort. Given a database schema and its data, AutoQA automatically generates a large set of high-quality questions for training that covers different database operations. It uses automatic paraphrasing combined with template-based parsing to find alternative expressions of an attribute in different parts of speech. It also uses a novel filtered auto-paraphraser to generate correct paraphrases of entire sentences. We apply AutoQA to the Schema2QA dataset and obtain an average logical form accuracy of 62.9% when tested on natural questions, which is only 6.4% lower than a model trained with expert natural language annotations and paraphrase data collected from crowdworkers. To demonstrate the generality of AutoQA, we also apply it to the Overnight dataset. AutoQA achieves 69.8% answer accuracy, 16.4% higher than the state-of-the-art zero-shot models and only 5.2% lower than the same model trained with human data.

Recent advances in modeling 3D objects mostly rely on synthetic datasets due to the lack of large-scale realscanned 3D databases. To facilitate the development of 3D perception, reconstruction, and generation in the real world, we propose OmniObject3D, a large vocabulary 3D object dataset with massive high-quality real-scanned 3D objects. OmniObject3D has several appealing properties: 1) Large Vocabulary: It comprises 6,000 scanned objects in 190 daily categories, sharing common classes with popular 2D datasets (e.g., ImageNet and LVIS), benefiting the pursuit of generalizable 3D representations. 2) Rich Annotations: Each 3D object is captured with both 2D and 3D sensors, providing textured meshes, point clouds, multiview rendered images, and multiple real-captured videos. 3) Realistic Scans: The professional scanners support highquality object scans with precise shapes and realistic appearances. With the vast exploration space offered by OmniObject3D, we carefully set up four evaluation tracks: a) robust 3D perception, b) novel-view synthesis, c) neural surface reconstruction, and d) 3D object generation. Extensive studies are performed on these four benchmarks, revealing new observations, challenges, and opportunities for future research in realistic 3D vision.

Large language models (LLMs) have made impressive progress in chemistry applications, including molecular property prediction, molecular generation, experimental protocol design, etc. However, the community lacks a dialogue-based model specifically designed for chemistry. The challenge arises from the fact that most chemical data and scientific knowledge are primarily stored in structured databases, and the direct use of these structured data compromises the model's ability to maintain coherent dialogue. To tackle this issue, we develop a novel template-based instruction construction method that transforms structured knowledge into plain dialogue, making it suitable for language model training. By leveraging this approach, we develop ChemLLM, the first large language model dedicated to chemistry, capable of performing various tasks across chemical disciplines with smooth dialogue interaction. ChemLLM beats GPT-3.5 on all three principal tasks in chemistry, i.e., name conversion, molecular caption, and reaction prediction, and surpasses GPT-4 on two of them. Remarkably, ChemLLM also shows exceptional adaptability to related mathematical and physical tasks despite being trained mainly on chemical-centric corpora. Furthermore, ChemLLM demonstrates proficiency in specialized NLP tasks within chemistry, such as literature translation and cheminformatic programming. ChemLLM opens up a new avenue for exploration within chemical studies, while our method of integrating structured chemical knowledge into dialogue systems sets a new frontier for developing LLMs across various scientific fields. Codes, Datasets, and Model weights are publicly accessible at hf.co/AI4Chem/ChemLLM-7B-Chat.

Gene set knowledge discovery is essential for advancing human functional genomics. Recent studies have shown promising performance by harnessing the power of Large Language Models (LLMs) on this task. Nonetheless, their results are subject to several limitations common in LLMs such as hallucinations. In response, we present GeneAgent, a first-of-its-kind language agent featuring self-verification capability. It autonomously interacts with various biological databases and leverages relevant domain knowledge to improve accuracy and reduce hallucination occurrences. Benchmarking on 1,106 gene sets from different sources, GeneAgent consistently outperforms standard GPT-4 by a significant margin. Moreover, a detailed manual review confirms the effectiveness of the self-verification module in minimizing hallucinations and generating more reliable analytical narratives. To demonstrate its practical utility, we apply GeneAgent to seven novel gene sets derived from mouse B2905 melanoma cell lines, with expert evaluations showing that GeneAgent offers novel insights into gene functions and subsequently expedites knowledge discovery.

Large Language Models (LLMs) have drawn widespread attention and research due to their astounding performance in tasks such as text generation and reasoning. Derivative products, like ChatGPT, have been extensively deployed and highly sought after. Meanwhile, the evaluation and optimization of LLMs in software engineering tasks, such as code generation, have become a research focus. However, there is still a lack of systematic research on the application and evaluation of LLMs in the field of software engineering. Therefore, this paper is the first to comprehensively investigate and collate the research and products combining LLMs with software engineering, aiming to answer two questions: (1) What are the current integrations of LLMs with software engineering? (2) Can LLMs effectively handle software engineering tasks? To find the answers, we have collected related literature as extensively as possible from seven mainstream databases, and selected 123 papers for analysis. We have categorized these papers in detail and reviewed the current research status of LLMs from the perspective of seven major software engineering tasks, hoping this will help researchers better grasp the research trends and address the issues when applying LLMs. Meanwhile, we have also organized and presented papers with evaluation content to reveal the performance and effectiveness of LLMs in various software engineering tasks, providing guidance for researchers and developers to optimize.

The majority of data in businesses and industries is stored in tables, databases, and data warehouses. Reasoning with table-structured data poses significant challenges for large language models (LLMs) due to its hidden semantics, inherent complexity, and structured nature. One of these challenges is lacking an effective evaluation benchmark fairly reflecting the performances of LLMs on broad table reasoning abilities. In this paper, we fill in this gap, presenting a comprehensive table reasoning evolution benchmark, TReB, which measures both shallow table understanding abilities and deep table reasoning abilities, a total of 26 sub-tasks. We construct a high quality dataset through an iterative data processing procedure. We create an evaluation framework to robustly measure table reasoning capabilities with three distinct inference modes, TCoT, PoT and ICoT. Further, we benchmark over 20 state-of-the-art LLMs using this frame work and prove its effectiveness. Experimental results reveal that existing LLMs still have significant room for improvement in addressing the complex and real world Table related tasks. Both the dataset and evaluation framework are publicly available, with the dataset hosted on [HuggingFace] and the framework on [GitHub].

Large language models have demonstrated exceptional performance, yet struggle with complex tasks such as numerical reasoning, plan generation. Integrating external tools, such as calculators and databases, into large language models (LLMs) is crucial for enhancing problem-solving capabilities. Current methods assign a unique token to each tool, enabling LLMs to call tools through token prediction-similar to word generation. However, this approach fails to account for the relationship between tool and word tokens, limiting adaptability within pre-trained LLMs. To address this issue, we propose a novel token learning method that aligns tool tokens with the existing word embedding space from the perspective of initialization, thereby enhancing model performance. We begin by constructing prior token embeddings for each tool based on the tool's name or description, which are used to initialize and regularize the learnable tool token embeddings. This ensures the learned embeddings are well-aligned with the word token space, improving tool call accuracy. We evaluate the method on tasks such as numerical reasoning, knowledge-based question answering, and embodied plan generation using GSM8K-XL, FuncQA, KAMEL, and VirtualHome datasets. The results demonstrate clear improvements over recent baselines, including CoT, REACT, ICL, and ToolkenGPT, indicating that our approach effectively augments LLMs with tools through relevant tokens across diverse domains.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

Recent breakthroughs in large language models (LLMs) offer unprecedented natural language understanding and generation capabilities. However, existing surveys on LLMs in biomedicine often focus on specific applications or model architectures, lacking a comprehensive analysis that integrates the latest advancements across various biomedical domains. This review, based on an analysis of 484 publications sourced from databases including PubMed, Web of Science, and arXiv, provides an in-depth examination of the current landscape, applications, challenges, and prospects of LLMs in biomedicine, distinguishing itself by focusing on the practical implications of these models in real-world biomedical contexts. Firstly, we explore the capabilities of LLMs in zero-shot learning across a broad spectrum of biomedical tasks, including diagnostic assistance, drug discovery, and personalized medicine, among others, with insights drawn from 137 key studies. Then, we discuss adaptation strategies of LLMs, including fine-tuning methods for both uni-modal and multi-modal LLMs to enhance their performance in specialized biomedical contexts where zero-shot fails to achieve, such as medical question answering and efficient processing of biomedical literature. Finally, we discuss the challenges that LLMs face in the biomedicine domain including data privacy concerns, limited model interpretability, issues with dataset quality, and ethics due to the sensitive nature of biomedical data, the need for highly reliable model outputs, and the ethical implications of deploying AI in healthcare. To address these challenges, we also identify future research directions of LLM in biomedicine including federated learning methods to preserve data privacy and integrating explainable AI methodologies to enhance the transparency of LLMs.

General large language models (LLMs), represented by ChatGPT, have demonstrated significant potential in tasks such as code generation in software engineering. This has led to the development of specialized LLMs for software engineering, known as Code LLMs. A considerable portion of Code LLMs is derived from general LLMs through model fine-tuning. As a result, Code LLMs are often updated frequently and their performance can be influenced by the base LLMs. However, there is currently a lack of systematic investigation into Code LLMs and their performance. In this study, we conduct a comprehensive survey and analysis of the types of Code LLMs and their differences in performance compared to general LLMs. We aim to address three questions: (1) What LLMs are specifically designed for software engineering tasks, and what is the relationship between these Code LLMs? (2) Do Code LLMs really outperform general LLMs in software engineering tasks? (3) Which LLMs are more proficient in different software engineering tasks? To answer these questions, we first collect relevant literature and work from five major databases and open-source communities, resulting in 134 works for analysis. Next, we categorize the Code LLMs based on their publishers and examine their relationships with general LLMs and among themselves. Furthermore, we investigate the performance differences between general LLMs and Code LLMs in various software engineering tasks to demonstrate the impact of base models and Code LLMs. Finally, we comprehensively maintained the performance of LLMs across multiple mainstream benchmarks to identify the best-performing LLMs for each software engineering task. Our research not only assists developers of Code LLMs in choosing base models for the development of more advanced LLMs but also provides insights for practitioners to better understand key improvement directions for Code LLMs.

The rise in loosely-structured data available through text, images, and other modalities has called for new ways of querying them. Multimedia Information Retrieval has filled this gap and has witnessed exciting progress in recent years. Tasks such as search and retrieval of extensive multimedia archives have undergone massive performance improvements, driven to a large extent by recent developments in multimodal deep learning. However, methods in this field remain limited in the kinds of queries they support and, in particular, their inability to answer database-like queries. For this reason, inspired by recent work on neural databases, we propose a new framework, which we name Multimodal Neural Databases (MMNDBs). MMNDBs can answer complex database-like queries that involve reasoning over different input modalities, such as text and images, at scale. In this paper, we present the first architecture able to fulfill this set of requirements and test it with several baselines, showing the limitations of currently available models. The results show the potential of these new techniques to process unstructured data coming from different modalities, paving the way for future research in the area. Code to replicate the experiments will be released at https://github.com/GiovanniTRA/MultimodalNeuralDatabases

In many use-cases, information is stored in text but not available in structured data. However, extracting data from natural language text to precisely fit a schema, and thus enable querying, is a challenging task. With the rise of pre-trained Large Language Models (LLMs), there is now an effective solution to store and use information extracted from massive corpora of text documents. Thus, we envision the use of SQL queries to cover a broad range of data that is not captured by traditional databases by tapping the information in LLMs. To ground this vision, we present Galois, a prototype based on a traditional database architecture, but with new physical operators for querying the underlying LLM. The main idea is to execute some operators of the the query plan with prompts that retrieve data from the LLM. For a large class of SQL queries, querying LLMs returns well structured relations, with encouraging qualitative results. Preliminary experimental results make pre-trained LLMs a promising addition to the field of database systems, introducing a new direction for hybrid query processing. However, we pinpoint several research challenges that must be addressed to build a DBMS that exploits LLMs. While some of these challenges necessitate integrating concepts from the NLP literature, others offer novel research avenues for the DB community.

Learning how humans manipulate objects requires machines to acquire knowledge from two perspectives: one for understanding object affordances and the other for learning human's interactions based on the affordances. Even though these two knowledge bases are crucial, we find that current databases lack a comprehensive awareness of them. In this work, we propose a multi-modal and rich-annotated knowledge repository, OakInk, for visual and cognitive understanding of hand-object interactions. We start to collect 1,800 common household objects and annotate their affordances to construct the first knowledge base: Oak. Given the affordance, we record rich human interactions with 100 selected objects in Oak. Finally, we transfer the interactions on the 100 recorded objects to their virtual counterparts through a novel method: Tink. The recorded and transferred hand-object interactions constitute the second knowledge base: Ink. As a result, OakInk contains 50,000 distinct affordance-aware and intent-oriented hand-object interactions. We benchmark OakInk on pose estimation and grasp generation tasks. Moreover, we propose two practical applications of OakInk: intent-based interaction generation and handover generation. Our datasets and source code are publicly available at https://github.com/lixiny/OakInk.

Unequal access to costly datasets essential for empirical research has long hindered researchers from disadvantaged institutions, limiting their ability to contribute to their fields and advance their careers. Recent breakthroughs in Large Language Models (LLMs) have the potential to democratize data access by automating data collection from unstructured sources. We develop and evaluate a novel methodology using GPT-4o-mini within a Retrieval-Augmented Generation (RAG) framework to collect data from corporate disclosures. Our approach achieves human-level accuracy in collecting CEO pay ratios from approximately 10,000 proxy statements and Critical Audit Matters (CAMs) from more than 12,000 10-K filings, with LLM processing times of 9 and 40 minutes respectively, each at a cost under $10. This stands in stark contrast to the hundreds of hours needed for manual collection or the thousands of dollars required for commercial database subscriptions. To foster a more inclusive research community by empowering researchers with limited resources to explore new avenues of inquiry, we share our methodology and the resulting datasets.

Recently, there has been a significant upsurge of interest in leveraging large language models (LLMs) to assist scientific discovery. However, most LLMs only focus on general science, while they lack domain-specific knowledge, such as chemical molecules and amino acid sequences. To bridge these gaps, we introduce SciDFM, a mixture-of-experts LLM, which is trained from scratch and is able to conduct college-level scientific reasoning and understand molecules and amino acid sequences. We collect a large-scale training corpus containing numerous scientific papers and books from different disciplines as well as data from domain-specific databases. We further fine-tune the pre-trained model on lots of instruction data to improve performances on downstream benchmarks. From experiment results, we show that SciDFM achieves strong performance on general scientific benchmarks such as SciEval and SciQ, and it reaches a SOTA performance on domain-specific benchmarks among models of similar size. We further analyze the expert layers and show that the results of expert selection vary with data from different disciplines. To benefit the broader research community, we open-source SciDFM at https://huggingface.co/OpenDFM/SciDFM-MoE-A5.6B-v1.0.

In recent years, large language models (LLMs) have achieved remarkable success in natural language processing (NLP). LLMs require an extreme amount of parameters to attain high performance. As models grow into the trillion-parameter range, computational and memory costs increase significantly. This makes it difficult for many researchers to access the resources needed to train or apply these models. Optimizing LLM performance involves two main approaches: fine-tuning pre-trained models for specific tasks to achieve state-of-the-art performance, and reducing costs or improving training time while maintaining similar performance. This paper presents a systematic literature review (SLR) following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. We reviewed 65 publications out of 983 from 2017 to December 2023, retrieved from 5 databases. The study presents methods to optimize and accelerate LLMs while achieving cutting-edge results without sacrificing accuracy. We begin with an overview of the development of language modeling, followed by a detailed explanation of commonly used frameworks and libraries, and a taxonomy for improving and speeding up LLMs based on three classes: LLM training, LLM inference, and system serving. We then delve into recent optimization and acceleration strategies such as training optimization, hardware optimization, scalability and reliability, accompanied by the taxonomy and categorization of these strategies. Finally, we provide an in-depth comparison of each class and strategy, with two case studies on optimizing model training and enhancing inference efficiency. These case studies showcase practical approaches to address LLM resource limitations while maintaining performance.

Generative Large Language Models (LLMs) such as GPT-3 are capable of generating highly fluent responses to a wide variety of user prompts. However, LLMs are known to hallucinate facts and make non-factual statements which can undermine trust in their output. Existing fact-checking approaches either require access to token-level output probability distribution (which may not be available for systems such as ChatGPT) or external databases that are interfaced via separate, often complex, modules. In this work, we propose "SelfCheckGPT", a simple sampling-based approach that can be used to fact-check black-box models in a zero-resource fashion, i.e. without an external database. SelfCheckGPT leverages the simple idea that if a LLM has knowledge of a given concept, sampled responses are likely to be similar and contain consistent facts. However, for hallucinated facts, stochastically sampled responses are likely to diverge and contradict one another. We investigate this approach by using GPT-3 to generate passages about individuals from the WikiBio dataset, and manually annotate the factuality of the generated passages. We demonstrate that SelfCheckGPT can: i) detect non-factual and factual sentences; and ii) rank passages in terms of factuality. We compare our approach to several existing baselines and show that in sentence hallucination detection, our approach has AUC-PR scores comparable to grey-box methods, while SelfCheckGPT is best at passage factuality assessment.

During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based language models, many language models that learn characteristics of nucleotide sequences have also emerged. These models show good performance in classifying various features of nucleotide sequences. When classifying nucleotide sequences, not only the sequence itself, but also various background knowledge is utilized. In this study, we use not only a nucleotide sequence-based language model but also a text language model based on PubMed articles to reflect more biological background knowledge in the model. We propose a method to fine-tune the nucleotide sequence language model and the text language model based on various databases of antibiotic resistance genes. We also propose an LLM-based augmentation technique to supplement the data and an ensemble method to effectively combine the two models. We also propose a benchmark for evaluating the model. Our method achieved better performance than the nucleotide sequence language model in the drug resistance class prediction.

With the rapid development of Large Language Models (LLMs), it is crucial to have benchmarks which can evaluate the ability of LLMs on different domains. One common use of LLMs is performing tasks on scientific topics, such as writing algorithms, querying databases or giving mathematical proofs. Inspired by the way university students are evaluated on such tasks, in this paper, we propose SciEx - a benchmark consisting of university computer science exam questions, to evaluate LLMs ability on solving scientific tasks. SciEx is (1) multilingual, containing both English and German exams, and (2) multi-modal, containing questions that involve images, and (3) contains various types of freeform questions with different difficulty levels, due to the nature of university exams. We evaluate the performance of various state-of-the-art LLMs on our new benchmark. Since SciEx questions are freeform, it is not straightforward to evaluate LLM performance. Therefore, we provide human expert grading of the LLM outputs on SciEx. We show that the free-form exams in SciEx remain challenging for the current LLMs, where the best LLM only achieves 59.4\% exam grade on average. We also provide detailed comparisons between LLM performance and student performance on SciEx. To enable future evaluation of new LLMs, we propose using LLM-as-a-judge to grade the LLM answers on SciEx. Our experiments show that, although they do not perform perfectly on solving the exams, LLMs are decent as graders, achieving 0.948 Pearson correlation with expert grading.

Scientific progress increasingly depends on synthesizing knowledge across vast literature, yet most experimental data remains trapped in semi-structured formats that resist systematic extraction and analysis. Here, we present MatSKRAFT, a computational framework that automatically extracts and integrates materials science knowledge from tabular data at unprecedented scale. Our approach transforms tables into graph-based representations processed by constraint-driven GNNs that encode scientific principles directly into model architecture. MatSKRAFT significantly outperforms state-of-the-art large language models, achieving F1 scores of 88.68 for property extraction and 71.35 for composition extraction, while processing data 19-496times faster than them (compared to the slowest and the fastest models, respectively) with modest hardware requirements. Applied to nearly 69,000 tables from more than 47,000 research publications, we construct a comprehensive database containing over 535,000 entries, including 104,000 compositions that expand coverage beyond major existing databases, pending manual validation. This systematic approach reveals previously overlooked materials with distinct property combinations and enables data-driven discovery of composition-property relationships forming the cornerstone of materials and scientific discovery.

Translating users' natural language queries (NL) into SQL queries (i.e., NL2SQL) can significantly reduce barriers to accessing relational databases and support various commercial applications. The performance of NL2SQL has been greatly enhanced with the emergence of Large Language Models (LLMs). In this survey, we provide a comprehensive review of NL2SQL techniques powered by LLMs, covering its entire lifecycle from the following four aspects: (1) Model: NL2SQL translation techniques that tackle not only NL ambiguity and under-specification, but also properly map NL with database schema and instances; (2) Data: From the collection of training data, data synthesis due to training data scarcity, to NL2SQL benchmarks; (3) Evaluation: Evaluating NL2SQL methods from multiple angles using different metrics and granularities; and (4) Error Analysis: analyzing NL2SQL errors to find the root cause and guiding NL2SQL models to evolve. Moreover, we provide a rule of thumb for developing NL2SQL solutions. Finally, we discuss the research challenges and open problems of NL2SQL in the LLMs era.

Electronic health records (EHRs) contain vast amounts of complex data, but harmonizing and processing this information remains a challenging and costly task requiring significant clinical expertise. While large language models (LLMs) have shown promise in various healthcare applications, their potential for abstracting medical concepts from EHRs remains largely unexplored. We introduce EHRmonize, a framework leveraging LLMs to abstract medical concepts from EHR data. Our study uses medication data from two real-world EHR databases to evaluate five LLMs on two free-text extraction and six binary classification tasks across various prompting strategies. GPT-4o's with 10-shot prompting achieved the highest performance in all tasks, accompanied by Claude-3.5-Sonnet in a subset of tasks. GPT-4o achieved an accuracy of 97% in identifying generic route names, 82% for generic drug names, and 100% in performing binary classification of antibiotics. While EHRmonize significantly enhances efficiency, reducing annotation time by an estimated 60%, we emphasize that clinician oversight remains essential. Our framework, available as a Python package, offers a promising tool to assist clinicians in EHR data abstraction, potentially accelerating healthcare research and improving data harmonization processes.

This paper introduces a scholarly Question Answering (QA) system on top of the NFDI4DataScience Gateway, employing a Retrieval Augmented Generation-based (RAG) approach. The NFDI4DS Gateway, as a foundational framework, offers a unified and intuitive interface for querying various scientific databases using federated search. The RAG-based scholarly QA, powered by a Large Language Model (LLM), facilitates dynamic interaction with search results, enhancing filtering capabilities and fostering a conversational engagement with the Gateway search. The effectiveness of both the Gateway and the scholarly QA system is demonstrated through experimental analysis.

One impressive emergent capability of large language models (LLMs) is generation of code, including Structured Query Language (SQL) for databases. For the task of converting natural language text to SQL queries, Text-to-SQL, adaptation of LLMs is of paramount importance, both in in-context learning and fine-tuning settings, depending on the amount of adaptation data used. In this paper, we propose an LLM-based Text-to-SQL model SQL-PaLM, leveraging on PaLM-2, that pushes the state-of-the-art in both settings. Few-shot SQL-PaLM is based on an execution-based self-consistency prompting approach designed for Text-to-SQL, and achieves 77.3% in test-suite accuracy on Spider, which to our best knowledge is the first to outperform previous state-of-the-art with fine-tuning by a significant margin, 4%. Furthermore, we demonstrate that the fine-tuned SQL-PALM outperforms it further by another 1%. Towards applying SQL-PaLM to real-world scenarios we further evaluate its robustness on other challenging variants of Spider and demonstrate the superior generalization capability of SQL-PaLM. In addition, via extensive case studies, we demonstrate the impressive intelligent capabilities and various success enablers of LLM-based Text-to-SQL.

Traditional benchmarks for large language models (LLMs) typically rely on static evaluations through storytelling or opinion expression, which fail to capture the dynamic requirements of real-time information processing in contemporary applications. To address this limitation, we present DynamicBench, a benchmark designed to evaluate the proficiency of LLMs in storing and processing up-to-the-minute data. DynamicBench utilizes a dual-path retrieval pipeline, integrating web searches with local report databases. It necessitates domain-specific knowledge, ensuring accurate responses report generation within specialized fields. By evaluating models in scenarios that either provide or withhold external documents, DynamicBench effectively measures their capability to independently process recent information or leverage contextual enhancements. Additionally, we introduce an advanced report generation system adept at managing dynamic information synthesis. Our experimental results confirm the efficacy of our approach, with our method achieving state-of-the-art performance, surpassing GPT4o in document-free and document-assisted scenarios by 7.0% and 5.8%, respectively. The code and data will be made publicly available.

Tumor documentation in Germany is largely done manually, requiring reading patient records and entering data into structured databases. Large language models (LLMs) could potentially enhance this process by improving efficiency and reliability. This evaluation tests eleven different open source LLMs with sizes ranging from 1-70 billion model parameters on three basic tasks of the tumor documentation process: identifying tumor diagnoses, assigning ICD-10 codes, and extracting the date of first diagnosis. For evaluating the LLMs on these tasks, a dataset of annotated text snippets based on anonymized doctors' notes from urology was prepared. Different prompting strategies were used to investigate the effect of the number of examples in few-shot prompting and to explore the capabilities of the LLMs in general. The models Llama 3.1 8B, Mistral 7B, and Mistral NeMo 12 B performed comparably well in the tasks. Models with less extensive training data or having fewer than 7 billion parameters showed notably lower performance, while larger models did not display performance gains. Examples from a different medical domain than urology could also improve the outcome in few-shot prompting, which demonstrates the ability of LLMs to handle tasks needed for tumor documentation. Open source LLMs show a strong potential for automating tumor documentation. Models from 7-12 billion parameters could offer an optimal balance between performance and resource efficiency. With tailored fine-tuning and well-designed prompting, these models might become important tools for clinical documentation in the future. The code for the evaluation is available from https://github.com/stefan-m-lenz/UroLlmEval. We also release the dataset as a new valuable resource that addresses the shortage of authentic and easily accessible benchmarks in German-language medical NLP.

Large Language Model (LLM) techniques play an increasingly important role in Natural Language to SQL (NL2SQL) translation. LLMs trained by extensive corpora have strong natural language understanding and basic SQL generation abilities without additional tuning specific to NL2SQL tasks. Existing LLMs-based NL2SQL approaches try to improve the translation by enhancing the LLMs with an emphasis on user intention understanding. However, LLMs sometimes fail to generate appropriate SQL due to their lack of knowledge in organizing complex logical operator composition. A promising method is to input the LLMs with demonstrations, which include known NL2SQL translations from various databases. LLMs can learn to organize operator compositions from the input demonstrations for the given task. In this paper, we propose PURPLE (Pre-trained models Utilized to Retrieve Prompts for Logical Enhancement), which improves accuracy by retrieving demonstrations containing the requisite logical operator composition for the NL2SQL task on hand, thereby guiding LLMs to produce better SQL translation. PURPLE achieves a new state-of-the-art performance of 80.5% exact-set match accuracy and 87.8% execution match accuracy on the validation set of the popular NL2SQL benchmark Spider. PURPLE maintains high accuracy across diverse benchmarks, budgetary constraints, and various LLMs, showing robustness and cost-effectiveness.

Many organizations rely on data from government and third-party sources, and those sources rarely follow the same data formatting. This introduces challenges in integrating data from multiple sources or aligning external sources with internal databases. Commercial database systems do not offer adequate support for integrating data from heterogeneous sources, and manual integration is both time-consuming and inefficient. State-of-the-art data integration approaches that rely on similarity functions and textual transformations often fail to handle challenging cases where multiple mappings are required, or the mappings go beyond simple textual transformations. In this paper, we study the potentials of deep neural models for transforming tables for joinability. In particular, we cast the problem as a prediction task and develop a framework that leverages large deep-learning language models to transform tabular data from a source formatting to a desired target representation. Our framework can efficiently learn the patterns for mapping a source formatting into an expected target using just a few examples, which can then be used for tasks such as table joining, filling in missing values, and error detection. Compared to state-of-the-art mapping and joining approaches, our framework delivers noticeably more accurate and scalable performance on both real-world and synthetic datasets. Our experimental evaluation also shows that the performance of the proposed framework using our fine-tuned model is at par or better than large language models such as GPT-3, despite the significant difference in size, and that using large language models within our framework improves their performance.

Radio frequency (RF) signal mapping, which is the process of analyzing and predicting the RF signal strength and distribution across specific areas, is crucial for cellular network planning and deployment. Traditional approaches to RF signal mapping rely on statistical models constructed based on measurement data, which offer low complexity but often lack accuracy, or ray tracing tools, which provide enhanced precision for the target area but suffer from increased computational complexity. Recently, machine learning (ML) has emerged as a data-driven method for modeling RF signal propagation, which leverages models trained on synthetic datasets to perform RF signal mapping in "unseen" areas. In this paper, we present Geo2SigMap, an ML-based framework for efficient and high-fidelity RF signal mapping using geographic databases. First, we develop an automated framework that seamlessly integrates three open-source tools: OpenStreetMap (geographic databases), Blender (computer graphics), and Sionna (ray tracing), enabling the efficient generation of large-scale 3D building maps and ray tracing models. Second, we propose a cascaded U-Net model, which is pre-trained on synthetic datasets and employed to generate detailed RF signal maps, leveraging environmental information and sparse measurement data. Finally, we evaluate the performance of Geo2SigMap via a real-world measurement campaign, where three types of user equipment (UE) collect over 45,000 data points related to cellular information from six LTE cells operating in the citizens broadband radio service (CBRS) band. Our results show that Geo2SigMap achieves an average root-mean-square-error (RMSE) of 6.04 dB for predicting the reference signal received power (RSRP) at the UE, representing an average RMSE improvement of 3.59 dB compared to existing methods.

Many users communicate with chatbots and AI assistants in order to help them with various tasks. A key component of the assistant is the ability to understand and answer a user's natural language questions for question-answering (QA). Because data can be usually stored in a structured manner, an essential step involves turning a natural language question into its corresponding query language. However, in order to train most natural language-to-query-language state-of-the-art models, a large amount of training data is needed first. In most domains, this data is not available and collecting such datasets for various domains can be tedious and time-consuming. In this work, we propose a novel method for accelerating the training dataset collection for developing the natural language-to-query-language machine learning models. Our system allows one to generate conversational multi-term data, where multiple turns define a dialogue session, enabling one to better utilize chatbot interfaces. We train two current state-of-the-art NL-to-QL models, on both an SQL and SPARQL-based datasets in order to showcase the adaptability and efficacy of our created data.

We present a system for generating indoor scenes in response to text prompts. The prompts are not limited to a fixed vocabulary of scene descriptions, and the objects in generated scenes are not restricted to a fixed set of object categories -- we call this setting indoor scene generation. Unlike most prior work on indoor scene generation, our system does not require a large training dataset of existing 3D scenes. Instead, it leverages the world knowledge encoded in pre-trained large language models (LLMs) to synthesize programs in a domain-specific layout language that describe objects and spatial relations between them. Executing such a program produces a specification of a constraint satisfaction problem, which the system solves using a gradient-based optimization scheme to produce object positions and orientations. To produce object geometry, the system retrieves 3D meshes from a database. Unlike prior work which uses databases of category-annotated, mutually-aligned meshes, we develop a pipeline using vision-language models (VLMs) to retrieve meshes from massive databases of un-annotated, inconsistently-aligned meshes. Experimental evaluations show that our system outperforms generative models trained on 3D data for traditional, closed-universe scene generation tasks; it also outperforms a recent LLM-based layout generation method on open-universe scene generation.

The problem of verifying whether a textual hypothesis holds based on the given evidence, also known as fact verification, plays an important role in the study of natural language understanding and semantic representation. However, existing studies are mainly restricted to dealing with unstructured evidence (e.g., natural language sentences and documents, news, etc), while verification under structured evidence, such as tables, graphs, and databases, remains under-explored. This paper specifically aims to study the fact verification given semi-structured data as evidence. To this end, we construct a large-scale dataset called TabFact with 16k Wikipedia tables as the evidence for 118k human-annotated natural language statements, which are labeled as either ENTAILED or REFUTED. TabFact is challenging since it involves both soft linguistic reasoning and hard symbolic reasoning. To address these reasoning challenges, we design two different models: Table-BERT and Latent Program Algorithm (LPA). Table-BERT leverages the state-of-the-art pre-trained language model to encode the linearized tables and statements into continuous vectors for verification. LPA parses statements into programs and executes them against the tables to obtain the returned binary value for verification. Both methods achieve similar accuracy but still lag far behind human performance. We also perform a comprehensive analysis to demonstrate great future opportunities. The data and code of the dataset are provided in https://github.com/wenhuchen/Table-Fact-Checking.

Natural Language to SQL (NL2SQL) has emerged as a critical task for enabling seamless interaction with databases. Recent advancements in Large Language Models (LLMs) have demonstrated remarkable performance in this domain. However, existing NL2SQL methods predominantly rely on closed-source LLMs leveraging prompt engineering, while open-source models typically require fine-tuning to acquire domain-specific knowledge. Despite these efforts, open-source LLMs struggle with complex NL2SQL tasks due to the indirect expression of user query objectives and the semantic gap between user queries and database schemas. Inspired by the application of reinforcement learning in mathematical problem-solving to encourage step-by-step reasoning in LLMs, we propose LearNAT (Learning NL2SQL with AST-guided Task Decomposition), a novel framework that improves the performance of open-source LLMs on complex NL2SQL tasks through task decomposition and reinforcement learning. LearNAT introduces three key components: (1) a Decomposition Synthesis Procedure that leverages Abstract Syntax Trees (ASTs) to guide efficient search and pruning strategies for task decomposition, (2) Margin-aware Reinforcement Learning, which employs fine-grained step-level optimization via DPO with AST margins, and (3) Adaptive Demonstration Reasoning, a mechanism for dynamically selecting relevant examples to enhance decomposition capabilities. Extensive experiments on two benchmark datasets, Spider and BIRD, demonstrate that LearNAT enables a 7B-parameter open-source LLM to achieve performance comparable to GPT-4, while offering improved efficiency and accessibility.

Large language models (LLMs), such as ChatGPT, are able to generate human-like, fluent responses for many downstream tasks, e.g., task-oriented dialog and question answering. However, applying LLMs to real-world, mission-critical applications remains challenging mainly due to their tendency to generate hallucinations and their inability to use external knowledge. This paper proposes a LLM-Augmenter system, which augments a black-box LLM with a set of plug-and-play modules. Our system makes the LLM generate responses grounded in external knowledge, e.g., stored in task-specific databases. It also iteratively revises LLM prompts to improve model responses using feedback generated by utility functions, e.g., the factuality score of a LLM-generated response. The effectiveness of LLM-Augmenter is empirically validated on two types of scenarios, task-oriented dialog and open-domain question answering. LLM-Augmenter significantly reduces ChatGPT's hallucinations without sacrificing the fluency and informativeness of its responses. We make the source code and models publicly available.

Large language models (LLMs) have demonstrated remarkable performance on single-turn text-to-SQL tasks, but real-world database applications predominantly require multi-turn interactions to handle ambiguous queries, execution errors, and evolving user requirements. Existing multi-turn benchmarks fall short by treating conversation histories as static context or limiting evaluation to read-only operations, failing to reflect production-grade database assistant challenges. We introduce BIRD-INTERACT, a benchmark that restores this realism through: (1) a comprehensive interaction environment coupling each database with a hierarchical knowledge base, metadata files, and a function-driven user simulator, enabling models to solicit clarifications, retrieve knowledge, and recover from errors without human supervision; (2) two evaluation settings consisting of a pre-defined conversational protocol (c-Interact) and an open-ended agentic setting (a-Interact) where models autonomously decide when to query the user simulator or explore the environment; (3) a challenging task suite covering the full CRUD spectrum for business-intelligence and operational use cases, guarded by executable test cases. Each task features ambiguous and follow-up sub-tasks requiring dynamic interaction. The suite comprises BIRD-INTERACT-FULL (600 tasks, up to 11,796 interactions) for comprehensive performance assessment, and BIRD-INTERACT-LITE (300 tasks with simplified databases) for detailed behavioral analysis and rapid method development. Our empirical results highlight BIRD-INTERACT's difficulty: GPT-5 completes only 8.67% of tasks in c-Interact and 17.00% in a-Interact. Analysis via memory grafting and Interaction Test-time Scaling validates the importance of effective interaction for complex, dynamic text-to-SQL tasks.

Text-to-SQL parsing, which aims at converting natural language instructions into executable SQLs, has gained increasing attention in recent years. In particular, Codex and ChatGPT have shown impressive results in this task. However, most of the prevalent benchmarks, i.e., Spider, and WikiSQL, focus on database schema with few rows of database contents leaving the gap between academic study and real-world applications. To mitigate this gap, we present Bird, a big benchmark for large-scale database grounded in text-to-SQL tasks, containing 12,751 pairs of text-to-SQL data and 95 databases with a total size of 33.4 GB, spanning 37 professional domains. Our emphasis on database values highlights the new challenges of dirty database contents, external knowledge between NL questions and database contents, and SQL efficiency, particularly in the context of massive databases. To solve these problems, text-to-SQL models must feature database value comprehension in addition to semantic parsing. The experimental results demonstrate the significance of database values in generating accurate text-to-SQLs for big databases. Furthermore, even the most effective text-to-SQL models, i.e. ChatGPT, only achieves 40.08% in execution accuracy, which is still far from the human result of 92.96%, proving that challenges still stand. Besides, we also provide an efficiency analysis to offer insights into generating text-to-efficient-SQLs that are beneficial to industries. We believe that BIRD will contribute to advancing real-world applications of text-to-SQL research. The leaderboard and source code are available: https://bird-bench.github.io/.

Data-driven materials discovery requires large-scale experimental datasets, yet most of the information remains trapped in unstructured literature. Existing extraction efforts often focus on a limited set of features and have not addressed the integrated composition-processing-microstructure-property relationships essential for understanding materials behavior, thereby posing challenges for building comprehensive databases. To address this gap, we propose a multi-stage information extraction pipeline powered by large language models, which captures 47 features spanning composition, processing, microstructure, and properties exclusively from experimentally reported materials. The pipeline integrates iterative extraction with source tracking to enhance both accuracy and reliability. Evaluations at the feature level (independent attributes) and tuple level (interdependent features) yielded F1 scores around 0.96. Compared with single-pass extraction without source tracking, our approach improved F1 scores of microstructure category by 10.0% (feature level) and 13.7% (tuple level), and reduced missed materials from 49 to 13 out of 396 materials in 100 articles on precipitate-containing multi-principal element alloys (miss rate reduced from 12.4% to 3.3%). The pipeline enables scalable and efficient literature mining, producing databases with high precision, minimal omissions, and zero false positives. These datasets provide trustworthy inputs for machine learning and materials informatics, while the modular design generalizes to diverse material classes, enabling comprehensive materials information extraction.

Feature representation in the form of spatio-spectral decomposition is one of the robust techniques adopted in automatic handwritten character recognition systems. In this regard, we propose a new image representation approach for unconstrained handwritten alphanumeric characters using sparse concept coded Tetrolets. Tetrolets, which does not use fixed dyadic square blocks for spectral decomposition like conventional wavelets, preserve the localized variations in handwritings by adopting tetrominoes those capture the shape geometry. The sparse concept coding of low entropy Tetrolet representation is found to extract the important hidden information (concept) for superior pattern discrimination. Large scale experimentation using ten databases in six different scripts (Bangla, Devanagari, Odia, English, Arabic and Telugu) has been performed. The proposed feature representation along with standard classifiers such as random forest, support vector machine (SVM), nearest neighbor and modified quadratic discriminant function (MQDF) is found to achieve state-of-the-art recognition performance in all the databases, viz. 99.40% (MNIST); 98.72% and 93.24% (IITBBS); 99.38% and 99.22% (ISI Kolkata). The proposed OCR system is shown to perform better than other sparse based techniques such as PCA, SparsePCA and SparseLDA, as well as better than existing transforms (Wavelet, Slantlet and Stockwell).

Large Language Models (LLMs) have shown impressive capabilities in transforming natural language questions about relational databases into SQL queries. Despite recent improvements, small LLMs struggle to handle questions involving multiple tables and complex SQL patterns under a Zero-Shot Learning (ZSL) setting. Supervised Fine-Tuning (SFT) partially compensate the knowledge deficits in pretrained models but falls short while dealing with queries involving multi-hop reasoning. To bridge this gap, different LLM training strategies to reinforce reasoning capabilities have been proposed, ranging from leveraging a thinking process within ZSL, including reasoning traces in SFT, or adopt Reinforcement Learning (RL) strategies. However, the influence of reasoning on Text2SQL performance is still largely unexplored. This paper investigates to what extent LLM reasoning capabilities influence their Text2SQL performance on four benchmark datasets. To this end, it considers the following LLM settings: (1) ZSL, including general-purpose reasoning or not; (2) SFT, with and without task-specific reasoning traces; (3) RL, leveraging execution accuracy as primary reward function; (4) SFT+RL, i.e, a two-stage approach that combines SFT and RL. The results show that general-purpose reasoning under ZSL proves to be ineffective in tackling complex Text2SQL cases. Small LLMs benefit from SFT with reasoning much more than larger ones, bridging the gap of their (weaker) model pretraining. RL is generally beneficial across all tested models and datasets, particularly when SQL queries involve multi-hop reasoning and multiple tables. Small LLMs with SFT+RL excel on most complex datasets thanks to a strategic balance between generality of the reasoning process and optimization of the execution accuracy. Thanks to RL, the7B Qwen-Coder-2.5 model performs on par with 100+ Billion ones on the Bird dataset.

Large language models (LLMs) have demonstrated strong capabilities in translating natural language questions about relational databases into SQL queries. In particular, test-time scaling techniques such as Self-Consistency and Self-Correction can enhance SQL generation accuracy by increasing computational effort during inference. However, these methods have notable limitations: Self-Consistency may select suboptimal outputs despite majority votes, while Self-Correction typically addresses only syntactic errors. To leverage the strengths of both approaches, we propose CSC-SQL, a novel method that integrates Self-Consistency and Self-Correction. CSC-SQL selects the two most frequently occurring outputs from parallel sampling and feeds them into a merge revision model for correction. Additionally, we employ the Group Relative Policy Optimization (GRPO) algorithm to fine-tune both the SQL generation and revision models via reinforcement learning, significantly enhancing output quality. Experimental results confirm the effectiveness and generalizability of CSC-SQL. On the BIRD development set, our 3B model achieves 65.28% execution accuracy, while the 7B model achieves 69.19%. The code will be open sourced at https://github.com/CycloneBoy/csc_sql.

The availability of large-scale authentic face databases has been crucial to the significant advances made in face recognition research over the past decade. However, legal and ethical concerns led to the recent retraction of many of these databases by their creators, raising questions about the continuity of future face recognition research without one of its key resources. Synthetic datasets have emerged as a promising alternative to privacy-sensitive authentic data for face recognition development. However, recent synthetic datasets that are used to train face recognition models suffer either from limitations in intra-class diversity or cross-class (identity) discrimination, leading to less optimal accuracies, far away from the accuracies achieved by models trained on authentic data. This paper targets this issue by proposing IDiff-Face, a novel approach based on conditional latent diffusion models for synthetic identity generation with realistic identity variations for face recognition training. Through extensive evaluations, our proposed synthetic-based face recognition approach pushed the limits of state-of-the-art performances, achieving, for example, 98.00% accuracy on the Labeled Faces in the Wild (LFW) benchmark, far ahead from the recent synthetic-based face recognition solutions with 95.40% and bridging the gap to authentic-based face recognition with 99.82% accuracy.

The advent of artificial intelligence (AI) has enabled a comprehensive exploration of materials for various applications. However, AI models often prioritize frequently encountered materials in the scientific literature, limiting the selection of suitable candidates based on inherent physical and chemical properties. To address this imbalance, we have generated a dataset of 1,494,017 natural language-material paragraphs based on combined OQMD, Materials Project, JARVIS, COD and AFLOW2 databases, which are dominated by ab initio calculations and tend to be much more evenly distributed on the periodic table. The generated text narratives were then polled and scored by both human experts and ChatGPT-4, based on three rubrics: technical accuracy, language and structure, and relevance and depth of content, showing similar scores but with human-scored depth of content being the most lagging. The merger of multi-modality data sources and large language model (LLM) holds immense potential for AI frameworks to help the exploration and discovery of solid-state materials for specific applications.

Accurate diagnosis of heart arrhythmias requires the interpretation of electrocardiograms (ECG), which capture the electrical activity of the heart. Automating this process through machine learning is challenging due to the need for large annotated datasets, which are difficult and costly to collect. To address this issue, transfer learning is often employed, where models are pre-trained on large datasets and fine-tuned for specific ECG classification tasks with limited labeled data. Self-supervised learning has become a widely adopted pre-training method, enabling models to learn meaningful representations from unlabeled datasets. In this work, we explore the joint-embedding predictive architecture (JEPA) for self-supervised learning from ECG data. Unlike invariance-based methods, JEPA does not rely on hand-crafted data augmentations, and unlike generative methods, it predicts latent features rather than reconstructing input data. We create a large unsupervised pre-training dataset by combining ten public ECG databases, amounting to over one million records. We pre-train Vision Transformers using JEPA on this dataset and fine-tune them on various PTB-XL benchmarks. Our results show that JEPA outperforms existing invariance-based and generative approaches, achieving an AUC of 0.945 on the PTB-XL all statements task. JEPA consistently learns the highest quality representations, as demonstrated in linear evaluations, and proves advantageous for pre-training even in the absence of additional data.

A vector database is used to store high-dimensional data that cannot be characterized by traditional DBMS. Although there are not many articles describing existing or introducing new vector database architectures, the approximate nearest neighbor search problem behind vector databases has been studied for a long time, and considerable related algorithmic articles can be found in the literature. This article attempts to comprehensively review relevant algorithms to provide a general understanding of this booming research area. The basis of our framework categorises these studies by the approach of solving ANNS problem, respectively hash-based, tree-based, graph-based and quantization-based approaches. Then we present an overview of existing challenges for vector databases. Lastly, we sketch how vector databases can be combined with large language models and provide new possibilities.

Tables stored in databases and tables which are present in web pages and articles account for a large part of semi-structured data that is available on the internet. It then becomes pertinent to develop a modeling approach with large language models (LLMs) that can be used to solve diverse table tasks such as semantic parsing, question answering as well as classification problems. Traditionally, there existed separate models specialized for each task individually. It raises the question of how far can we go to build a unified model that works well on some table tasks without significant degradation on others. To that end, we attempt at creating a shared modeling approach in the pretraining stage with encoder-decoder style LLMs that can cater to diverse tasks. We evaluate our approach that continually pretrains and finetunes different model families of T5 with data from tables and surrounding context, on these downstream tasks at different model scales. Through multiple ablation studies, we observe that our pretraining with self-supervised objectives can significantly boost the performance of the models on these tasks. As an example of one improvement, we observe that the instruction finetuned public models which come specialized on text question answering (QA) and have been trained on table data still have room for improvement when it comes to table specific QA. Our work is the first attempt at studying the advantages of a unified approach to table specific pretraining when scaled from 770M to 11B sequence to sequence models while also comparing the instruction finetuned variants of the models.