Daily Papers

Scientific research involves complex information-seeking and reasoning workflows across heterogeneous sources. However, existing benchmarks primarily emphasize general-domain retrieval or static scientific question answering, and therefore fail to assess key capabilities required in realistic scientific research workflows. We introduce SciExplore, a benchmark designed to evaluate scientific information-seeking and reasoning capabilities of LLMs and agents. SciExplore comprises four task types covering 103 expert-curated tasks across more than ten scientific disciplines: scientific database navigation, ambiguous literature retrieval, missing reference completion, and cross-source structured knowledge synthesis, which probe progressively higher-level abilities from entity-level reasoning and document-level identification to evidence-level grounding and domain-level synthesis. We evaluate over ten state-of-the-art LLMs and autonomous agents on SciExplore, revealing substantial performance gaps with performance degrading sharply as task complexity increases and extremely low accuracy on the most challenging structured synthesis tasks. These results highlight significant limitations of current models and agents in realistic scientific information-seeking scenarios.

The exponential growth of scientific literature necessitates advanced tools for effective knowledge exploration. We present Knowledge Navigator, a system designed to enhance exploratory search abilities by organizing and structuring the retrieved documents from broad topical queries into a navigable, two-level hierarchy of named and descriptive scientific topics and subtopics. This structured organization provides an overall view of the research themes in a domain, while also enabling iterative search and deeper knowledge discovery within specific subtopics by allowing users to refine their focus and retrieve additional relevant documents. Knowledge Navigator combines LLM capabilities with cluster-based methods to enable an effective browsing method. We demonstrate our approach's effectiveness through automatic and manual evaluations on two novel benchmarks, CLUSTREC-COVID and SCITOC. Our code, prompts, and benchmarks are made publicly available.

Scholarly data are largely fragmented across siloed databases with divergent metadata and missing linkages among them. We present the Science Data Lake, a locally-deployable infrastructure built on DuckDB and simple Parquet files that unifies eight open sources - Semantic Scholar, OpenAlex, SciSciNet, Papers with Code, Retraction Watch, Reliance on Science, a preprint-to-published mapping, and Crossref - via DOI normalization while preserving source-level schemas. The resource comprises approximately 960GB of Parquet files spanning ~293 million uniquely identifiable papers across ~22 schemas and ~153 SQL views. An embedding-based ontology alignment using BGE-large sentence embeddings maps 4,516 OpenAlex topics to 13 scientific ontologies (~1.3 million terms), yielding 16,150 mappings covering 99.8% of topics (geq 0.65 threshold) with F1 = 0.77 at the recommended geq 0.85 operating point, outperforming TF-IDF, BM25, and Jaro-Winkler baselines on a 300-pair gold-standard evaluation. We validate through 10 automated checks, cross-source citation agreement analysis (pairwise Pearson r = 0.76 - 0.87), and stratified manual annotation. Four vignettes demonstrate cross-source analyses infeasible with any single database. The resource is open source, deployable on a single drive or queryable remotely via HuggingFace, and includes structured documentation suitable for large language model (LLM) based research agents.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

The exponential growth of astronomical literature poses significant challenges for researchers navigating and synthesizing general insights or even domain-specific knowledge. We present Pathfinder, a machine learning framework designed to enable literature review and knowledge discovery in astronomy, focusing on semantic searching with natural language instead of syntactic searches with keywords. Utilizing state-of-the-art large language models (LLMs) and a corpus of 350,000 peer-reviewed papers from the Astrophysics Data System (ADS), Pathfinder offers an innovative approach to scientific inquiry and literature exploration. Our framework couples advanced retrieval techniques with LLM-based synthesis to search astronomical literature by semantic context as a complement to currently existing methods that use keywords or citation graphs. It addresses complexities of jargon, named entities, and temporal aspects through time-based and citation-based weighting schemes. We demonstrate the tool's versatility through case studies, showcasing its application in various research scenarios. The system's performance is evaluated using custom benchmarks, including single-paper and multi-paper tasks. Beyond literature review, Pathfinder offers unique capabilities for reformatting answers in ways that are accessible to various audiences (e.g. in a different language or as simplified text), visualizing research landscapes, and tracking the impact of observatories and methodologies. This tool represents a significant advancement in applying AI to astronomical research, aiding researchers at all career stages in navigating modern astronomy literature.

Finding relevant tables among databases, lakes, and repositories is the first step in extracting value from data. Such a task remains difficult because assessing whether a table is relevant to a problem does not always depend only on its content but also on the context, which is usually tribal knowledge known to the individual or team. While tools like data catalogs and academic data discovery systems target this problem, they rely on keyword search or more complex interfaces, limiting non-technical users' ability to find relevant data. The advent of large language models (LLMs) offers a unique opportunity for users to ask questions directly in natural language, making dataset discovery more intuitive, accessible, and efficient. In this paper, we introduce Pneuma, a retrieval-augmented generation (RAG) system designed to efficiently and effectively discover tabular data. Pneuma leverages large language models (LLMs) for both table representation and table retrieval. For table representation, Pneuma preserves schema and row-level information to ensure comprehensive data understanding. For table retrieval, Pneuma augments LLMs with traditional information retrieval techniques, such as full-text and vector search, harnessing the strengths of both to improve retrieval performance. To evaluate Pneuma, we generate comprehensive benchmarks that simulate table discovery workload on six real-world datasets including enterprise data, scientific databases, warehousing data, and open data. Our results demonstrate that Pneuma outperforms widely used table search systems (such as full-text search and state-of-the-art RAG systems) in accuracy and resource efficiency.

The accessibility of documents within a collection holds a pivotal role in Information Retrieval, signifying the ease of locating specific content in a collection of documents. This accessibility can be achieved via two distinct avenues. The first is through some retrieval model using a keyword or other feature-based search, and the other is where a document can be navigated using links associated with them, if available. Metrics such as PageRank, Hub, and Authority illuminate the pathways through which documents can be discovered within the network of content while the concept of Retrievability is used to quantify the ease with which a document can be found by a retrieval model. In this paper, we compare these two perspectives, PageRank and retrievability, as they quantify the importance and discoverability of content in a corpus. Through empirical experimentation on benchmark datasets, we demonstrate a subtle similarity between retrievability and PageRank particularly distinguishable for larger datasets.

Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including 65 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.

Relational databases play an important role in business, science, and more. However, many users cannot fully unleash the analytical power of relational databases, because they are not familiar with database languages such as SQL. Many techniques have been proposed to automatically generate SQL from natural language, but they suffer from two issues: (1) they still make many mistakes, particularly for complex queries, and (2) they do not provide a flexible way for non-expert users to validate and refine incorrect queries. To address these issues, we introduce a new interaction mechanism that allows users to directly edit a step-by-step explanation of a query to fix errors. Our experiments on multiple datasets, as well as a user study with 24 participants, demonstrate that our approach can achieve better performance than multiple SOTA approaches. Our code and datasets are available at https://github.com/magic-YuanTian/STEPS.

The exponential growth of scientific literature requires effective management and extraction of valuable insights. While existing scientific search engines excel at delivering search results based on relational databases, they often neglect the analysis of collaborations between scientific entities and the evolution of ideas, as well as the in-depth analysis of content within scientific publications. The representation of heterogeneous graphs and the effective measurement, analysis, and mining of such graphs pose significant challenges. To address these challenges, we present AceMap, an academic system designed for knowledge discovery through academic graph. We present advanced database construction techniques to build the comprehensive AceMap database with large-scale academic entities that contain rich visual, textual, and numerical information. AceMap also employs innovative visualization, quantification, and analysis methods to explore associations and logical relationships among academic entities. AceMap introduces large-scale academic network visualization techniques centered on nebular graphs, providing a comprehensive view of academic networks from multiple perspectives. In addition, AceMap proposes a unified metric based on structural entropy to quantitatively measure the knowledge content of different academic entities. Moreover, AceMap provides advanced analysis capabilities, including tracing the evolution of academic ideas through citation relationships and concept co-occurrence, and generating concise summaries informed by this evolutionary process. In addition, AceMap uses machine reading methods to generate potential new ideas at the intersection of different fields. Exploring the integration of large language models and knowledge graphs is a promising direction for future research in idea evolution. Please visit https://www.acemap.info for further exploration.

The aim of the Prague Relational Learning Repository is to support machine learning research with multi-relational data. The repository currently contains 148 SQL databases hosted on a public MySQL server located at https://relational.fel.cvut.cz. The server is provided by the Czech Technical University (CTU). A searchable meta-database provides metadata (e.g., the number of tables in the database, the number of rows and columns in the tables, the number of self-relationships).

Large language models (LLMs) have grown in their usage to provide support for question answering across numerous disciplines. The models on their own have already shown promise for answering basic questions, however fail quickly where expert domain knowledge is required or the question is nuanced. Scientific research often involves searching for relevant literature, distilling pertinent information from that literature and analysing how the findings support or contradict one another. The information is often encapsulated in the full text body of research articles, rather than just in the abstracts. Statements within these articles frequently require the wider article context to be fully understood. We have built an LLM-based system that performs such search and distillation of information encapsulated in scientific literature, and we evaluate our keyword based search and information distillation system against a set of biology related questions from previously released literature benchmarks. We demonstrate sparse retrieval methods exhibit results close to state of the art without the need for dense retrieval, with its associated infrastructure and complexity overhead. We also show how to increase the coverage of relevant documents for literature review generation.

High-quality medical systematic reviews require comprehensive literature searches to ensure the recommendations and outcomes are sufficiently reliable. Indeed, searching for relevant medical literature is a key phase in constructing systematic reviews and often involves domain (medical researchers) and search (information specialists) experts in developing the search queries. Queries in this context are highly complex, based on Boolean logic, include free-text terms and index terms from standardised terminologies (e.g., MeSH), and are difficult and time-consuming to build. The use of MeSH terms, in particular, has been shown to improve the quality of the search results. However, identifying the correct MeSH terms to include in a query is difficult: information experts are often unfamiliar with the MeSH database and unsure about the appropriateness of MeSH terms for a query. Naturally, the full value of the MeSH terminology is often not fully exploited. This paper investigates methods to suggest MeSH terms based on an initial Boolean query that includes only free-text terms. These methods promise to automatically identify highly effective MeSH terms for inclusion in a systematic review query. Our study contributes an empirical evaluation of several MeSH term suggestion methods. We perform an extensive analysis of the retrieval, ranking, and refinement of MeSH term suggestions for each method and how these suggestions impact the effectiveness of Boolean queries.

Recent text-to-SQL systems powered by large language models (LLMs) have demonstrated remarkable performance in translating natural language queries into SQL. However, these systems often struggle with complex database structures and domain-specific queries, as they primarily focus on enhancing logical reasoning and SQL syntax while overlooking the critical need for comprehensive database understanding. To address this limitation, we propose DB-Explore, a novel framework that systematically aligns LLMs with database knowledge through automated exploration and instruction synthesis. DB-Explore constructs database graphs to capture complex relational schemas, leverages GPT-4 to systematically mine structural patterns and semantic knowledge, and synthesizes instructions to distill this knowledge for efficient fine-tuning of LLMs. Our framework enables comprehensive database understanding through diverse sampling strategies and automated instruction generation, bridging the gap between database structures and language models. Experiments conducted on the SPIDER and BIRD benchmarks validate the effectiveness of DB-Explore, achieving an execution accuracy of 52.1% on BIRD and 84.0% on SPIDER. Notably, our open-source implementation, based on the Qwen2.5-coder-7B model, outperforms multiple GPT-4-driven text-to-SQL systems in comparative evaluations, and achieves near state-of-the-art performance with minimal computational cost.

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.

We present SymbioticRAG, a novel framework that fundamentally reimagines Retrieval-Augmented Generation~(RAG) systems by establishing a bidirectional learning relationship between humans and machines. Our approach addresses two critical challenges in current RAG systems: the inherently human-centered nature of relevance determination and users' progression from "unconscious incompetence" in query formulation. SymbioticRAG introduces a two-tier solution where Level 1 enables direct human curation of retrieved content through interactive source document exploration, while Level 2 aims to build personalized retrieval models based on captured user interactions. We implement Level 1 through three key components: (1)~a comprehensive document processing pipeline with specialized models for layout detection, OCR, and extraction of tables, formulas, and figures; (2)~an extensible retriever module supporting multiple retrieval strategies; and (3)~an interactive interface that facilitates both user engagement and interaction data logging. We experiment Level 2 implementation via a retriever strategy incorporated LLM summarized user intention from user interaction logs. To maintain high-quality data preparation, we develop a human-on-the-loop validation interface that improves pipeline output while advancing research in specialized extraction tasks. Evaluation across three scenarios (literature review, geological exploration, and education) demonstrates significant improvements in retrieval relevance and user satisfaction compared to traditional RAG approaches. To facilitate broader research and further advancement of SymbioticRAG Level 2 implementation, we will make our system openly accessible to the research community.

The exponential growth of global academic output has confronted researchers and AI agents with an unprecedented ``information explosion,'' where fragmented and unstructured knowledge organization impedes deep interdisciplinary integration. Current academic retrieval tools predominantly rely on superficial keyword matching or vector-space semantic retrieval, which lack the topological reasoning capabilities required to navigate complex logical connections. Agentic deep-research-based frameworks are often prone to logical hallucinations and consuming high inference costs. To bridge this gap, in this report, we introduce SciAtlas, a large-scale, multi-disciplinary, heterogeneous academic resource knowledge graph designed as a panoramic scientific evolution network. By integrating over 43M papers from 26 disciplines, and a total of 157M entities and 3B triplets, SciAtlas provides a structured topological cognitive substrate that dismantles disciplinary barriers and furnishes AI agents with a global perspective. Furthermore, we develop a neuro-symbolic retrieval algorithm featuring tri-path collaborative recall and graph reranking, achieving a seamless transition from simple semantic matching to deterministic association discovery. We also present key application directions of SciAtlas, including literature review, automated research trend synthesis, idea positioning, and academic trajectory exploration, to demonstrate that SciAtlas can serve as an effective ``cognitive map'' to empower the full loop of automated scientific research while significantly reducing reasoning costs. We have released the interfaces for KG retrieval and various downstream tasks in our GitHub repo.

Scientific progress depends on researchers' ability to synthesize the growing body of literature. Can large language models (LMs) assist scientists in this task? We introduce OpenScholar, a specialized retrieval-augmented LM that answers scientific queries by identifying relevant passages from 45 million open-access papers and synthesizing citation-backed responses. To evaluate OpenScholar, we develop ScholarQABench, the first large-scale multi-domain benchmark for literature search, comprising 2,967 expert-written queries and 208 long-form answers across computer science, physics, neuroscience, and biomedicine. On ScholarQABench, OpenScholar-8B outperforms GPT-4o by 5% and PaperQA2 by 7% in correctness, despite being a smaller, open model. While GPT4o hallucinates citations 78 to 90% of the time, OpenScholar achieves citation accuracy on par with human experts. OpenScholar's datastore, retriever, and self-feedback inference loop also improves off-the-shelf LMs: for instance, OpenScholar-GPT4o improves GPT-4o's correctness by 12%. In human evaluations, experts preferred OpenScholar-8B and OpenScholar-GPT4o responses over expert-written ones 51% and 70% of the time, respectively, compared to GPT4o's 32%. We open-source all of our code, models, datastore, data and a public demo.

Datasets play a critical role in medical imaging research, yet issues such as label quality, shortcuts, and metadata are often overlooked. This lack of attention may harm the generalizability of algorithms and, consequently, negatively impact patient outcomes. While existing medical imaging literature reviews mostly focus on machine learning (ML) methods, with only a few focusing on datasets for specific applications, these reviews remain static -- they are published once and not updated thereafter. This fails to account for emerging evidence, such as biases, shortcuts, and additional annotations that other researchers may contribute after the dataset is published. We refer to these newly discovered findings of datasets as research artifacts. To address this gap, we propose a living review that continuously tracks public datasets and their associated research artifacts across multiple medical imaging applications. Our approach includes a framework for the living review to monitor data documentation artifacts, and an SQL database to visualize the citation relationships between research artifact and dataset. Lastly, we discuss key considerations for creating medical imaging datasets, review best practices for data annotation, discuss the significance of shortcuts and demographic diversity, and emphasize the importance of managing datasets throughout their entire lifecycle. Our demo is publicly available at http://inthepicture.itu.dk/.

Current Information Seeking (InfoSeeking) agents struggle to maintain focus and coherence during long-horizon exploration, as tracking search states, including planning procedure and massive search results, within one plain-text context is inherently fragile. To address this, we introduce Table-as-Search (TaS), a structured planning framework that reformulates the InfoSeeking task as a Table Completion task. TaS maps each query into a structured table schema maintained in an external database, where rows represent search candidates and columns denote constraints or required information. This table precisely manages the search states: filled cells strictly record the history and search results, while empty cells serve as an explicit search plan. Crucially, TaS unifies three distinct InfoSeeking tasks: Deep Search, Wide Search, and the challenging DeepWide Search. Extensive experiments demonstrate that TaS significantly outperforms numerous state-of-the-art baselines across three kinds of benchmarks, including multi-agent framework and commercial systems. Furthermore, our analysis validates the TaS's superior robustness in long-horizon InfoSeeking, alongside its efficiency, scalability and flexibility. Code and datasets are publicly released at https://github.com/AIDC-AI/Marco-Search-Agent.

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

Boolean query construction is often critical for medical systematic review literature search. To create an effective Boolean query, systematic review researchers typically spend weeks coming up with effective query terms and combinations. One challenge to creating an effective systematic review Boolean query is the selection of effective MeSH Terms to include in the query. In our previous work, we created neural MeSH term suggestion methods and compared them to state-of-the-art MeSH term suggestion methods. We found neural MeSH term suggestion methods to be highly effective. In this demonstration, we build upon our previous work by creating (1) a Web-based MeSH term suggestion prototype system that allows users to obtain suggestions from a number of underlying methods and (2) a Python library that implements ours and others' MeSH term suggestion methods and that is aimed at researchers who want to further investigate, create or deploy such type of methods. We describe the architecture of the web-based system and how to use it for the MeSH term suggestion task. For the Python library, we describe how the library can be used for advancing further research and experimentation, and we validate the results of the methods contained in the library on standard datasets. Our web-based prototype system is available at http://ielab-mesh-suggest.uqcloud.net, while our Python library is at https://github.com/ielab/meshsuggestlib.

The Land Matrix initiative (https://landmatrix.org) and its global observatory aim to provide reliable data on large-scale land acquisitions to inform debates and actions in sectors such as agriculture, extraction, or energy in low- and middle-income countries. Although these data are recognized in the academic world, they remain underutilized in public policy, mainly due to the complexity of access and exploitation, which requires technical expertise and a good understanding of the database schema. The objective of this work is to simplify access to data from different database systems. The methods proposed in this article are evaluated using data from the Land Matrix. This work presents various comparisons of Large Language Models (LLMs) as well as combinations of LLM adaptations (Prompt Engineering, RAG, Agents) to query different database systems (GraphQL and REST queries). The experiments are reproducible, and a demonstration is available online: https://github.com/tetis-nlp/landmatrix-graphql-python.

The recent breakthroughs in large language models (LLMs) are positioned to transition many areas of software. Database technologies particularly have an important entanglement with LLMs as efficient and intuitive database interactions are paramount. In this paper, we present DB-GPT, a revolutionary and production-ready project that integrates LLMs with traditional database systems to enhance user experience and accessibility. DB-GPT is designed to understand natural language queries, provide context-aware responses, and generate complex SQL queries with high accuracy, making it an indispensable tool for users ranging from novice to expert. The core innovation in DB-GPT lies in its private LLM technology, which is fine-tuned on domain-specific corpora to maintain user privacy and ensure data security while offering the benefits of state-of-the-art LLMs. We detail the architecture of DB-GPT, which includes a novel retrieval augmented generation (RAG) knowledge system, an adaptive learning mechanism to continuously improve performance based on user feedback and a service-oriented multi-model framework (SMMF) with powerful data-driven agents. Our extensive experiments and user studies confirm that DB-GPT represents a paradigm shift in database interactions, offering a more natural, efficient, and secure way to engage with data repositories. The paper concludes with a discussion of the implications of DB-GPT framework on the future of human-database interaction and outlines potential avenues for further enhancements and applications in the field. The project code is available at https://github.com/eosphoros-ai/DB-GPT. Experience DB-GPT for yourself by installing it with the instructions https://github.com/eosphoros-ai/DB-GPT#install and view a concise 10-minute video at https://www.youtube.com/watch?v=KYs4nTDzEhk.

The existing search tools for exploring the NASA Astrophysics Data System (ADS) can be quite rich and empowering (e.g., similar and trending operators), but researchers are not yet allowed to fully leverage semantic search. For example, a query for "results from the Planck mission" should be able to distinguish between all the various meanings of Planck (person, mission, constant, institutions and more) without further clarification from the user. At ADS, we are applying modern machine learning and natural language processing techniques to our dataset of recent astronomy publications to train astroBERT, a deeply contextual language model based on research at Google. Using astroBERT, we aim to enrich the ADS dataset and improve its discoverability, and in particular we are developing our own named entity recognition tool. We present here our preliminary results and lessons learned.

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.

Text-to-SQL systems powered by Large Language Models have excelled on academic benchmarks but struggle in complex enterprise environments. The primary limitation lies in their reliance on static schema representations, which fails to resolve semantic ambiguity and scale effectively to large, complex databases. To address this, we propose APEX-SQL, an Agentic Text-to-SQL Framework that shifts the paradigm from passive translation to agentic exploration. Our framework employs a hypothesis-verification loop to ground model reasoning in real data. In the schema linking phase, we use logical planning to verbalize hypotheses, dual-pathway pruning to reduce the search space, and parallel data profiling to validate column roles against real data, followed by global synthesis to ensure topological connectivity. For SQL generation, we introduce a deterministic mechanism to retrieve exploration directives, allowing the agent to effectively explore data distributions, refine hypotheses, and generate semantically accurate SQLs. Experiments on BIRD (70.65% execution accuracy) and Spider 2.0-Snow (51.01% execution accuracy) demonstrate that APEX-SQL outperforms competitive baselines with reduced token consumption. Further analysis reveals that agentic exploration acts as a performance multiplier, unlocking the latent reasoning potential of foundation models in enterprise settings. Ablation studies confirm the critical contributions of each component in ensuring robust and accurate data analysis.

Scientific discovery is a cumulative process and requires new ideas to be situated within an ever-expanding landscape of existing knowledge. An emerging and critical challenge is how to identify conceptually relevant prior work from rapidly growing literature, and assess how a new idea differentiates from existing research. Current embedding approaches typically conflate distinct conceptual aspects into single representations and cannot support fine-grained literature retrieval; meanwhile, LLM-based evaluators are subject to sycophancy biases, failing to provide discriminative novelty assessment. To tackle these challenges, we introduce the Ideation Space, a structured representation that decomposes scientific knowledge into three distinct dimensions, i.e., research problem, methodology, and core findings, each learned through contrastive training. This framework enables principled measurement of conceptual distance between ideas, and modeling of ideation transitions that capture the logical connections within a proposed idea. Building upon this representation, we propose a Hierarchical Sub-Space Retrieval framework for efficient, targeted literature retrieval, and a Decomposed Novelty Assessment algorithm that identifies which aspects of an idea are novel. Extensive experiments demonstrate substantial improvements, where our approach achieves Recall@30 of 0.329 (16.7% over baselines), our ideation transition retrieval reaches Hit Rate@30 of 0.643, and novelty assessment attains 0.37 correlation with expert judgments. In summary, our work provides a promising paradigm for future research on accelerating and evaluating scientific discovery.

Scientific researchers need intensive information about datasets to effectively evaluate and develop theories and methodologies. The information needs regarding datasets are implicitly embedded in particular research tasks, rather than explicitly expressed in search queries. However, existing scientific retrieval and question-answering (QA) datasets typically address straightforward questions, which do not align with the distribution of real-world research inquiries. To bridge this gap, we developed ScIRGen, a dataset generation framework for scientific QA \& retrieval that more accurately reflects the information needs of professional science researchers, and uses it to create a large-scale scientific retrieval-augmented generation (RAG) dataset with realistic queries, datasets and papers. Technically, we designed a dataset-oriented information extraction method that leverages academic papers to augment the dataset representation. We then proposed a question generation framework by employing cognitive taxonomy to ensure the quality of synthesized questions. We also design a method to automatically filter synthetic answers based on the perplexity shift of LLMs, which is highly aligned with human judgment of answers' validity. Collectively, these methodologies culminated in the creation of the 61k QA dataset, ScIRGen-Geo. We benchmarked representative methods on the ScIRGen-Geo dataset for their question-answering and retrieval capabilities, finding out that current methods still suffer from reasoning from complex questions. This work advances the development of more sophisticated tools to support the intricate information needs of the scientific community.

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

Chemistry literature synthesis often requires assembling specific findings scattered across many publications, yet existing literature-search systems primarily return ranked document lists. As a result, scientists and AI agents need to locate relevant information, verify their provenance, and assemble cross-paper answers manually. We present AskChem, a claim-centered infrastructure for cross-paper chemistry search. AskChem changes the unit of retrieval from the paper to the provenance-carrying claim: each paper is converted into atomic, typed claims, each grounded by a source DOI and a verbatim quote or an explicit evidence locator. Over this shared claim store, AskChem exposes complementary structures for search and synthesis: a stabilized faceted taxonomy for hierarchical retrieval and browsing, an evidence graph linking claims through relations, and an exploratory living taxonomy that situates indexed papers under scientific principles. AskChem currently indexes 2.4M claims from 147K papers and provides a web interface, as well as REST, SDK, and MCP access for AI agents. On AskChem-Bench, grounding a GPT-5.5 reader in AskChem yields 100% resolvable DOIs, compared with 88.3% without retrieval, and the highest citation density among five tested systems. AskChem is live at https://askchem.org.

The data landscape is rich with structured data, often of high value to organizations, driving important applications in data analysis and machine learning. Recent progress in representation learning and generative models for such data has led to the development of natural language interfaces to structured data, including those leveraging text-to-SQL. Contextualizing interactions, either through conversational interfaces or agentic components, in structured data through retrieval-augmented generation can provide substantial benefits in the form of freshness, accuracy, and comprehensiveness of answers. The key question is: how do we retrieve the right table(s) for the analytical query or task at hand? To this end, we introduce TARGET: a benchmark for evaluating TAble Retrieval for GEnerative Tasks. With TARGET we analyze the retrieval performance of different retrievers in isolation, as well as their impact on downstream tasks. We find that dense embedding-based retrievers far outperform a BM25 baseline which is less effective than it is for retrieval over unstructured text. We also surface the sensitivity of retrievers across various metadata (e.g., missing table titles), and demonstrate a stark variation of retrieval performance across datasets and tasks. TARGET is available at https://target-benchmark.github.io.

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

Schema linking -- the process of aligning natural language questions with database schema elements -- is a critical yet underexplored component of Text-to-SQL systems. While recent methods have focused primarily on improving SQL generation, they often neglect the retrieval of relevant schema elements, which can lead to hallucinations and execution failures. In this work, we propose a context-aware bidirectional schema retrieval framework that treats schema linking as a standalone problem. Our approach combines two complementary strategies: table-first retrieval followed by column selection, and column-first retrieval followed by table selection. It is further augmented with techniques such as question decomposition, keyword extraction, and keyphrase extraction. Through comprehensive evaluations on challenging benchmarks such as BIRD and Spider, we demonstrate that our method significantly improves schema recall while reducing false positives. Moreover, SQL generation using our retrieved schema consistently outperforms full-schema baselines and closely approaches oracle performance, all without requiring query refinement. Notably, our method narrows the performance gap between full and perfect schema settings by 50\%. Our findings highlight schema linking as a powerful lever for enhancing Text-to-SQL accuracy and efficiency.

Query rewriting aims to generate a new query that can complement the original query to improve the information retrieval system. Recent studies on query rewriting, such as query2doc (Q2D), query2expand (Q2E) and querey2cot (Q2C), rely on the internal knowledge of Large Language Models (LLMs) to generate a relevant passage to add information to the query. Nevertheless, the efficacy of these methodologies may markedly decline in instances where the requisite knowledge is not encapsulated within the model's intrinsic parameters. In this paper, we propose a novel structured query rewriting method called Crafting the Path tailored for retrieval systems. Crafting the Path involves a three-step process that crafts query-related information necessary for finding the passages to be searched in each step. Specifically, the Crafting the Path begins with Query Concept Comprehension, proceeds to Query Type Identification, and finally conducts Expected Answer Extraction. Experimental results show that our method outperforms previous rewriting methods, especially in less familiar domains for LLMs. We demonstrate that our method is less dependent on the internal parameter knowledge of the model and generates queries with fewer factual inaccuracies. Furthermore, we observe that Crafting the Path has less latency compared to the baselines.

Identifying the intent of a citation in scientific papers (e.g., background information, use of methods, comparing results) is critical for machine reading of individual publications and automated analysis of the scientific literature. We propose structural scaffolds, a multitask model to incorporate structural information of scientific papers into citations for effective classification of citation intents. Our model achieves a new state-of-the-art on an existing ACL anthology dataset (ACL-ARC) with a 13.3% absolute increase in F1 score, without relying on external linguistic resources or hand-engineered features as done in existing methods. In addition, we introduce a new dataset of citation intents (SciCite) which is more than five times larger and covers multiple scientific domains compared with existing datasets. Our code and data are available at: https://github.com/allenai/scicite.

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.

Scientific reading is an active process that frequently requires consulting external resources, but manual keyword searching interrupts the reading flow and imposes a high cognitive load. Existing proactive information retrieval systems often suffer from context ambiguity, as they rely solely on on-screen text and ignore the reader's specific background and intent. In this demonstration, we present H-MAPS (Hierarchical Memory-Augmented Proactive Search Assistant), a proactive literature exploration assistant that resolves this ambiguity by leveraging a three-layered hierarchical memory. Triggered by implicit reading behaviors, H-MAPS articulates the user's latent information needs into explicit natural language questions and performs neural retrieval entirely on the local device to ensure privacy. We demonstrate H-MAPS using a scenario where two researchers, specializing in NLP and HCI, read the same paper. In response, the system generates profile-specific questions and retrieves distinct literature tailored to each user.

Scientific literature searches are often exploratory, whereby users are not yet familiar with a particular field or concept but are interested in learning more about it. However, existing systems for scientific literature search are typically tailored to keyword-based lookup searches, limiting the possibilities for exploration. We propose NLP-KG, a feature-rich system designed to support the exploration of research literature in unfamiliar natural language processing (NLP) fields. In addition to a semantic search, NLP-KG allows users to easily find survey papers that provide a quick introduction to a field of interest. Further, a Fields of Study hierarchy graph enables users to familiarize themselves with a field and its related areas. Finally, a chat interface allows users to ask questions about unfamiliar concepts or specific articles in NLP and obtain answers grounded in knowledge retrieved from scientific publications. Our system provides users with comprehensive exploration possibilities, supporting them in investigating the relationships between different fields, understanding unfamiliar concepts in NLP, and finding relevant research literature. Demo, video, and code are available at: https://github.com/NLP-Knowledge-Graph/NLP-KG-WebApp.

Scientists increasingly rely on open-source tools to support their research workflows, yet discovering relevant software among over 600 million GitHub repositories remains challenging. Existing code search benchmarks focus on general software engineering tasks and fail to capture the domain-specific vocabulary and needs of scientific computing. We present a curated corpus of 5,264 high-quality, domain-classified scientific repositories spanning five NASA Science Mission Directorate divisions -- Earth Science, Astrophysics, Planetary Science, Heliophysics, and Biological & Physical Sciences -- enriched with cleaned READMEs, extracted topics, and additional context from crawled links. Building on this corpus, we introduce two novel information retrieval benchmarks: (1) a repository search benchmark with 219 expert-curated queries designed by domain scientists, and (2) a large-scale code snippet retrieval benchmark containing 117,950 code snippets and 119,720 queries across seven programming languages. Baseline evaluations on repository search reveal significant performance variation across scientific domains. Code snippet retrieval proves equally challenging, with substantial variation driven by differing documentation practices, coding standards, and programming language conventions across scientific communities. All datasets and benchmarks are publicly released on HuggingFace to support research on scientific tool discovery.

Model cards describe model behavior through a mixture of textual descriptions and structured artifacts, including performance, configuration, and dataset tables. Existing model search systems rely predominantly on semantic similarity over text, which can produce homogeneous result sets and limit exploration of alternatives. We argue that model search is inherently comparative: users want models that are task-aligned yet differentiated in measurable ways. We hypothesize that this balance requires retrieval over condensed, high-quality evidence rather than verbose descriptions, and much of that evidence is concentrated in structured tables. We present StructuredSemanticSearch, a table-driven model search framework built on the ModelTables benchmark. Given a query, StructuredSemanticSearch combines a semantic baseline for task alignment with a structure-aware pipeline that discovers query-related model-card tables using table discovery operators such as unionability, joinability, and keyword search. Retrieved tables are mapped back to model cards under a controlled top-k budget, enabling fair comparison between text-based and table-based retrieval. Beyond retrieval, StructuredSemanticSearch adapts table integration to the model-table domain through orientation-aware integration, producing compact integrated views of tables from partially overlapping and sometimes transposed evidence tables. For evaluation, we introduce a nugget-based, auditable protocol that extracts compact evidence items from model cards, matches queries to condition- or intent-specific nuggets, and measures evidence coverage and diversity over retrieved model-card candidate sets. This protocol also provides a scalable path toward approximate, evidence-based labeling in dynamic model lakes. Experiments on 597 model-recommendation queries show improved nugget coverage for the structure-aware pipeline than semantic baseline

Most scientific materials compress reasoning, presenting conclusions while omitting the derivational chains that justify them. This compression hinders verification by lacking explicit, step-wise justifications and inhibits cross-domain links by collapsing the very pathways that establish the logical and causal connections between concepts. We introduce a scalable framework that decompresses scientific reasoning, constructing a verifiable Long Chain-of-Thought (LCoT) knowledge base and projecting it into an emergent encyclopedia, SciencePedia. Our pipeline operationalizes an endpoint-driven, reductionist strategy: a Socratic agent, guided by a curriculum of around 200 courses, generates approximately 3 million first-principles questions. To ensure high fidelity, multiple independent solver models generate LCoTs, which are then rigorously filtered by prompt sanitization and cross-model answer consensus, retaining only those with verifiable endpoints. This verified corpus powers the Brainstorm Search Engine, which performs inverse knowledge search -- retrieving diverse, first-principles derivations that culminate in a target concept. This engine, in turn, feeds the Plato synthesizer, which narrates these verified chains into coherent articles. The initial SciencePedia comprises approximately 200,000 fine-grained entries spanning mathematics, physics, chemistry, biology, engineering, and computation. In evaluations across six disciplines, Plato-synthesized articles (conditioned on retrieved LCoTs) exhibit substantially higher knowledge-point density and significantly lower factual error rates than an equally-prompted baseline without retrieval (as judged by an external LLM). Built on this verifiable LCoT knowledge base, this reasoning-centric approach enables trustworthy, cross-domain scientific synthesis at scale and establishes the foundation for an ever-expanding encyclopedia.

Researchers and scientists increasingly rely on specialized information retrieval (IR) or recommendation systems (RS) to support them in their daily research tasks. Paper recommender systems are one such tool scientists use to stay on top of the ever-increasing number of academic publications in their field. Improving research paper recommender systems is an active research field. However, less research has focused on how the interfaces of research paper recommender systems can be tailored to suit the needs of different research domains. For example, in the field of biomedicine and chemistry, researchers are not only interested in textual relevance but may also want to discover or compare the contained chemical entity information found in a paper's full text. Existing recommender systems for academic literature do not support the discovery of this non-textual, but semantically valuable, chemical entity data. We present the first implementation of a specialized chemistry paper recommender system capable of visualizing the contained chemical structures, chemical formulae, and synonyms for chemical compounds within the document's full text. We review existing tools and related research in this field before describing the implementation of our ChemVis system. With the help of chemists, we are expanding the functionality of ChemVis, and will perform an evaluation of recommendation performance and usability in future work.

There has been a surge of interest in harnessing the reasoning capabilities of Large Language Models (LLMs) to accelerate scientific discovery. While existing approaches rely on grounding the discovery process within the relevant literature, effectiveness varies significantly with the quality and nature of the retrieved literature. We address the challenge of retrieving prior work whose concepts can inspire solutions for a given research problem, a task we define as Methodology Inspiration Retrieval (MIR). We construct a novel dataset tailored for training and evaluating retrievers on MIR, and establish baselines. To address MIR, we build the Methodology Adjacency Graph (MAG); capturing methodological lineage through citation relationships. We leverage MAG to embed an "intuitive prior" into dense retrievers for identifying patterns of methodological inspiration beyond superficial semantic similarity. This achieves significant gains of +5.4 in Recall@3 and +7.8 in Mean Average Precision (mAP) over strong baselines. Further, we adapt LLM-based re-ranking strategies to MIR, yielding additional improvements of +4.5 in Recall@3 and +4.8 in mAP. Through extensive ablation studies and qualitative analyses, we exhibit the promise of MIR in enhancing automated scientific discovery and outline avenues for advancing inspiration-driven retrieval.

Subject classification schemes are foundational to the organization, evaluation, and navigation of scientific knowledge. While expert-curated systems like Scopus provide widely used taxonomies, they often suffer from coarse granularity, subjectivity, and limited adaptability to emerging interdisciplinary fields. Data-driven alternatives based on citation networks show promise but lack rigorous, external validation against the semantic content of scientific literature. Here, we propose a novel quantitative framework that leverages classification tasks to evaluate the effectiveness of journal classification schemes. Using over 23 million paper abstracts, we demonstrate that labels derived from k-means clustering on Periodical2Vec (P2V)--a periodical embedding learned from paper-level citations--yield significantly higher classification performance than both Scopus and other data-driven baselines (e.g., citation, co-citation, and Node2Vec variants). By comparing journal partitions across classification schemes, two structural patterns emerge on the map of science: (1) the reorganization of disciplinary boundaries--splitting overly broad categories (e.g., "Medicine" into "Oncology", "Cardiology", and other specialties) while merging artificially fragmented ones (e.g., "Chemistry" and "Chemical Engineering"); and (2) the identification of coherent interdisciplinary clusters--such as "Biomedical Engineering", "Medical Ethics", and "Information Management"--that are dispersed across multiple categories but unified in citation space. These findings underscore that citation-derived periodical embeddings not only outperform traditional taxonomies in predictive validity but also offer a dynamic, fine-grained map of science that better reflects both the specialization and interdisciplinarity inherent in contemporary research.

Information retrieval is a rapidly evolving field. However it still faces significant limitations in the scientific and industrial vast amounts of information, such as semantic divergence and vocabulary gaps in sparse retrieval, low precision and lack of interpretability in semantic search, or hallucination and outdated information in generative models. In this paper, we introduce a two-block approach to tackle these hurdles for long documents. The first block enhances language understanding in sparse retrieval by query expansion to retrieve relevant documents. The second block deepens the result by providing comprehensive and informative answers to the complex question using only the information spread in the long document, enabling bidirectional engagement. At various stages of the pipeline, intermediate results are presented to users to facilitate understanding of the system's reasoning. We believe this bidirectional approach brings significant advancements in terms of transparency, logical thinking, and comprehensive understanding in the field of scientific information retrieval.

ResearchPilot is an open-source, self-hostable multi-agent system for literature-review assistance. Given a natural-language research question, it retrieves papers from Semantic Scholar and arXiv, extracts structured findings from paper abstracts, synthesizes cross-paper patterns, and drafts a citation-aware related-work section. The system combines FastAPI, Next.js, DSPy, SQLite, and Qdrant in a local-first architecture that supports bring-your-own-key model access and remote-or-local embeddings. This paper describes the system design, typed agent interfaces, persistence and history-search mechanisms, and the engineering tradeoffs involved in building a transparent research assistant. Rather than claiming algorithmic novelty, we present ResearchPilot as a systems contribution and evaluate it through automated tests and end-to-end local runs. We discuss limitations including external API rate limits, abstract-only extraction, incomplete corpus coverage, and the lack of citation verification.

The rapid acceleration of scientific publishing has created substantial challenges for researchers attempting to discover, contextualize, and interpret relevant literature. Traditional keyword-based search systems provide limited semantic understanding, while existing AI-driven tools typically focus on isolated tasks such as retrieval, clustering, or bibliometric visualization. This paper presents an integrated system for scientific literature exploration that combines large-scale data acquisition, hybrid retrieval, semantic topic modeling, and heterogeneous knowledge graph construction. The system builds a comprehensive corpus by merging full-text data from arXiv with structured metadata from OpenAlex. A hybrid retrieval architecture fuses BM25 lexical search with embedding-based semantic search using Reciprocal Rank Fusion. Topic modeling is performed on retrieved results using BERTopic or non-negative matrix factorization depending on computational resources. A knowledge graph unifies papers, authors, institutions, countries, and extracted topics into an interpretable structure. The system provides a multi-layered exploration environment that reveals not only relevant publications but also the conceptual and relational landscape surrounding a query. Evaluation across multiple queries demonstrates improvements in retrieval relevance, topic coherence, and interpretability. The proposed framework contributes an extensible foundation for AI-assisted scientific discovery.

Scientific progress depends on sequences of enabling contributions, yet existing AI4Science benchmarks largely focus on citation prediction, literature retrieval, or idea generation rather than the dependencies that make progress possible. In this paper, we introduce discovery pathway forecasting: given a target scientific contribution and the prior literature available at a specified time, the task is to (1) identify the enabling contributions required to realize it and (2) ground each in prior work when such prior work exists. We present SciPaths, a benchmark of 262 expert-annotated gold pathways and 2,444 silver pathways constructed from machine learning and natural language processing papers, where each pathway records enabling contributions, roles, rationales, and prior-work groundings or unmapped decisions. Evaluating frontier and open-weight language models, we find that the best model reaches only 0.189 F1 under strict semantic matching, with core methodological dependencies hardest to recover. Prior-work grounding improves substantially when gold enabling contributions are provided, showing that decomposition quality is a major bottleneck for end-to-end pathway recovery. SciPaths therefore shifts evaluation toward a missing capability in scientific forecasting: reasoning backward from a target contribution to the enabling scientific building blocks and prior-work dependencies that make it feasible.

Schema linking is a crucial step in Text-to-SQL pipelines, which translate natural language queries into SQL. The goal of schema linking is to retrieve relevant tables and columns (signal) while disregarding irrelevant ones (noise). However, imperfect schema linking can often exclude essential columns needed for accurate query generation. In this work, we revisit the need for schema linking when using the latest generation of large language models (LLMs). We find empirically that newer models are adept at identifying relevant schema elements during generation, without the need for explicit schema linking. This allows Text-to-SQL pipelines to bypass schema linking entirely and instead pass the full database schema to the LLM, eliminating the risk of excluding necessary information. Furthermore, as alternatives to schema linking, we propose techniques that improve Text-to-SQL accuracy without compromising on essential schema information. Our approach achieves 71.83\% execution accuracy on the BIRD benchmark, ranking first at the time of submission.

Scientific discovery workflows usually contain and rely heavily on lab notes, where researchers record observations, interpret uncertain results, and plan follow-up experiments. Such informative lab notes preserve evolving scientific reasoning and author uncertainty, rather than polished final results exhibited in publications, providing a valuable opportunity for AI to engage in scientific exploration at a more comprehensive and deeper level. However, most prior work on scientific text focuses on papers, protocols, or structured databases, leaving informal laboratory notes underexplored as inputs to AI agents for science. This gap matters because lab notes often intermingle validated observations, tentative judgments, and possible experimental next steps within the same passage. If these signals are conflated, an AI agent may mistake uncertain scientific judgments for confirmed conclusions or executable actions. To this end, we present Notes2Skills, a two-stage framework for turning lab notebooks into verifiable skills for scientific AI agents while preserving the author's certainty. Across seven conditions and three wet-lab sessions, Notes2Skills is the only configuration that neither mistakes uncertain notes for firm instructions nor discards firm ones. We show that certainty preservation is the missing piece between lab notebooks and reliable agent skills, opening a path toward safer AI co-scientist systems.

Scientific literature search often requires more than retrieving papers from a single query: users' intents are underspecified, preference-dependent, and evolve through interaction. Existing search agents typically rely on fixed pipelines or implicit language-only reasoning, making their search strategies difficult to control, inspect, and refine. We introduce PaperPilot, a multi-turn literature search agent that frames scientific search as workflow induction. Given an anchor paper and a user query, PaperPilot constructs an executable DAG of paper-search operators, including keyword search, citation expansion, filtering, scoring, reranking, and evidence extraction. User feedback is then used to refine both the query and the workflow itself. We train PaperPilot with supervised workflow imitation and preference optimization over controlled workflow corruptions. Experiments show that PaperPilot-9B improves over the base Qwen3.5-9B toolset agent under multi-turn interaction, increasing Hit@5 from 58.0 to 77.0, MRR from 47.5 to 59.4, and nDCG@10 from 26.8 to 32.5, while reducing workflow execution errors from 9.5% to 0%. These results show that explicit, editable search workflows provide an effective and controllable interface for aligning literature search agents with complex scientific intent.

Hypothesis ranking is a crucial component of automated scientific discovery, particularly in natural sciences where wet-lab experiments are costly and throughput-limited. Existing approaches focus on pre-experiment ranking, relying solely on large language model's internal reasoning without incorporating empirical outcomes from experiments. We introduce the task of experiment-guided ranking, which aims to prioritize candidate hypotheses based on the results of previously tested ones. However, developing such strategies is challenging due to the impracticality of repeatedly conducting real experiments in natural science domains. To address this, we propose a simulator grounded in three domain-informed assumptions, modeling hypothesis performance as a function of similarity to a known ground truth hypothesis, perturbed by noise. We curate a dataset of 124 chemistry hypotheses with experimentally reported outcomes to validate the simulator. Building on this simulator, we develop a pseudo experiment-guided ranking method that clusters hypotheses by shared functional characteristics and prioritizes candidates based on insights derived from simulated experimental feedback. Experiments show that our method outperforms pre-experiment baselines and strong ablations.

Scientific paper retrieval is essential for supporting literature discovery and research. While dense retrieval methods demonstrate effectiveness in general-purpose tasks, they often fail to capture fine-grained scientific concepts that are essential for accurate understanding of scientific queries. Recent studies also use large language models (LLMs) for query understanding; however, these methods often lack grounding in corpus-specific knowledge and may generate unreliable or unfaithful content. To overcome these limitations, we propose SemRank, an effective and efficient paper retrieval framework that combines LLM-guided query understanding with a concept-based semantic index. Each paper is indexed using multi-granular scientific concepts, including general research topics and detailed key phrases. At query time, an LLM identifies core concepts derived from the corpus to explicitly capture the query's information need. These identified concepts enable precise semantic matching, significantly enhancing retrieval accuracy. Experiments show that SemRank consistently improves the performance of various base retrievers, surpasses strong existing LLM-based baselines, and remains highly efficient.

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

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.

Extraction and synthesis of structured knowledge from extensive scientific literature are crucial for advancing and disseminating scientific progress. Although many existing systems facilitate literature review and digest, they struggle to process multimodal, varied, and inconsistent information within and across the literature into structured data. We introduce SciDaSynth, a novel interactive system powered by large language models (LLMs) that enables researchers to efficiently build structured knowledge bases from scientific literature at scale. The system automatically creates data tables to organize and summarize users' interested knowledge in literature via question-answering. Furthermore, it provides multi-level and multi-faceted exploration of the generated data tables, facilitating iterative validation, correction, and refinement. Our within-subjects study with researchers demonstrates the effectiveness and efficiency of SciDaSynth in constructing quality scientific knowledge bases. We further discuss the design implications for human-AI interaction tools for data extraction and structuring.

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

Tabular data constitute a dominant form of information in modern data lakes and repositories, yet discovering the relevant tables to answer user questions remains challenging. Existing data discovery systems assume that each question can be answered by a single table and often rely on resource-intensive offline preprocessing, such as model training or large-scale content indexing. In practice, however, many questions require information spread across multiple tables -- either independently or through joins -- and users often seek specific cell values rather than entire tables. In this paper, we present Octopus, a lightweight, entity-aware, and training-free system for multi-table data discovery and cell-level value retrieval. Instead of embedding entire questions, Octopus identifies fine-grained entities (column mentions and value mentions) from natural-language queries using an LLM parser. It then matches these entities to table headers through a compact embedding index and scans table contents directly for value occurrences, eliminating the need for heavy content indexing or costly offline stages. The resulting fine-grained alignment not only improves table retrieval accuracy but also facilitates efficient downstream NL2SQL execution by reducing token usage and redundant LLM calls. To evaluate Octopus, we introduce a new benchmark covering both table- and cell-level discovery under multi-table settings, including five datasets for independent discovery and two for join-based discovery. Experimental results show that Octopus consistently outperforms existing systems while achieving substantially lower computational and token costs. Code is available at https://github.com/wenzhilics/octopus.

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

On October 19 and 20, 2023, the authors of this report convened in Cambridge, MA, to discuss the state of the database research field, its recent accomplishments and ongoing challenges, and future directions for research and community engagement. This gathering continues a long standing tradition in the database community, dating back to the late 1980s, in which researchers meet roughly every five years to produce a forward looking report. This report summarizes the key takeaways from our discussions. We begin with a retrospective on the academic, open source, and commercial successes of the community over the past five years. We then turn to future opportunities, with a focus on core data systems, particularly in the context of cloud computing and emerging hardware, as well as on the growing impact of data science, data governance, and generative AI. This document is not intended as an exhaustive survey of all technical challenges or industry innovations in the field. Rather, it reflects the perspectives of senior community members on the most pressing challenges and promising opportunities ahead.

The burgeoning integration of 3D medical imaging into healthcare has led to a substantial increase in the workload of medical professionals. To assist clinicians in their diagnostic processes and alleviate their workload, the development of a robust system for retrieving similar case studies presents a viable solution. While the concept holds great promise, the field of 3D medical text-image retrieval is currently limited by the absence of robust evaluation benchmarks and curated datasets. To remedy this, our study presents a groundbreaking dataset, BIMCV-R (This dataset will be released upon acceptance.), which includes an extensive collection of 8,069 3D CT volumes, encompassing over 2 million slices, paired with their respective radiological reports. Expanding upon the foundational work of our dataset, we craft a retrieval strategy, MedFinder. This approach employs a dual-stream network architecture, harnessing the potential of large language models to advance the field of medical image retrieval beyond existing text-image retrieval solutions. It marks our preliminary step towards developing a system capable of facilitating text-to-image, image-to-text, and keyword-based retrieval tasks.

Recent advancements in Text-to-SQL (Text2SQL) emphasize stimulating the large language models (LLM) on in-context learning, achieving significant results. Nevertheless, they face challenges when dealing with verbose database information and complex user intentions. This paper presents a two-stage framework to enhance the performance of current LLM-based natural language to SQL systems. We first introduce a novel prompt representation, called reference-enhanced representation, which includes schema information and randomly sampled cell values from tables to instruct LLMs in generating SQL queries. Then, in the first stage, question-SQL pairs are retrieved as few-shot demonstrations, prompting the LLM to generate a preliminary SQL (PreSQL). After that, the mentioned entities in PreSQL are parsed to conduct schema linking, which can significantly compact the useful information. In the second stage, with the linked schema, we simplify the prompt's schema information and instruct the LLM to produce the final SQL. Finally, as the post-refinement module, we propose using cross-consistency across different LLMs rather than self-consistency within a particular LLM. Our methods achieve new SOTA results on the Spider benchmark, with an execution accuracy of 87.6%.

Retrieval models are often evaluated on partially-annotated datasets. Each query is mapped to a few relevant texts and the remaining corpus is assumed to be irrelevant. As a result, models that successfully retrieve false negatives are punished in evaluation. Unfortunately, completely annotating all texts for every query is not resource efficient. In this work, we show that using partially-annotated datasets in evaluation can paint a distorted picture. We curate D-MERIT, a passage retrieval evaluation set from Wikipedia, aspiring to contain all relevant passages for each query. Queries describe a group (e.g., ``journals about linguistics'') and relevant passages are evidence that entities belong to the group (e.g., a passage indicating that Language is a journal about linguistics). We show that evaluating on a dataset containing annotations for only a subset of the relevant passages might result in misleading ranking of the retrieval systems and that as more relevant texts are included in the evaluation set, the rankings converge. We propose our dataset as a resource for evaluation and our study as a recommendation for balance between resource-efficiency and reliable evaluation when annotating evaluation sets for text retrieval.

Modern machine learning relies on datasets to develop and validate research ideas. Given the growth of publicly available data, finding the right dataset to use is increasingly difficult. Any research question imposes explicit and implicit constraints on how well a given dataset will enable researchers to answer this question, such as dataset size, modality, and domain. We operationalize the task of recommending datasets given a short natural language description of a research idea, to help people find relevant datasets for their needs. Dataset recommendation poses unique challenges as an information retrieval problem; datasets are hard to directly index for search and there are no corpora readily available for this task. To facilitate this task, we build the DataFinder Dataset which consists of a larger automatically-constructed training set (17.5K queries) and a smaller expert-annotated evaluation set (392 queries). Using this data, we compare various information retrieval algorithms on our test set and present a superior bi-encoder retriever for text-based dataset recommendation. This system, trained on the DataFinder Dataset, finds more relevant search results than existing third-party dataset search engines. To encourage progress on dataset recommendation, we release our dataset and models to the public.

There are a few prominent practices for conducting reviews of academic literature, including searching for specific keywords on Google Scholar or checking citations from some initial seed paper(s). These approaches serve a critical purpose for academic literature reviews, yet there remain challenges in identifying relevant literature when similar work may utilize different terminology (e.g., mixed-initiative visual analytics papers may not use the same terminology as papers on model-steering, yet the two topics are relevant to one another). In this paper, we introduce a system, VitaLITy, intended to complement existing practices. In particular, VitaLITy promotes serendipitous discovery of relevant literature using transformer language models, allowing users to find semantically similar papers in a word embedding space given (1) a list of input paper(s) or (2) a working abstract. VitaLITy visualizes this document-level embedding space in an interactive 2-D scatterplot using dimension reduction. VitaLITy also summarizes meta information about the document corpus or search query, including keywords and co-authors, and allows users to save and export papers for use in a literature review. We present qualitative findings from an evaluation of VitaLITy, suggesting it can be a promising complementary technique for conducting academic literature reviews. Furthermore, we contribute data from 38 popular data visualization publication venues in VitaLITy, and we provide scrapers for the open-source community to continue to grow the list of supported venues.

Recent advances in Tool-Integrated Large Language Models have made web search a core capability of information-seeking agents. However, as interaction histories grow, agents increasingly struggle to track task progress. When search attempts fail to yield useful evidence, current single- and multi-agent systems can become trapped in repetitive loops, wasting search budgets and ultimately compromising the quality and completeness of the final output. We introduce SearchOS, a system-level multi-agent framework that turns fragile, implicit search progress into explicit, persistent, and shared state. First, we formulate open-domain information seeking as relational schema completion with grounded citations, where agents discover entities, populate attributes across linked tables, and anchor each value to source evidence. Then we design Search-Oriented Context Management (SOCM), which externalizes the evolving state into Frontier Task, an Evidence Graph, a Coverage Map, and Failure Memory. Built on SOCM, SearchOS applies a pipeline-parallel scheduling mechanism that overlaps the execution of sub-agents and continuously refills freed slots with tasks targeting unresolved coverage gaps to improve utilization and throughput. To schedule and control the execution of search agents, SearchOS introduces a Search Tool Middleware Harness that intercepts model and tool interactions to record grounded evidence and react to stalls or budget exhaustion, and provides a reusable hierarchical skill system comprising strategy and access skills to augment the agents' search process and avoid repeating failed search patterns across runs. On WideSearch and GISA, SearchOS leads all metrics among the evaluated single- and multi-agent baselines, paving the way toward robust information-seeking collaboration.

Recent advances in Retrieval-Augmented Generation (RAG) have shifted from simple vector similarity to structure-aware approaches like HippoRAG, which leverage Knowledge Graphs (KGs) and Personalized PageRank (PPR) to capture multi-hop dependencies. However, these methods suffer from a "Static Graph Fallacy": they rely on fixed transition probabilities determined during indexing. This rigidity ignores the query-dependent nature of edge relevance, causing semantic drift where random walks are diverted into high-degree "hub" nodes before reaching critical downstream evidence. Consequently, models often achieve high partial recall but fail to retrieve the complete evidence chain required for multi-hop queries. To address this, we propose CatRAG, Context-Aware Traversal for robust RAG, a framework that builds on the HippoRAG 2 architecture and transforms the static KG into a query-adaptive navigation structure. We introduce a multi-faceted framework to steer the random walk: (1) Symbolic Anchoring, which injects weak entity constraints to regularize the random walk; (2) Query-Aware Dynamic Edge Weighting, which dynamically modulates graph structure, to prune irrelevant paths while amplifying those aligned with the query's intent; and (3) Key-Fact Passage Weight Enhancement, a cost-efficient bias that structurally anchors the random walk to likely evidence. Experiments across four multi-hop benchmarks demonstrate that CatRAG consistently outperforms state of the art baselines. Our analysis reveals that while standard Recall metrics show modest gains, CatRAG achieves substantial improvements in reasoning completeness, the capacity to recover the entire evidence path without gaps. These results reveal that our approach effectively bridges the gap between retrieving partial context and enabling fully grounded reasoning. Resources are available at https://github.com/kwunhang/CatRAG.

Measures for research activity and impact have become an integral ingredient in the assessment of a wide range of entities (individual researchers, organizations, instruments, regions, disciplines). Traditional bibliometric indicators, like publication and citation based indicators, provide an essential part of this picture, but cannot describe the complete picture. Since reading scholarly publications is an essential part of the research life cycle, it is only natural to introduce measures for this activity in attempts to quantify the efficiency, productivity and impact of an entity. Citations and reads are significantly different signals, so taken together, they provide a more complete picture of research activity. Most scholarly publications are now accessed online, making the study of reads and their patterns possible. Click-stream logs allow us to follow information access by the entire research community, real-time. Publication and citation datasets just reflect activity by authors. In addition, download statistics will help us identify publications with significant impact, but which do not attract many citations. Click-stream signals are arguably more complex than, say, citation signals. For one, they are a superposition of different classes of readers. Systematic downloads by crawlers also contaminate the signal, as does browsing behavior. We discuss the complexities associated with clickstream data and how, with proper filtering, statistically significant relations and conclusions can be inferred from download statistics. We describe how download statistics can be used to describe research activity at different levels of aggregation, ranging from organizations to countries. These statistics show a correlation with socio-economic indicators. A comparison will be made with traditional bibliometric indicators. We will argue that astronomy is representative of more general trends.

We present ModelTables, a benchmark of tables in Model Lakes that captures the structured semantics of performance and configuration tables often overlooked by text only retrieval. The corpus is built from Hugging Face model cards, GitHub READMEs, and referenced papers, linking each table to its surrounding model and publication context. Compared with open data lake tables, model tables are smaller yet exhibit denser inter table relationships, reflecting tightly coupled model and benchmark evolution. The current release covers over 60K models and 90K tables. To evaluate model and table relatedness, we construct a multi source ground truth using three complementary signals: (1) paper citation links, (2) explicit model card links and inheritance, and (3) shared training datasets. We present one extensive empirical use case for the benchmark which is table search. We compare canonical Data Lake search operators (unionable, joinable, keyword) and Information Retrieval baselines (dense, sparse, hybrid retrieval) on this benchmark. Union based semantic table retrieval attains 54.8 % P@1 overall (54.6 % on citation, 31.3 % on inheritance, 30.6 % on shared dataset signals); table based dense retrieval reaches 66.5 % P@1, and metadata hybrid retrieval achieves 54.1 %. This evaluation indicates clear room for developing better table search methods. By releasing ModelTables and its creation protocol, we provide the first large scale benchmark of structured data describing AI model. Our use case of table discovery in Model Lakes, provides intuition and evidence for developing more accurate semantic retrieval, structured comparison, and principled organization of structured model knowledge. Source code, data, and other artifacts have been made available at https://github.com/RJMillerLab/ModelTables.

Text-to-SQL systems allow non-SQL experts to interact with relational databases using natural language. However, their tendency to generate executable SQL for ambiguous, out-of-scope, or unanswerable queries introduces a hidden risk, as outputs may be misinterpreted as correct. This risk is especially serious in biomedical contexts, where precision is critical. We therefore present Query Carefully, a pipeline that integrates LLM-based SQL generation with explicit detection and handling of unanswerable inputs. Building on the OncoMX component of ScienceBenchmark, we construct OncoMX-NAQ (No-Answer Questions), a set of 80 no-answer questions spanning 8 categories (non-SQL, out-of-schema/domain, and multiple ambiguity types). Our approach employs llama3.3:70b with schema-aware prompts, explicit No-Answer Rules (NAR), and few-shot examples drawn from both answerable and unanswerable questions. We evaluate SQL exact match, result accuracy, and unanswerable-detection accuracy. On the OncoMX dev split, few-shot prompting with answerable examples increases result accuracy, and adding unanswerable examples does not degrade performance. On OncoMX-NAQ, balanced prompting achieves the highest unanswerable-detection accuracy (0.8), with near-perfect results for structurally defined categories (non-SQL, missing columns, out-of-domain) but persistent challenges for missing-value queries (0.5) and column ambiguity (0.3). A lightweight user interface surfaces interim SQL, execution results, and abstentions, supporting transparent and reliable text-to-SQL in biomedical applications.

The arXiv has collected 1.5 million pre-print articles over 28 years, hosting literature from scientific fields including Physics, Mathematics, and Computer Science. Each pre-print features text, figures, authors, citations, categories, and other metadata. These rich, multi-modal features, combined with the natural graph structure---created by citation, affiliation, and co-authorship---makes the arXiv an exciting candidate for benchmarking next-generation models. Here we take the first necessary steps toward this goal, by providing a pipeline which standardizes and simplifies access to the arXiv's publicly available data. We use this pipeline to extract and analyze a 6.7 million edge citation graph, with an 11 billion word corpus of full-text research articles. We present some baseline classification results, and motivate application of more exciting generative graph models.

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.

Utilizing large language models (LLMs) for transforming natural language questions into SQL queries (text-to-SQL) is a promising yet challenging approach, particularly when applied to real-world databases with complex and extensive schemas. In particular, effectively incorporating data catalogs and database values for SQL generation remains an obstacle, leading to suboptimal solutions. We address this problem by proposing a new pipeline that effectively retrieves relevant data and context, selects an efficient schema, and synthesizes correct and efficient SQL queries. To increase retrieval precision, our pipeline introduces a hierarchical retrieval method leveraging model-generated keywords, locality-sensitive hashing indexing, and vector databases. Additionally, we have developed an adaptive schema pruning technique that adjusts based on the complexity of the problem and the model's context size. Our approach generalizes to both frontier proprietary models like GPT-4 and open-source models such as Llama-3-70B. Through a series of ablation studies, we demonstrate the effectiveness of each component of our pipeline and its impact on the end-to-end performance. Our method achieves new state-of-the-art performance on the cross-domain challenging BIRD dataset.

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.

Keeping track of all relevant recent publications and experimental results for a research area is a challenging task. Prior work has demonstrated the efficacy of information extraction models in various scientific areas. Recently, several datasets have been released for the yet understudied materials science domain. However, these datasets focus on sub-problems such as parsing synthesis procedures or on sub-domains, e.g., solid oxide fuel cells. In this resource paper, we present MuLMS, a new dataset of 50 open-access articles, spanning seven sub-domains of materials science. The corpus has been annotated by domain experts with several layers ranging from named entities over relations to frame structures. We present competitive neural models for all tasks and demonstrate that multi-task training with existing related resources leads to benefits.

Data-driven scientific discovery requires iterative cycles of literature search, hypothesis generation, and data analysis. Substantial progress has been made towards AI agents that can automate scientific research, but all such agents remain limited in the number of actions they can take before losing coherence, thus limiting the depth of their findings. Here we present Kosmos, an AI scientist that automates data-driven discovery. Given an open-ended objective and a dataset, Kosmos runs for up to 12 hours performing cycles of parallel data analysis, literature search, and hypothesis generation before synthesizing discoveries into scientific reports. Unlike prior systems, Kosmos uses a structured world model to share information between a data analysis agent and a literature search agent. The world model enables Kosmos to coherently pursue the specified objective over 200 agent rollouts, collectively executing an average of 42,000 lines of code and reading 1,500 papers per run. Kosmos cites all statements in its reports with code or primary literature, ensuring its reasoning is traceable. Independent scientists found 79.4% of statements in Kosmos reports to be accurate, and collaborators reported that a single 20-cycle Kosmos run performed the equivalent of 6 months of their own research time on average. Furthermore, collaborators reported that the number of valuable scientific findings generated scales linearly with Kosmos cycles (tested up to 20 cycles). We highlight seven discoveries made by Kosmos that span metabolomics, materials science, neuroscience, and statistical genetics. Three discoveries independently reproduce findings from preprinted or unpublished manuscripts that were not accessed by Kosmos at runtime, while four make novel contributions to the scientific literature.

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.

Deep Research agents driven by LLMs have automated the scholarly discovery pipeline, from planning and query formulation to iterative web exploration. Yet they remain constrained by a static, ``one-size-fits-all'' retrieval paradigm. Current systems fail to adaptively adjust the depth and breadth of exploration based on the user's existing expertise or latent interests, frequently resulting in reports that are either redundant for experts or overly dense for novices. To address this, we introduce Personalized Deep Research (PDR), a framework that integrates dynamic user context into the core retrieval-reasoning loop. Rather than treating personalization as a post-hoc formatting step, PDR unifies user profile modeling with iterative query development, dual-stage (private/public) retrieval, and context-aware synthesis. This allows the system to autonomously align research sub-goals with user intent and optimize the stopping criteria for evidence collection. To facilitate benchmarking, we release the PDR Dataset, covering four realistic user tasks, and propose a hybrid evaluation framework combining lexical metrics with LLM-based judgments to assess factual accuracy and personalization alignment. Experimental results against commercial baselines demonstrate that PDR significantly improves retrieval utility and report relevance, effectively bridging the gap between generic information retrieval and personalized knowledge acquisition. The resource is available to the public at https://github.com/Applied-Machine-Learning-Lab/SIGIR2026_PDR.

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.

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.

Autonomous scientific discovery systems offer the potential to accelerate research by automating the process of hypothesis generation and validation. However, current systems operate within constrained search spaces or require predefined research questions, limiting their capacity for true open-ended inquiry. Furthermore, while they generate hypotheses iteratively, they largely lack the ability to explicitly synthesize their own accumulated findings to uncover complex, interconnected phenomena. We introduce DiscoPER, an autonomous large language model-powered framework that conducts open-ended research by dynamically generating and executing code to explore datasets without pre-specified research objectives. To ensure rigorous scientific validity, every proposed discovery must pass statistical testing. To overcome the limitations of isolated search, our framework introduces a second-order reasoning mechanism that periodically analyzes its own accumulated discoveries. By treating prior discoveries as empirical data, DiscoPER identifies structural patterns, confounds, and epistemic gaps, actively redirecting hypothesis exploration toward uncharted regions of the search space. The search space is further expanded by incorporating tool use, enabling the system to explore hypotheses beyond structured metadata by seamlessly processing and extracting useful information from multimodal sources like images. Evaluated on iNatDisco, a new multimodal ecological knowledge benchmark with pattern-level ground truth obtained from peer-reviewed literature, DiscoPER recovers 8 of 9 known patterns with a 72.7% hypothesis support rate, outperforming both classical causal discovery and LLM-guided baselines. Ablations show that DiscoPER scales with more data, and confirms the benefits of second-order meta-reflection.

With the future striving toward data-centric decision-making, seamless access to databases is of utmost importance. There is extensive research on creating an efficient text-to-sql (TEXT2SQL) model to access data from the database. Using a Natural language is one of the best interfaces that can bridge the gap between the data and results by accessing the database efficiently, especially for non-technical users. It will open the doors and create tremendous interest among users who are well versed in technical skills or not very skilled in query languages. Even if numerous deep learning-based algorithms are proposed or studied, there still is very challenging to have a generic model to solve the data query issues using natural language in a real-work scenario. The reason is the use of different datasets in different studies, which comes with its limitations and assumptions. At the same time, we do lack a thorough understanding of these proposed models and their limitations with the specific dataset it is trained on. In this paper, we try to present a holistic overview of 24 recent neural network models studied in the last couple of years, including their architectures involving convolutional neural networks, recurrent neural networks, pointer networks, reinforcement learning, generative models, etc. We also give an overview of the 11 datasets that are widely used to train the models for TEXT2SQL technologies. We also discuss the future application possibilities of TEXT2SQL technologies for seamless data queries.

Large language models (LLMs) are rapidly changing how researchers in materials science and chemistry discover, organize, and act on scientific knowledge. This paper analyzes a broad set of community-developed LLM applications in an effort to identify emerging patterns in how these systems can be used across the scientific research lifecycle. We organize the projects into two complementary categories: Knowledge Infrastructure, systems that structure, retrieve, synthesize, and validate scientific information; and Action Systems, systems that execute, coordinate, or automate scientific work across computational and experimental environments. The submissions reveal a shift from single-purpose LLM tools toward integrated, multi-agent workflows that combine retrieval, reasoning, tool use, and domain-specific validation. Prominent themes include retrieval-augmented generation as grounding infrastructure, persistent structured knowledge representations, multimodal and multilingual scientific inputs, and early progress toward laboratory-integrated closed-loop systems. Together, these results suggest that LLMs are evolving from general-purpose assistants into composable infrastructure for scientific reasoning and action. This work provides a community snapshot of that transition and a practical taxonomy for understanding emerging LLM-enabled workflows in materials science and chemistry.

When conducting literature reviews, scientists often create literature review tables - tables whose rows are publications and whose columns constitute a schema, a set of aspects used to compare and contrast the papers. Can we automatically generate these tables using language models (LMs)? In this work, we introduce a framework that leverages LMs to perform this task by decomposing it into separate schema and value generation steps. To enable experimentation, we address two main challenges: First, we overcome a lack of high-quality datasets to benchmark table generation by curating and releasing arxivDIGESTables, a new dataset of 2,228 literature review tables extracted from ArXiv papers that synthesize a total of 7,542 research papers. Second, to support scalable evaluation of model generations against human-authored reference tables, we develop DecontextEval, an automatic evaluation method that aligns elements of tables with the same underlying aspects despite differing surface forms. Given these tools, we evaluate LMs' abilities to reconstruct reference tables, finding this task benefits from additional context to ground the generation (e.g. table captions, in-text references). Finally, through a human evaluation study we find that even when LMs fail to fully reconstruct a reference table, their generated novel aspects can still be useful.

This paper presents multi- and interdisciplinary approaches for finding the appropriate AI technologies for research information. Professional research information management (RIM) is becoming increasingly important as an expressly data-driven tool for researchers. It is not only the basis of scientific knowledge processes, but also related to other data. A concept and a process model of the elementary phases from the start of the project to the ongoing operation of the AI methods in the RIM is presented, portraying the implementation of an AI project, meant to enable universities and research institutions to support their researchers in dealing with incorrect and incomplete research information, while it is being stored in their RIMs. Our aim is to show how research information harmonizes with the challenges of data literacy and data quality issues, related to AI, also wanting to underline that any project can be successful if the research institutions and various departments of universities, involved work together and appropriate support is offered to improve research information and data management.

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.

The development of Large Language Models (LLMs) has revolutionized Q&A across various industries, including the database domain. However, there is still a lack of a comprehensive benchmark to evaluate the capabilities of different LLMs and their modular components in database Q&A. To this end, we introduce DQA, the first comprehensive database Q&A benchmark. DQA features an innovative LLM-based method for automating the generation, cleaning, and rewriting of database Q&A, resulting in over 240,000 Q&A pairs in English and Chinese. These Q&A pairs cover nearly all aspects of database knowledge, including database manuals, database blogs, and database tools. This inclusion allows for additional assessment of LLMs' Retrieval-Augmented Generation (RAG) and Tool Invocation Generation (TIG) capabilities in the database Q&A task. Furthermore, we propose a comprehensive LLM-based database Q&A testbed on DQA. This testbed is highly modular and scalable, with both basic and advanced components like Question Classification Routing (QCR), RAG, TIG, and Prompt Template Engineering (PTE). Besides, DQA provides a complete evaluation pipeline, featuring diverse metrics and a standardized evaluation process to ensure comprehensiveness, accuracy, and fairness. We use DQA to evaluate the database Q&A capabilities under the proposed testbed comprehensively. The evaluation reveals findings like (i) the strengths and limitations of nine different LLM-based Q&A bots and (ii) the performance impact and potential improvements of various service components (e.g., QCR, RAG, TIG). We hope our benchmark and findings will better guide the future development of LLM-based database Q&A research.

Effective scientific communication depends on accurate citations that validate sources and guide readers to supporting evidence. Yet academic literature faces mounting challenges: semantic citation errors that misrepresent sources, AI-generated hallucinated references, and traditional citation formats that point to entire papers without indicating which sections substantiate specific claims. We introduce SemanticCite, an AI-powered system that verifies citation accuracy through full-text source analysis while providing rich contextual information via detailed reasoning and relevant text snippets. Our approach combines multiple retrieval methods with a four-class classification system (Supported, Partially Supported, Unsupported, Uncertain) that captures nuanced claim-source relationships and enables appropriate remedial actions for different error types. Our experiments show that fine-tuned lightweight language models achieve performance comparable to large commercial systems with significantly lower computational requirements, making large-scale citation verification practically feasible. The system provides transparent, evidence-based explanations that support user understanding and trust. We contribute a comprehensive dataset of over 1,000 citations with detailed alignments, functional classifications, semantic annotations, and bibliometric metadata across eight disciplines, alongside fine-tuned models and the complete verification framework as open-source software. SemanticCite addresses critical challenges in research integrity through scalable citation verification, streamlined peer review, and quality control for AI-generated content, providing an open-source foundation for maintaining citation accuracy at scale.

Finding relevant literature underpins the practice of evidence-based medicine. From 2014 to 2016, TREC conducted a clinical decision support track, wherein participants were tasked with finding articles relevant to clinical questions posed by physicians. In total, 87 teams have participated over the past three years, generating 395 runs. During this period, each team has trialled a variety of methods. While there was significant overlap in the methods employed by different teams, the results were varied. Due to the diversity of the platforms used, the results arising from the different techniques are not directly comparable, reducing the ability to build on previous work. By using a stable platform, we have been able to compare different document and query processing techniques, allowing us to experiment with different search parameters. We have used our system to reproduce leading teams runs, and compare the results obtained. By benchmarking our indexing and search techniques, we can statistically test a variety of hypotheses, paving the way for further research.

To enable materials databases supporting computational and experimental research, it is critical to develop platforms that both facilitate access to the data and provide the tools used to generate/analyze it - all while considering the diversity of users' experience levels and usage needs. The recently formulated FAIR principles (Findable, Accessible, Interoperable, and Reusable) establish a common framework to aid these efforts. This article describes aflow_org, a web ecosystem developed to provide FAIR - compliant access to the AFLOW databases. Graphical and programmatic retrieval methods are offered, ensuring accessibility for all experience levels and data needs. aflow_org goes beyond data-access by providing applications to important features of the AFLOW software, assisting users in their own calculations without the need to install the entire high-throughput framework. Outreach commitments to provide AFLOW tutorials and materials science education to a global and diverse audiences will also be presented.

Skillful mobile operation in three-dimensional environments is a primary topic of study in Artificial Intelligence. The past two years have seen a surge of creative work on navigation. This creative output has produced a plethora of sometimes incompatible task definitions and evaluation protocols. To coordinate ongoing and future research in this area, we have convened a working group to study empirical methodology in navigation research. The present document summarizes the consensus recommendations of this working group. We discuss different problem statements and the role of generalization, present evaluation measures, and provide standard scenarios that can be used for benchmarking.

Literature-Based Discovery (LBD) aims to discover new scientific knowledge by mining papers and generating hypotheses. Standard LBD is limited to predicting pairwise relations between discrete concepts (e.g., drug-disease links), and ignores critical contexts like experimental settings (e.g., a specific patient population where a drug is evaluated) and background motivations (e.g., to find drugs without specific side effects). We address these limitations with a novel formulation of contextualized-LBD (C-LBD): generating scientific hypotheses in natural language, while grounding them in a context that controls the hypothesis search space. We present a modeling framework using retrieval of ``inspirations'' from past scientific papers. Our evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our inspiration prompting approaches partially mitigate this issue. Our work represents a first step toward building language models that generate new ideas derived from scientific literature.

We present SciRIFF (Scientific Resource for Instruction-Following and Finetuning), a dataset of 137K instruction-following demonstrations for 54 tasks covering five essential scientific literature understanding capabilities: information extraction, summarization, question answering, claim verification, and classification. SciRIFF demonstrations are notable for their long input contexts, detailed task specifications, and complex structured outputs. While instruction-following resources are available in specific domains such as clinical medicine and chemistry, SciRIFF is the first dataset focused on extracting and synthesizing information from research literature across a wide range of scientific fields. To demonstrate the utility of SciRIFF, we develop a sample-efficient strategy to adapt a general instruction-following model for science by performing additional finetuning on a mix of general-domain and SciRIFF demonstrations. In evaluations on nine held-out scientific tasks, our model -- called SciTulu -- improves over a strong LLM baseline by 28.1% and 6.5% at the 7B and 70B scales respectively, while maintaining general instruction-following performance within 2% of the baseline. We are optimistic that SciRIFF will facilitate the development and evaluation of LLMs to help researchers navigate the ever-growing body of scientific literature. We release our dataset, model checkpoints, and data processing and evaluation code to enable further research.

SciLaD is a novel, large-scale dataset of scientific language constructed entirely using open-source frameworks and publicly available data sources. It comprises a curated English split containing over 10 million scientific publications and a multilingual, unfiltered TEI XML split including more than 35 million publications. We also publish the extensible pipeline for generating SciLaD. The dataset construction and processing workflow demonstrates how open-source tools can enable large-scale, scientific data curation while maintaining high data quality. Finally, we pre-train a RoBERTa model on our dataset and evaluate it across a comprehensive set of benchmarks, achieving performance comparable to other scientific language models of similar size, validating the quality and utility of SciLaD. We publish the dataset and evaluation pipeline to promote reproducibility, transparency, and further research in natural scientific language processing and understanding including scholarly document processing.

Large-scale clinical databases offer opportunities for medical research, but their complexity creates barriers to effective use. The Medical Information Mart for Intensive Care (MIMIC-IV), one of the world's largest open-source electronic health record databases, traditionally requires both SQL proficiency and clinical domain expertise. We introduce M3, a system that enables natural language querying of MIMIC-IV data through the Model Context Protocol. With a single command, M3 retrieves MIMIC-IV from PhysioNet, launches a local SQLite instance or connects to hosted BigQuery, and allows researchers to pose clinical questions in plain English. We evaluated M3 using one hundred questions from the EHRSQL 2024 benchmark with two language models: the proprietary Claude Sonnet 4 achieved 94% accuracy, while the open-source gpt-oss-20B (deployable locally on consumer hardware) achieved 93% accuracy. Both models translate natural language into SQL, execute queries against MIMIC-IV, and return structured results alongside the underlying query for verification. Error analysis revealed that most failures stemmed from complex temporal reasoning or ambiguous question phrasing rather than fundamental architectural limitations. The comparable performance of a smaller open-source model demonstrates that privacy-preserving local deployment is viable for sensitive clinical data analysis. M3 lowers technical barriers to critical care data analysis while maintaining security through OAuth2 authentication, query validation, and comprehensive audit logging.

The exponential growth of knowledge and the increasing complexity of interdisciplinary research pose significant challenges for researchers, including information overload and difficulties in exploring novel ideas. The advancements in large language models (LLMs), such as GPT-4, have shown great potential in enhancing idea proposals, but how to effectively utilize large models for reasonable idea proposal has not been thoroughly explored. This paper proposes a scientific paper idea proposer (SciPIP). Based on a user-provided research background, SciPIP retrieves helpful papers from a literature database while leveraging the capabilities of LLMs to generate more novel and feasible ideas. To this end, 1) we construct a literature retrieval database, extracting lots of papers' multi-dimension information for fast access. Then, a literature retrieval method based on semantics, entity, and citation co-occurrences is proposed to search relevant literature from multiple aspects based on the user-provided background. 2) After literature retrieval, we introduce dual-path idea proposal strategies, where one path infers solutions from the retrieved literature and the other path generates original ideas through model brainstorming. We then combine the two to achieve a good balance between feasibility and originality. Through extensive experiments on the natural language processing (NLP) field, we demonstrate that SciPIP can retrieve citations similar to those of existing top conference papers and generate many ideas consistent with them. Additionally, we evaluate the originality of other ideas generated by SciPIP using large language models, further validating the effectiveness of our proposed method. The code and the database are released at https://github.com/cheerss/SciPIP.

The proposed research aims to develop an innovative semantic query processing system that enables users to obtain comprehensive information about research works produced by Computer Science (CS) researchers at the Australian National University (ANU). The system integrates Large Language Models (LLMs) with the ANU Scholarly Knowledge Graph (ASKG), a structured repository of all research-related artifacts produced at ANU in the CS field. Each artifact and its parts are represented as textual nodes stored in a Knowledge Graph (KG). To address the limitations of traditional scholarly KG construction and utilization methods, which often fail to capture fine-grained details, we propose a novel framework that integrates the Deep Document Model (DDM) for comprehensive document representation and the KG-enhanced Query Processing (KGQP) for optimized complex query handling. DDM enables a fine-grained representation of the hierarchical structure and semantic relationships within academic papers, while KGQP leverages the KG structure to improve query accuracy and efficiency with LLMs. By combining the ASKG with LLMs, our approach enhances knowledge utilization and natural language understanding capabilities. The proposed system employs an automatic LLM-SPARQL fusion to retrieve relevant facts and textual nodes from the ASKG. Initial experiments demonstrate that our framework is superior to baseline methods in terms of accuracy retrieval and query efficiency. We showcase the practical application of our framework in academic research scenarios, highlighting its potential to revolutionize scholarly knowledge management and discovery. This work empowers researchers to acquire and utilize knowledge from documents more effectively and provides a foundation for developing precise and reliable interactions with LLMs.

Large-scale data sets on scholarly publications are the basis for a variety of bibliometric analyses and natural language processing (NLP) applications. Especially data sets derived from publication's full-text have recently gained attention. While several such data sets already exist, we see key shortcomings in terms of their domain and time coverage, citation network completeness, and representation of full-text content. To address these points, we propose a new version of the data set unarXive. We base our data processing pipeline and output format on two existing data sets, and improve on each of them. Our resulting data set comprises 1.9 M publications spanning multiple disciplines and 32 years. It furthermore has a more complete citation network than its predecessors and retains a richer representation of document structure as well as non-textual publication content such as mathematical notation. In addition to the data set, we provide ready-to-use training/test data for citation recommendation and IMRaD classification. All data and source code is publicly available at https://github.com/IllDepence/unarXive.

Recently, context-dependent text-to-SQL semantic parsing which translates natural language into SQL in an interaction process has attracted a lot of attention. Previous works leverage context-dependence information either from interaction history utterances or the previous predicted SQL queries but fail in taking advantage of both since of the mismatch between natural language and logic-form SQL. In this work, we propose a History Information Enhanced text-to-SQL model (HIE-SQL) to exploit context-dependence information from both history utterances and the last predicted SQL query. In view of the mismatch, we treat natural language and SQL as two modalities and propose a bimodal pre-trained model to bridge the gap between them. Besides, we design a schema-linking graph to enhance connections from utterances and the SQL query to the database schema. We show our history information enhanced methods improve the performance of HIE-SQL by a significant margin, which achieves new state-of-the-art results on the two context-dependent text-to-SQL benchmarks, the SparC and CoSQL datasets, at the writing time.

The exponential surge in online health information, coupled with its increasing use by non-experts, highlights the pressing need for advanced Health Information Retrieval models that consider not only topical relevance but also the factual accuracy of the retrieved information, given the potential risks associated with health misinformation. To this aim, this paper introduces a solution driven by Retrieval-Augmented Generation (RAG), which leverages the capabilities of generative Large Language Models (LLMs) to enhance the retrieval of health-related documents grounded in scientific evidence. In particular, we propose a three-stage model: in the first stage, the user's query is employed to retrieve topically relevant passages with associated references from a knowledge base constituted by scientific literature. In the second stage, these passages, alongside the initial query, are processed by LLMs to generate a contextually relevant rich text (GenText). In the last stage, the documents to be retrieved are evaluated and ranked both from the point of view of topical relevance and factual accuracy by means of their comparison with GenText, either through stance detection or semantic similarity. In addition to calculating factual accuracy, GenText can offer a layer of explainability for it, aiding users in understanding the reasoning behind the retrieval. Experimental evaluation of our model on benchmark datasets and against baseline models demonstrates its effectiveness in enhancing the retrieval of both topically relevant and factually accurate health information, thus presenting a significant step forward in the health misinformation mitigation problem.

In many scientific fields, large language models (LLMs) have revolutionized the way text and other modalities of data (e.g., molecules and proteins) are handled, achieving superior performance in various applications and augmenting the scientific discovery process. Nevertheless, previous surveys on scientific LLMs often concentrate on one or two fields or a single modality. In this paper, we aim to provide a more holistic view of the research landscape by unveiling cross-field and cross-modal connections between scientific LLMs regarding their architectures and pre-training techniques. To this end, we comprehensively survey over 260 scientific LLMs, discuss their commonalities and differences, as well as summarize pre-training datasets and evaluation tasks for each field and modality. Moreover, we investigate how LLMs have been deployed to benefit scientific discovery. Resources related to this survey are available at https://github.com/yuzhimanhua/Awesome-Scientific-Language-Models.

The goal of database question answering is to enable natural language querying of real-life relational databases in diverse application domains. Recently, large-scale datasets such as Spider and WikiSQL facilitated novel modeling techniques for text-to-SQL parsing, improving zero-shot generalization to unseen databases. In this work, we examine the challenges that still prevent these techniques from practical deployment. First, we present KaggleDBQA, a new cross-domain evaluation dataset of real Web databases, with domain-specific data types, original formatting, and unrestricted questions. Second, we re-examine the choice of evaluation tasks for text-to-SQL parsers as applied in real-life settings. Finally, we augment our in-domain evaluation task with database documentation, a naturally occurring source of implicit domain knowledge. We show that KaggleDBQA presents a challenge to state-of-the-art zero-shot parsers but a more realistic evaluation setting and creative use of associated database documentation boosts their accuracy by over 13.2%, doubling their performance.

As scientific research proliferates, researchers face the daunting task of navigating and reading vast amounts of literature. Existing solutions, such as document QA, fail to provide personalized and up-to-date information efficiently. We present Paper Copilot, a self-evolving, efficient LLM system designed to assist researchers, based on thought-retrieval, user profile and high performance optimization. Specifically, Paper Copilot can offer personalized research services, maintaining a real-time updated database. Quantitative evaluation demonstrates that Paper Copilot saves 69.92\% of time after efficient deployment. This paper details the design and implementation of Paper Copilot, highlighting its contributions to personalized academic support and its potential to streamline the research process.

Deploying Large Language Models (LLMs) for regulatory compliance demands rigorous traceability via comprehensive citations across multi-tiered authority structures. Unlike traditional multi-hop or legal QA, this task requires structured procedural lookups and evidence-set closure rather than entity resolution or case-law reasoning. Existing RAG systems struggle here due to flattened citation edges, fragmented retrieval expansions, and fragile post-hoc attribution. We formalize Regulatory Compliance QA with RegOps-Bench, a novel benchmark featuring an Operational Knowledge Graph derived from complex national R\&D regulations. To address these bottlenecks, we propose RefWalk, a unified framework driven by a shared topic anchor. RefWalk traverses cross-document citations, fuses multi-view candidates via max-based aggregation, and enforces per-rule attribution to explicitly map claims to sources. We establish a strong baseline with substantial improvements in retrieval recall and citation accuracy. Finally, a contrastive evaluation on a U.S. health compliance dataset (HIPAA) reveals that existing systems exhibit saturation on flat-structure rules, underscoring the need for RegOps-Bench. Our code is available at https://github.com/yeongjoonJu/RefWalk.

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/.

In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about synthetic procedures. By taking advantage of recent advances in natural language processing for procedural texts, SynKB supports more flexible queries about reaction conditions, and thus has the potential to help chemists search the literature for conditions used in relevant reactions as they design new synthetic routes. Using customized Transformer models to automatically extract information from 6 million synthesis procedures described in U.S. and EU patents, we show that for many queries, SynKB has higher recall than Reaxsys, while maintaining high precision. We plan to make SynKB available as an open-source tool; in contrast, proprietary chemistry databases require costly subscriptions.

We explore using T5 (Raffel et al. (2019)) to directly translate natural language questions into SQL statements. General purpose natural language that interfaces to information stored within databases requires flexibly translating natural language questions into database queries. The best performing text-to-SQL systems approach this task by first converting questions into an intermediate logical form (LF) (Lyu et al. (2020)). While LFs provide a convenient intermediate representation and simplify query generation, they introduce an additional layer of complexity and annotation requirements. However, weakly supervised modeling that directly converts questions to SQL statements has proven more difficult without the scaffolding provided by LFs (Min et al. (2019)). We approach direct conversion of questions to SQL statements using T5 (Raffel et al. (2019)), a pre-trained textto-text generation model, modified to support pointer-generator style decoding (See et al. (2017)). We explore using question augmentation with table schema information and the use of automatically generated silver training data. The resulting model achieves 90.5% execution accuracy on the WikiSQL (Zhong et al. (2017)) test data set, a new state-of-the-art on weakly supervised SQL generation. The performance improvement is 6.6% absolute over the prior state-of-the-art (Min et al. (2019)) and approaches the performance of state-ofthe-art systems making use of LFs.

Tables have gained significant attention in large language models (LLMs) and multimodal large language models (MLLMs) due to their complex and flexible structure. Unlike linear text inputs, tables are two-dimensional, encompassing formats that range from well-structured database tables to complex, multi-layered spreadsheets, each with different purposes. This diversity in format and purpose has led to the development of specialized methods and tasks, instead of universal approaches, making navigation of table understanding tasks challenging. To address these challenges, this paper introduces key concepts through a taxonomy of tabular input representations and an introduction of table understanding tasks. We highlight several critical gaps in the field that indicate the need for further research: (1) the predominance of retrieval-focused tasks that require minimal reasoning beyond mathematical and logical operations; (2) significant challenges faced by models when processing complex table structures, large-scale tables, length context, or multi-table scenarios; and (3) the limited generalization of models across different tabular representations and formats.

We present a new regular grid search algorithm for quick fixed-radius nearest-neighbor lookup developed in Python. This module indexes a set of k-dimensional points in a regular grid, with optional periodic conditions, providing a fast approach for nearest neighbors queries. In this first installment we provide three types of queries: bubble, shell and the nth-nearest; as well as three different metrics of interest in astronomy: the euclidean and two distance functions in spherical coordinates of varying precision, haversine and Vincenty; and the possibility of providing a custom distance function. This package results particularly useful for large datasets where a brute-force search turns impractical.

Retrieval in the SQL setting has largely been studied as the task of finding, within a large collection of SQL statements, the statement that answers a natural-language question. At scale, however, a more fundamental retrieval problem precedes generation: schema retrieval, identifying the tables and columns a question requires in a database that may contain thousands of them, far more than fit in a model's context. We argue that this step warrants first-class evaluation. To this end, we recast five text-to-SQL datasets (Spider, BIRD, BEAVER, and two LiveSQLBench variants) as retrieval tasks at both table and column granularity, covering realistic and enterprise-scale schemas under two document representations, and we show that off-the-shelf text and code embedders transfer poorly to this setting. We then propose corpus-adaptive fine-tuning: natural-language queries are synthesized directly from the target schema corpus, granularity-aware hard negatives are mined, and a 305M-parameter embedder is fine-tuned contrastively. This procedure raises average recall@10 from 60.4 to 75.6 (nDCG@10 from 51.9 to 68.0), making the 305M model the strongest retriever under one billion parameters and competitive with state-of-the-art embedders of 4-8B parameters, more than an order of magnitude larger. The same recipe improves an 8B state-of-the-art embedder from 77.8 to 78.4 recall@10, matching the best result on the benchmark and indicating that the adaptation is backbone-agnostic. Leave-one-corpus-out experiments and a leakage audit show that these gains reflect a transferable schema-retrieval ability rather than memorization of the evaluation data. Our results establish schema linking as a standalone retrieval task and lightweight, label-free corpus adaptation as a practical route to deploying it at enterprise scale.

The Natural Language Interface to Databases (NLIDB) empowers non-technical users with database access through intuitive natural language (NL) interactions. Advanced approaches, utilizing neural sequence-to-sequence models or large-scale language models, typically employ auto-regressive decoding to generate unique SQL queries sequentially. While these translation models have greatly improved the overall translation accuracy, surpassing 70% on NLIDB benchmarks, the use of auto-regressive decoding to generate single SQL queries may result in sub-optimal outputs, potentially leading to erroneous translations. In this paper, we propose Metasql, a unified generate-then-rank framework that can be flexibly incorporated with existing NLIDBs to consistently improve their translation accuracy. Metasql introduces query metadata to control the generation of better SQL query candidates and uses learning-to-rank algorithms to retrieve globally optimized queries. Specifically, Metasql first breaks down the meaning of the given NL query into a set of possible query metadata, representing the basic concepts of the semantics. These metadata are then used as language constraints to steer the underlying translation model toward generating a set of candidate SQL queries. Finally, Metasql ranks the candidates to identify the best matching one for the given NL query. Extensive experiments are performed to study Metasql on two public NLIDB benchmarks. The results show that the performance of the translation models can be effectively improved using Metasql.

Recent advances in large language models and tool-using agents have expanded the range of benchmarked web tasks. Yet an important class of specialized retrieval tasks remains undercharacterized. On many specialized data-retrieval websites, answer-bearing evidence becomes accessible only after establishing the correct site-specific retrieval state through filters, views, hierarchies, or scopes. We term this capability state-gated retrieval (SGR). We introduce SGR-Bench, a benchmark for this setting containing 100 expert-curated tasks spanning six source families and 12 public data ecosystems. Each task requires discovering the appropriate website and configuring its site-specific retrieval state to produce a structured answer. SGR-Bench pairs constraint-guided and goal-oriented formulations of the same underlying problems, enabling controlled comparisons between explicit and implicit guidance for state-gated retrieval. We evaluate eight CLI-based agentic LLM systems and three commercial search-agent products. On SGR-Bench, the strongest system reaches only 66.18% item-level F1, while row-level F1 remains much lower. A manual audit of 156 analyzable failed CLI trajectories shows why: agents often reach a relevant web source, but establish the wrong site-specific retrieval state. Retrieval-scope drift (37.2%) and criterion mismatch (27.6%) dominate, whereas final answer composition accounts for only 10.3%. The dataset and single-case evaluation instructions are available at https://huggingface.co/datasets/PKUAIWeb/SGR-BENCH.

Query rewrite, which aims to generate more efficient queries by altering a SQL query's structure without changing the query result, has been an important research problem. In order to maintain equivalence between the rewritten query and the original one during rewriting, traditional query rewrite methods always rewrite the queries following certain rewrite rules. However, some problems still remain. Firstly, existing methods of finding the optimal choice or sequence of rewrite rules are still limited and the process always costs a lot of resources. Methods involving discovering new rewrite rules typically require complicated proofs of structural logic or extensive user interactions. Secondly, current query rewrite methods usually rely highly on DBMS cost estimators which are often not accurate. In this paper, we address these problems by proposing a novel method of query rewrite named LLM-R2, adopting a large language model (LLM) to propose possible rewrite rules for a database rewrite system. To further improve the inference ability of LLM in recommending rewrite rules, we train a contrastive model by curriculum to learn query representations and select effective query demonstrations for the LLM. Experimental results have shown that our method can significantly improve the query execution efficiency and outperform the baseline methods. In addition, our method enjoys high robustness across different datasets.

In this paper we introduce the olog, or ontology log, a category-theoretic model for knowledge representation (KR). Grounded in formal mathematics, ologs can be rigorously formulated and cross-compared in ways that other KR models (such as semantic networks) cannot. An olog is similar to a relational database schema; in fact an olog can serve as a data repository if desired. Unlike database schemas, which are generally difficult to create or modify, ologs are designed to be user-friendly enough that authoring or reconfiguring an olog is a matter of course rather than a difficult chore. It is hoped that learning to author ologs is much simpler than learning a database definition language, despite their similarity. We describe ologs carefully and illustrate with many examples. As an application we show that any primitive recursive function can be described by an olog. We also show that ologs can be aligned or connected together into a larger network using functors. The various methods of information flow and institutions can then be used to integrate local and global world-views. We finish by providing several different avenues for future research.

Masader (Alyafeai et al., 2021) created a metadata structure to be used for cataloguing Arabic NLP datasets. However, developing an easy way to explore such a catalogue is a challenging task. In order to give the optimal experience for users and researchers exploring the catalogue, several design and user experience challenges must be resolved. Furthermore, user interactions with the website may provide an easy approach to improve the catalogue. In this paper, we introduce Masader Plus, a web interface for users to browse Masader. We demonstrate data exploration, filtration, and a simple API that allows users to examine datasets from the backend. Masader Plus can be explored using this link https://arbml.github.io/masader. A video recording explaining the interface can be found here https://www.youtube.com/watch?v=SEtdlSeqchk.

Meta-analysis is a demanding form of evidence synthesis that combines literature retrieval, PI/ECO-guided study selection, and statistical aggregation. Its structured, verifiable workflow makes it an ideal substrate for evaluating systematic scientific reasoning, yet existing benchmarks lack ground truth across the full retrieval-screening-synthesis pipeline. We introduce MetaSyn, a dataset of 442 expert-curated meta-analyses from Nature Portfolio journals. Each entry pairs a research question with PI/ECO criteria, a retrieval corpus of 140k PubMed articles, verified positive studies, hard negatives that are topically similar but PI/ECO-ineligible, and complete search strategies and date bounds. Benchmarking twelve pipeline configurations (nine RAG variants and a protocol-driven agent) reveals a critical screening bottleneck: despite a retrieval ceiling of 90.9% recall at K=200, no system recovers more than 52.7% of ground-truth included literature. Current LLMs fail to reliably separate eligible studies from PI/ECO-failing distractors in pools of comparable topical relevance. Stage-attributed metrics capture where systems succeed and fail; a single end-to-end score does not.

Within the past few decades we have witnessed digital revolution, which moved scholarly communication to electronic media and also resulted in a substantial increase in its volume. Nowadays keeping track with the latest scientific achievements poses a major challenge for the researchers. Scientific information overload is a severe problem that slows down scholarly communication and knowledge propagation across the academia. Modern research infrastructures facilitate studying scientific literature by providing intelligent search tools, proposing similar and related documents, visualizing citation and author networks, assessing the quality and impact of the articles, and so on. In order to provide such high quality services the system requires the access not only to the text content of stored documents, but also to their machine-readable metadata. Since in practice good quality metadata is not always available, there is a strong demand for a reliable automatic method of extracting machine-readable metadata directly from source documents. This research addresses these problems by proposing an automatic, accurate and flexible algorithm for extracting wide range of metadata directly from scientific articles in born-digital form. Extracted information includes basic document metadata, structured full text and bibliography section. Designed as a universal solution, proposed algorithm is able to handle a vast variety of publication layouts with high precision and thus is well-suited for analyzing heterogeneous document collections. This was achieved by employing supervised and unsupervised machine-learning algorithms trained on large, diverse datasets. The evaluation we conducted showed good performance of proposed metadata extraction algorithm. The comparison with other similar solutions also proved our algorithm performs better than competition for most metadata types.

Passage ranking involves two stages: passage retrieval and passage re-ranking, which are important and challenging topics for both academics and industries in the area of Information Retrieval (IR). However, the commonly-used datasets for passage ranking usually focus on the English language. For non-English scenarios, such as Chinese, the existing datasets are limited in terms of data scale, fine-grained relevance annotation and false negative issues. To address this problem, we introduce T2Ranking, a large-scale Chinese benchmark for passage ranking. T2Ranking comprises more than 300K queries and over 2M unique passages from real-world search engines. Expert annotators are recruited to provide 4-level graded relevance scores (fine-grained) for query-passage pairs instead of binary relevance judgments (coarse-grained). To ease the false negative issues, more passages with higher diversities are considered when performing relevance annotations, especially in the test set, to ensure a more accurate evaluation. Apart from the textual query and passage data, other auxiliary resources are also provided, such as query types and XML files of documents which passages are generated from, to facilitate further studies. To evaluate the dataset, commonly used ranking models are implemented and tested on T2Ranking as baselines. The experimental results show that T2Ranking is challenging and there is still scope for improvement. The full data and all codes are available at https://github.com/THUIR/T2Ranking/