Daily Papers

Recent advances in large language models (LLMs) have opened new opportunities for academic literature retrieval. However, existing systems often rely on rigid pipelines and exhibit limited reasoning capabilities. We introduce SPAR, a multi-agent framework that incorporates RefChain-based query decomposition and query evolution to enable more flexible and effective search. To facilitate systematic evaluation, we also construct SPARBench, a challenging benchmark with expert-annotated relevance labels. Experimental results demonstrate that SPAR substantially outperforms strong baselines, achieving up to +56% F1 on AutoScholar and +23% F1 on SPARBench over the best-performing baseline. Together, SPAR and SPARBench provide a scalable, interpretable, and high-performing foundation for advancing research in scholarly retrieval. Code and data will be available at: https://github.com/xiaofengShi/SPAR

This paper presents the development and application of a Large Language Model Retrieval-Augmented Generation (LLM-RAG) system tailored for nanotechnology research. The system leverages the capabilities of a sophisticated language model to serve as an intelligent research assistant, enhancing the efficiency and comprehensiveness of literature reviews in the nanotechnology domain. Central to this LLM-RAG system is its advanced query backend retrieval mechanism, which integrates data from multiple reputable sources. The system retrieves relevant literature by utilizing Google Scholar's advanced search, and scraping open-access papers from Elsevier, Springer Nature, and ACS Publications. This multifaceted approach ensures a broad and diverse collection of up-to-date scholarly articles and papers. The proposed system demonstrates significant potential in aiding researchers by providing a streamlined, accurate, and exhaustive literature retrieval process, thereby accelerating research advancements in nanotechnology. The effectiveness of the LLM-RAG system is validated through rigorous testing, illustrating its capability to significantly reduce the time and effort required for comprehensive literature reviews, while maintaining high accuracy, query relevance and outperforming standard, publicly available LLMS.

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.

Meta-analysis is a systematic research methodology that synthesizes data from multiple existing studies to derive comprehensive conclusions. This approach not only mitigates limitations inherent in individual studies but also facilitates novel discoveries through integrated data analysis. Traditional meta-analysis involves a complex multi-stage pipeline including literature retrieval, paper screening, and data extraction, which demands substantial human effort and time. However, while LLM-based methods can accelerate certain stages, they still face significant challenges, such as hallucinations in paper screening and data extraction. In this paper, we propose a multi-agent system, Manalyzer, which achieves end-to-end automated meta-analysis through tool calls. The hybrid review, hierarchical extraction, self-proving, and feedback checking strategies implemented in Manalyzer significantly alleviate these two hallucinations. To comprehensively evaluate the performance of meta-analysis, we construct a new benchmark comprising 729 papers across 3 domains, encompassing text, image, and table modalities, with over 10,000 data points. Extensive experiments demonstrate that Manalyzer achieves significant performance improvements over the LLM baseline in multi meta-analysis tasks. Project page: https://black-yt.github.io/meta-analysis-page/ .

Advances in AI-assisted research have introduced powerful tools for literature retrieval, hypothesis generation, experimentation, and manuscript preparation. However, systems remain fragmented and lack human-centred workflows. To address these gaps, we introduce AIssistant, an agentic, open-source Human-AI collaborative framework designed to simplify the end-to-end creation of scientific workflows. Since our development is still in an early stage, we present here the first experiments with AIssistant for perspective and review research papers in machine learning. Our system integrates modular tools and agents for literature synthesis, section-wise experimentation, citation management, and automatic LaTeX paper text generation, while maintaining human oversight at every stage to ensure accuracy, coherence, and scholarly rigour. We conducted a comprehensive evaluation across three layers: (1) Independent Human Review, following NeurIPS double-blind standards; (2) Automated LLM Review, using GPT-5 as a scalable human review proxy; and (3) Program Chair Oversight, where the chair monitors the entire review process and makes final validation and acceptance decisions. The results demonstrate that AIssistant improves drafting efficiency and thematic consistency. Nonetheless, Human-AI collaboration remains essential for maintaining factual correctness, methodological soundness, and ethical compliance. Despite its effectiveness, we identify key limitations, including hallucinated citations, difficulty adapting to dynamic paper structures, and incomplete integration of multimodal content.

Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantities such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines. Here, we introduce CellForge, an agentic system that leverages a multi-agent framework that transforms presented biological datasets and research objectives directly into optimized computational models for virtual cells. More specifically, given only raw single-cell multi-omics data and task descriptions as input, CellForge outputs both an optimized model architecture and executable code for training virtual cell models and inference. The framework integrates three core modules: Task Analysis for presented dataset characterization and relevant literature retrieval, Method Design, where specialized agents collaboratively develop optimized modeling strategies, and Experiment Execution for automated generation of code. The agents in the Design module are separated into experts with differing perspectives and a central moderator, and have to collaboratively exchange solutions until they achieve a reasonable consensus. We demonstrate CellForge's capabilities in single-cell perturbation prediction, using six diverse datasets that encompass gene knockouts, drug treatments, and cytokine stimulations across multiple modalities. CellForge consistently outperforms task-specific state-of-the-art methods. Overall, CellForge demonstrates how iterative interaction between LLM agents with differing perspectives provides better solutions than directly addressing a modeling challenge. Our code is publicly available at https://github.com/gersteinlab/CellForge.

Peer review is fundamental to scientific research, but the growing volume of publications has intensified the challenges of this expertise-intensive process. While LLMs show promise in various scientific tasks, their potential to assist with peer review, particularly in identifying paper limitations, remains understudied. We first present a comprehensive taxonomy of limitation types in scientific research, with a focus on AI. Guided by this taxonomy, for studying limitations, we present LimitGen, the first comprehensive benchmark for evaluating LLMs' capability to support early-stage feedback and complement human peer review. Our benchmark consists of two subsets: LimitGen-Syn, a synthetic dataset carefully created through controlled perturbations of high-quality papers, and LimitGen-Human, a collection of real human-written limitations. To improve the ability of LLM systems to identify limitations, we augment them with literature retrieval, which is essential for grounding identifying limitations in prior scientific findings. Our approach enhances the capabilities of LLM systems to generate limitations in research papers, enabling them to provide more concrete and constructive feedback.

Advances in LLMs have produced agents with knowledge and operational capabilities comparable to human scientists, suggesting potential to assist, accelerate, and automate research. However, existing studies mainly evaluate such systems on well-defined benchmarks or general tasks like literature retrieval, limiting their end-to-end problem-solving ability in open scientific scenarios. This is particularly true in physics, which is abstract, mathematically intensive, and requires integrating analytical reasoning with code-based computation. To address this, we propose PhysMaster, an LLM-based agent functioning as an autonomous theoretical and computational physicist. PhysMaster couples absract reasoning with numerical computation and leverages LANDAU, the Layered Academic Data Universe, which preserves retrieved literature, curated prior knowledge, and validated methodological traces, enhancing decision reliability and stability. It also employs an adaptive exploration strategy balancing efficiency and open-ended exploration, enabling robust performance in ultra-long-horizon tasks. We evaluate PhysMaster on problems from high-energy theory, condensed matter theory to astrophysics, including: (i) acceleration, compressing labor-intensive research from months to hours; (ii) automation, autonomously executing hypothesis-driven loops ; and (iii) autonomous discovery, independently exploring open problems.

This technical report introduces Uni-Parser, an industrial-grade document parsing engine tailored for scientific literature and patents, delivering high throughput, robust accuracy, and cost efficiency. Unlike pipeline-based document parsing methods, Uni-Parser employs a modular, loosely coupled multi-expert architecture that preserves fine-grained cross-modal alignments across text, equations, tables, figures, and chemical structures, while remaining easily extensible to emerging modalities. The system incorporates adaptive GPU load balancing, distributed inference, dynamic module orchestration, and configurable modes that support either holistic or modality-specific parsing. Optimized for large-scale cloud deployment, Uni-Parser achieves a processing rate of up to 20 PDF pages per second on 8 x NVIDIA RTX 4090D GPUs, enabling cost-efficient inference across billions of pages. This level of scalability facilitates a broad spectrum of downstream applications, ranging from literature retrieval and summarization to the extraction of chemical structures, reaction schemes, and bioactivity data, as well as the curation of large-scale corpora for training next-generation large language models and AI4Science models.

Automatic survey generation has emerged as a key task in scientific document processing. While large language models (LLMs) have shown promise in generating survey texts, the lack of standardized evaluation datasets critically hampers rigorous assessment of their performance against human-written surveys. In this work, we present SurveyGen, a large-scale dataset comprising over 4,200 human-written surveys across diverse scientific domains, along with 242,143 cited references and extensive quality-related metadata for both the surveys and the cited papers. Leveraging this resource, we build QUAL-SG, a novel quality-aware framework for survey generation that enhances the standard Retrieval-Augmented Generation (RAG) pipeline by incorporating quality-aware indicators into literature retrieval to assess and select higher-quality source papers. Using this dataset and framework, we systematically evaluate state-of-the-art LLMs under varying levels of human involvement - from fully automatic generation to human-guided writing. Experimental results and human evaluations show that while semi-automatic pipelines can achieve partially competitive outcomes, fully automatic survey generation still suffers from low citation quality and limited critical analysis.

Peer review is essential for scientific progress but faces growing challenges due to increasing submission volumes and reviewer fatigue. Existing automated review approaches struggle with factual accuracy, rating consistency, and analytical depth, often generating superficial or generic feedback lacking the insights characteristic of high-quality human reviews. We introduce ReviewRL, a reinforcement learning framework for generating comprehensive and factually grounded scientific paper reviews. Our approach combines: (1) an ArXiv-MCP retrieval-augmented context generation pipeline that incorporates relevant scientific literature, (2) supervised fine-tuning that establishes foundational reviewing capabilities, and (3) a reinforcement learning procedure with a composite reward function that jointly enhances review quality and rating accuracy. Experiments on ICLR 2025 papers demonstrate that ReviewRL significantly outperforms existing methods across both rule-based metrics and model-based quality assessments. ReviewRL establishes a foundational framework for RL-driven automatic critique generation in scientific discovery, demonstrating promising potential for future development in this domain. The implementation of ReviewRL will be released at GitHub.

Large Language Models (LLMs) have shown promise in automating code generation and software engineering tasks, yet they often struggle with complex, multi-file projects due to context limitations and knowledge gaps. We propose a novel context engineering workflow that combines multiple AI components: an Intent Translator (GPT-5) for clarifying user requirements, an Elicit-powered semantic literature retrieval for injecting domain knowledge, NotebookLM-based document synthesis for contextual understanding, and a Claude Code multi-agent system for code generation and validation. Our integrated approach leverages intent clarification, retrieval-augmented generation, and specialized sub-agents orchestrated via Claude's agent framework. We demonstrate that this method significantly improves the accuracy and reliability of code assistants in real-world repositories, yielding higher single-shot success rates and better adherence to project context than baseline single-agent approaches. Qualitative results on a large Next.js codebase show the multi-agent system effectively plans, edits, and tests complex features with minimal human intervention. We compare our system with recent frameworks like CodePlan, MASAI, and HyperAgent, highlighting how targeted context injection and agent role decomposition lead to state-of-the-art performance. Finally, we discuss the implications for deploying LLM-based coding assistants in production, along with lessons learned on context management and future research directions.

Large Language Models (LLMs) are increasingly utilized in scientific research assessment, particularly in automated paper review. However, existing LLM-based review systems face significant challenges, including limited domain expertise, hallucinated reasoning, and a lack of structured evaluation. To address these limitations, we introduce DeepReview, a multi-stage framework designed to emulate expert reviewers by incorporating structured analysis, literature retrieval, and evidence-based argumentation. Using DeepReview-13K, a curated dataset with structured annotations, we train DeepReviewer-14B, which outperforms CycleReviewer-70B with fewer tokens. In its best mode, DeepReviewer-14B achieves win rates of 88.21\% and 80.20\% against GPT-o1 and DeepSeek-R1 in evaluations. Our work sets a new benchmark for LLM-based paper review, with all resources publicly available. The code, model, dataset and demo have be released in http://ai-researcher.net.

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.

Researchers struggle to efficiently locate and manage relevant literature within the exponentially growing body of scientific publications. We present WisPaper, an intelligent academic retrieval and literature management platform that addresses this challenge through three integrated capabilities: (1) Scholar Search, featuring both quick keyword-based and deep agentic search modes for efficient paper discovery; (2) Library, a customizable knowledge base for systematic literature organization; and (3) AI Feeds, an intelligent recommendation system that automatically delivers relevant new publications based on user interests. Unlike existing academic tools, WisPaper provides a closed-loop workflow that seamlessly connects literature discovery, management, and continuous tracking of research frontiers. Our multilingual and multidisciplinary system significantly reduces the time researchers from diverse backgrounds spend on paper screening and management, enabling them to focus on their core research activities. The platform is publicly accessible and serves researchers across academia and industry.

Existing approaches typically rely on large-scale fine-tuning to adapt LLMs for information reranking tasks, which is computationally expensive. In this work, we demonstrate that modern LLMs can be effectively adapted using only minimal, high-quality supervision. To enable this, we design LIMRANK-SYNTHESIZER, a reusable and open-source pipeline for generating diverse, challenging, and realistic reranking examples. Using this synthetic data, we fine-tune our reranker model, LIMRANK. We evaluate LIMRANK on two challenging benchmarks, i.e., BRIGHT for reasoning-intensive retrieval and FollowIR for instruction-following retrieval. Our experiments demonstrate that LIMRANK achieves competitive performance, while being trained on less than 5% of the data typically used in prior work. Further ablation studies demonstrate the effectiveness of LIMRANK-SYNTHESIZER and the strong generalization capabilities of LIMRANK across downstream tasks, including scientific literature search and retrieval-augmented generation for knowledge-intensive problem solving.

Literature search questions, such as "where can I find research on the evaluation of consistency in generated summaries?" pose significant challenges for modern search engines and retrieval systems. These questions often require a deep understanding of research concepts and the ability to reason over entire articles. In this work, we introduce LitSearch, a retrieval benchmark comprising 597 realistic literature search queries about recent ML and NLP papers. LitSearch is constructed using a combination of (1) questions generated by GPT-4 based on paragraphs containing inline citations from research papers and (2) questions about recently published papers, manually written by their authors. All LitSearch questions were manually examined or edited by experts to ensure high quality. We extensively benchmark state-of-the-art retrieval models and also evaluate two LLM-based reranking pipelines. We find a significant performance gap between BM25 and state-of-the-art dense retrievers, with a 24.8% difference in absolute recall@5. The LLM-based reranking strategies further improve the best-performing dense retriever by 4.4%. Additionally, commercial search engines and research tools like Google Search perform poorly on LitSearch, lagging behind the best dense retriever by 32 points. Taken together, these results show that LitSearch is an informative new testbed for retrieval systems while catering to a real-world use case.

Language Models [LMs] are now playing an increasingly large role in information generation and synthesis; the representation of scientific knowledge in these systems needs to be highly accurate. A prime challenge is hallucination; that is, generating apparently plausible but actually false information, including invented citations and nonexistent research papers. This kind of inaccuracy is dangerous in all the domains that require high levels of factual correctness, such as academia and education. This work presents a pipeline for evaluating the frequency with which language models hallucinate in generating responses in the scientific literature. We propose ArxEval, an evaluation pipeline with two tasks using ArXiv as a repository: Jumbled Titles and Mixed Titles. Our evaluation includes fifteen widely used language models and provides comparative insights into their reliability in handling scientific literature.

This research presents and compares multiple approaches to automate the generation of literature reviews using several Natural Language Processing (NLP) techniques and retrieval-augmented generation (RAG) with a Large Language Model (LLM). The ever-increasing number of research articles provides a huge challenge for manual literature review. It has resulted in an increased demand for automation. Developing a system capable of automatically generating the literature reviews from only the PDF files as input is the primary objective of this research work. The effectiveness of several Natural Language Processing (NLP) strategies, such as the frequency-based method (spaCy), the transformer model (Simple T5), and retrieval-augmented generation (RAG) with Large Language Model (GPT-3.5-turbo), is evaluated to meet the primary objective. The SciTLDR dataset is chosen for this research experiment and three distinct techniques are utilized to implement three different systems for auto-generating the literature reviews. The ROUGE scores are used for the evaluation of all three systems. Based on the evaluation, the Large Language Model GPT-3.5-turbo achieved the highest ROUGE-1 score, 0.364. The transformer model comes in second place and spaCy is at the last position. Finally, a graphical user interface is created for the best system based on the large language model.

Large Language Models (LLMs) generalize well across language tasks, but suffer from hallucinations and uninterpretability, making it difficult to assess their accuracy without ground-truth. Retrieval-Augmented Generation (RAG) models have been proposed to reduce hallucinations and provide provenance for how an answer was generated. Applying such models to the scientific literature may enable large-scale, systematic processing of scientific knowledge. We present PaperQA, a RAG agent for answering questions over the scientific literature. PaperQA is an agent that performs information retrieval across full-text scientific articles, assesses the relevance of sources and passages, and uses RAG to provide answers. Viewing this agent as a question answering model, we find it exceeds performance of existing LLMs and LLM agents on current science QA benchmarks. To push the field closer to how humans perform research on scientific literature, we also introduce LitQA, a more complex benchmark that requires retrieval and synthesis of information from full-text scientific papers across the literature. Finally, we demonstrate PaperQA's matches expert human researchers on LitQA.

Text retrieval is a long-standing research topic on information seeking, where a system is required to return relevant information resources to user's queries in natural language. From classic retrieval methods to learning-based ranking functions, the underlying retrieval models have been continually evolved with the ever-lasting technical innovation. To design effective retrieval models, a key point lies in how to learn the text representation and model the relevance matching. The recent success of pretrained language models (PLMs) sheds light on developing more capable text retrieval approaches by leveraging the excellent modeling capacity of PLMs. With powerful PLMs, we can effectively learn the representations of queries and texts in the latent representation space, and further construct the semantic matching function between the dense vectors for relevance modeling. Such a retrieval approach is referred to as dense retrieval, since it employs dense vectors (a.k.a., embeddings) to represent the texts. Considering the rapid progress on dense retrieval, in this survey, we systematically review the recent advances on PLM-based dense retrieval. Different from previous surveys on dense retrieval, we take a new perspective to organize the related work by four major aspects, including architecture, training, indexing and integration, and summarize the mainstream techniques for each aspect. We thoroughly survey the literature, and include 300+ related reference papers on dense retrieval. To support our survey, we create a website for providing useful resources, and release a code repertory and toolkit for implementing dense retrieval models. This survey aims to provide a comprehensive, practical reference focused on the major progress for dense text retrieval.

Literature reviews are an essential component of scientific research, but they remain time-intensive and challenging to write, especially due to the recent influx of research papers. This paper explores the zero-shot abilities of recent Large Language Models (LLMs) in assisting with the writing of literature reviews based on an abstract. We decompose the task into two components: 1. Retrieving related works given a query abstract, and 2. Writing a literature review based on the retrieved results. We analyze how effective LLMs are for both components. For retrieval, we introduce a novel two-step search strategy that first uses an LLM to extract meaningful keywords from the abstract of a paper and then retrieves potentially relevant papers by querying an external knowledge base. Additionally, we study a prompting-based re-ranking mechanism with attribution and show that re-ranking doubles the normalized recall compared to naive search methods, while providing insights into the LLM's decision-making process. In the generation phase, we propose a two-step approach that first outlines a plan for the review and then executes steps in the plan to generate the actual review. To evaluate different LLM-based literature review methods, we create test sets from arXiv papers using a protocol designed for rolling use with newly released LLMs to avoid test set contamination in zero-shot evaluations. We release this evaluation protocol to promote additional research and development in this regard. Our empirical results suggest that LLMs show promising potential for writing literature reviews when the task is decomposed into smaller components of retrieval and planning. Our project page including a demonstration system and toolkit can be accessed here: https://litllm.github.io.

Profiting from large-scale training datasets, advances in neural architecture design and efficient inference, joint embeddings have become the dominant approach for tackling cross-modal retrieval. In this work we first show that, despite their effectiveness, state-of-the-art joint embeddings suffer significantly from the longstanding "hubness problem" in which a small number of gallery embeddings form the nearest neighbours of many queries. Drawing inspiration from the NLP literature, we formulate a simple but effective framework called Querybank Normalisation (QB-Norm) that re-normalises query similarities to account for hubs in the embedding space. QB-Norm improves retrieval performance without requiring retraining. Differently from prior work, we show that QB-Norm works effectively without concurrent access to any test set queries. Within the QB-Norm framework, we also propose a novel similarity normalisation method, the Dynamic Inverted Softmax, that is significantly more robust than existing approaches. We showcase QB-Norm across a range of cross modal retrieval models and benchmarks where it consistently enhances strong baselines beyond the state of the art. Code is available at https://vladbogo.github.io/QB-Norm/.

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.

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.

PubTator 3.0 (https://www.ncbi.nlm.nih.gov/research/pubtator3/) is a biomedical literature resource using state-of-the-art AI techniques to offer semantic and relation searches for key concepts like proteins, genetic variants, diseases, and chemicals. It currently provides over one billion entity and relation annotations across approximately 36 million PubMed abstracts and 6 million full-text articles from the PMC open access subset, updated weekly. PubTator 3.0's online interface and API utilize these precomputed entity relations and synonyms to provide advanced search capabilities and enable large-scale analyses, streamlining many complex information needs. We showcase the retrieval quality of PubTator 3.0 using a series of entity pair queries, demonstrating that PubTator 3.0 retrieves a greater number of articles than either PubMed or Google Scholar, with higher precision in the top 20 results. We further show that integrating ChatGPT (GPT-4) with PubTator APIs dramatically improves the factuality and verifiability of its responses. In summary, PubTator 3.0 offers a comprehensive set of features and tools that allow researchers to navigate the ever-expanding wealth of biomedical literature, expediting research and unlocking valuable insights for scientific discovery.

The use of Retrieval-Augmented Generation (RAG) has improved Large Language Models (LLMs) in collaborating with external data, yet significant challenges exist in real-world scenarios. In areas such as academic literature and finance question answering, data are often found in raw text and tables in HTML or PDF formats, which can be lengthy and highly unstructured. In this paper, we introduce a benchmark suite, namely Unstructured Document Analysis (UDA), that involves 2,965 real-world documents and 29,590 expert-annotated Q&A pairs. We revisit popular LLM- and RAG-based solutions for document analysis and evaluate the design choices and answer qualities across multiple document domains and diverse query types. Our evaluation yields interesting findings and highlights the importance of data parsing and retrieval. We hope our benchmark can shed light and better serve real-world document analysis applications. The benchmark suite and code can be found at https://github.com/qinchuanhui/UDA-Benchmark.

Knowledge-Intensive Visual Question Answering (KI-VQA) refers to answering a question about an image whose answer does not lie in the image. This paper presents a new pipeline for KI-VQA tasks, consisting of a retriever and a reader. First, we introduce DEDR, a symmetric dual encoding dense retrieval framework in which documents and queries are encoded into a shared embedding space using uni-modal (textual) and multi-modal encoders. We introduce an iterative knowledge distillation approach that bridges the gap between the representation spaces in these two encoders. Extensive evaluation on two well-established KI-VQA datasets, i.e., OK-VQA and FVQA, suggests that DEDR outperforms state-of-the-art baselines by 11.6% and 30.9% on OK-VQA and FVQA, respectively. Utilizing the passages retrieved by DEDR, we further introduce MM-FiD, an encoder-decoder multi-modal fusion-in-decoder model, for generating a textual answer for KI-VQA tasks. MM-FiD encodes the question, the image, and each retrieved passage separately and uses all passages jointly in its decoder. Compared to competitive baselines in the literature, this approach leads to 5.5% and 8.5% improvements in terms of question answering accuracy on OK-VQA and FVQA, respectively.

A common thread of retrieval-augmented methods in the existing literature focuses on retrieving encyclopedic knowledge, such as Wikipedia, which facilitates well-defined entity and relation spaces that can be modeled. However, applying such methods to commonsense reasoning tasks faces two unique challenges, i.e., the lack of a general large-scale corpus for retrieval and a corresponding effective commonsense retriever. In this paper, we systematically investigate how to leverage commonsense knowledge retrieval to improve commonsense reasoning tasks. We proposed a unified framework of retrieval-augmented commonsense reasoning (called RACo), including a newly constructed commonsense corpus with over 20 million documents and novel strategies for training a commonsense retriever. We conducted experiments on four different commonsense reasoning tasks. Extensive evaluation results showed that our proposed RACo can significantly outperform other knowledge-enhanced method counterparts, achieving new SoTA performance on the CommonGen and CREAK leaderboards.

Existing neural ranking models follow the text matching paradigm, where document-to-query relevance is estimated through predicting the matching score. Drawing from the rich literature of classical generative retrieval models, we introduce and formalize the paradigm of deep generative retrieval models defined via the cumulative probabilities of generating query terms. This paradigm offers a grounded probabilistic view on relevance estimation while still enabling the use of modern neural architectures. In contrast to the matching paradigm, the probabilistic nature of generative rankers readily offers a fine-grained measure of uncertainty. We adopt several current neural generative models in our framework and introduce a novel generative ranker (T-PGN), which combines the encoding capacity of Transformers with the Pointer Generator Network model. We conduct an extensive set of evaluation experiments on passage retrieval, leveraging the MS MARCO Passage Re-ranking and TREC Deep Learning 2019 Passage Re-ranking collections. Our results show the significantly higher performance of the T-PGN model when compared with other generative models. Lastly, we demonstrate that exploiting the uncertainty information of deep generative rankers opens new perspectives to query/collection understanding, and significantly improves the cut-off prediction task.

Improvements in language models' capabilities have pushed their applications towards longer contexts, making long-context evaluation and development an active research area. However, many disparate use-cases are grouped together under the umbrella term of "long-context", defined simply by the total length of the model's input, including - for example - Needle-in-a-Haystack tasks, book summarization, and information aggregation. Given their varied difficulty, in this position paper we argue that conflating different tasks by their context length is unproductive. As a community, we require a more precise vocabulary to understand what makes long-context tasks similar or different. We propose to unpack the taxonomy of long-context based on the properties that make them more difficult with longer contexts. We propose two orthogonal axes of difficulty: (I) Diffusion: How hard is it to find the necessary information in the context? (II) Scope: How much necessary information is there to find? We survey the literature on long-context, provide justification for this taxonomy as an informative descriptor, and situate the literature with respect to it. We conclude that the most difficult and interesting settings, whose necessary information is very long and highly diffused within the input, is severely under-explored. By using a descriptive vocabulary and discussing the relevant properties of difficulty in long-context, we can implement more informed research in this area. We call for a careful design of tasks and benchmarks with distinctly long context, taking into account the characteristics that make it qualitatively different from shorter context.

The exponential growth of scientific literature has made it increasingly difficult for researchers to keep up with the literature. In an attempt to alleviate this problem, we propose CASPER, a sparse retrieval model for scientific search that utilizes tokens and keyphrases as representation units (i.e. dimensions in the sparse embedding space), enabling it to represent queries and documents with research concepts and match them at both granular and conceptual levels. To overcome the lack of suitable training data, we propose mining training data by leveraging scholarly references (i.e. signals that capture how research concepts of papers are expressed in different settings), including titles, citation contexts, author-assigned keyphrases, and co-citations. CASPER outperforms strong dense and sparse retrieval baselines on eight scientific retrieval benchmarks. Moreover, we demonstrate that through simple post-processing, CASPER can be effectively used for the keyphrase generation tasks, achieving competitive performance with the established CopyRNN while producing more diverse keyphrases and being nearly four times faster.

Retrieval-augmented generation (RAG) has emerged as a powerful framework for enhancing large language models (LLMs) with external knowledge, particularly in scientific domains that demand specialized and dynamic information. Despite its promise, the application of RAG in the chemistry domain remains underexplored, primarily due to the lack of high-quality, domain-specific corpora and well-curated evaluation benchmarks. In this work, we introduce ChemRAG-Bench, a comprehensive benchmark designed to systematically assess the effectiveness of RAG across a diverse set of chemistry-related tasks. The accompanying chemistry corpus integrates heterogeneous knowledge sources, including scientific literature, the PubChem database, PubMed abstracts, textbooks, and Wikipedia entries. In addition, we present ChemRAG-Toolkit, a modular and extensible RAG toolkit that supports five retrieval algorithms and eight LLMs. Using ChemRAG-Toolkit, we demonstrate that RAG yields a substantial performance gain -- achieving an average relative improvement of 17.4% over direct inference methods. We further conduct in-depth analyses on retriever architectures, corpus selection, and the number of retrieved passages, culminating in practical recommendations to guide future research and deployment of RAG systems in the chemistry domain. The code and data is available at https://chemrag.github.io.

Retrieval-Augmented Generation (RAG) has quickly grown into a pivotal paradigm in the development of Large Language Models (LLMs). While much of the current research in this field focuses on performance optimization, particularly in terms of accuracy and efficiency, the trustworthiness of RAG systems remains an area still under exploration. From a positive perspective, RAG systems are promising to enhance LLMs by providing them with useful and up-to-date knowledge from vast external databases, thereby mitigating the long-standing problem of hallucination. While from a negative perspective, RAG systems are at the risk of generating undesirable contents if the retrieved information is either inappropriate or poorly utilized. To address these concerns, we propose a unified framework that assesses the trustworthiness of RAG systems across six key dimensions: factuality, robustness, fairness, transparency, accountability, and privacy. Within this framework, we thoroughly review the existing literature on each dimension. Additionally, we create the evaluation benchmark regarding the six dimensions and conduct comprehensive evaluations for a variety of proprietary and open-source models. Finally, we identify the potential challenges for future research based on our investigation results. Through this work, we aim to lay a structured foundation for future investigations and provide practical insights for enhancing the trustworthiness of RAG systems in real-world applications.

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.

We consider the task of retrieving audio using free-form natural language queries. To study this problem, which has received limited attention in the existing literature, we introduce challenging new benchmarks for text-based audio retrieval using text annotations sourced from the Audiocaps and Clotho datasets. We then employ these benchmarks to establish baselines for cross-modal audio retrieval, where we demonstrate the benefits of pre-training on diverse audio tasks. We hope that our benchmarks will inspire further research into cross-modal text-based audio retrieval with free-form text queries.

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.

As AI tools become increasingly common for research ideation, robust evaluation is critical to ensure the validity and usefulness of generated ideas. We introduce ScholarEval, a retrieval augmented evaluation framework that assesses research ideas based on two fundamental criteria: soundness - the empirical validity of proposed methods based on existing literature, and contribution - the degree of advancement made by the idea across different dimensions relative to prior research. To evaluate ScholarEval, we introduce ScholarIdeas, the first expert-annotated dataset of multi-domain research ideas and reviews, comprised of 117 ideas across four disciplines: artificial intelligence, neuroscience, biochemistry, and ecology. Our evaluation shows that ScholarEval achieves significantly higher coverage of points mentioned in the human expert annotated rubrics in ScholarIdeas compared to all baselines. Furthermore, ScholarEval is consistently preferred over our strongest baseline o4-mini-deep-research, a reasoning and search-enabled agentic system by OpenAI, in terms of evaluation actionability, depth, and evidence support. Our large-scale user study also shows that ScholarEval significantly outperforms deep research in literature engagement, idea refinement, and usefulness. We openly release our code, dataset, and ScholarEval tool for the community to use and build on.

Universal multimodal retrieval (UMR), which aims to address complex retrieval tasks where both queries and candidates span diverse modalities, has been significantly advanced by the emergence of MLLMs. While state-of-the-art MLLM-based methods in the literature predominantly adopt contrastive learning principles, they often differ in their specific training recipes. Despite their success, the mechanisms underlying their retrieval capabilities remain largely unexplored, potentially resulting in suboptimal performance and limited generalization ability. To address these issues, we present a comprehensive study aimed at uncovering the key factors that drive effective embedding learning for UMR using MLLMs. We begin by implementing a general MLLM-based embedding learning pipeline, and systematically analyze the primary contributors to high-performing universal retrieval systems. Based on this, we explore various aspects of the details in embedding generation and training strategies, including progressive transition, hard negative mining and re-ranker distillation. Notably, our findings reveal that often-overlooked factors can have a substantial impact on model performance. Building on these discoveries, we introduce a unified framework termed U-MARVEL (Universal MultimodAl RetrieVal via Embedding Learning), which outperforms state-of-the-art competitors on the M-BEIR benchmark by a large margin in supervised settings, and also exihibits strong zero-shot performance on several tasks such as composed image retrieval and text-to-video retrieval. These results underscore the generalization potential of our framework across various embedding-based retrieval tasks. Code is available at https://github.com/chaxjli/U-MARVEL

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.

The emergence of advanced reasoning capabilities in Large Language Models (LLMs) marks a transformative development in healthcare applications. Beyond merely expanding functional capabilities, these reasoning mechanisms enhance decision transparency and explainability-critical requirements in medical contexts. This survey examines the transformation of medical LLMs from basic information retrieval tools to sophisticated clinical reasoning systems capable of supporting complex healthcare decisions. We provide a thorough analysis of the enabling technological foundations, with a particular focus on specialized prompting techniques like Chain-of-Thought and recent breakthroughs in Reinforcement Learning exemplified by DeepSeek-R1. Our investigation evaluates purpose-built medical frameworks while also examining emerging paradigms such as multi-agent collaborative systems and innovative prompting architectures. The survey critically assesses current evaluation methodologies for medical validation and addresses persistent challenges in field interpretation limitations, bias mitigation strategies, patient safety frameworks, and integration of multimodal clinical data. Through this survey, we seek to establish a roadmap for developing reliable LLMs that can serve as effective partners in clinical practice and medical research.

Retrieval-Augmented Generation (RAG) systems are increasingly vital for navigating the ever-expanding body of scientific literature, particularly in high-stakes domains such as chemistry. Despite the promise of RAG, foundational design choices -- such as how documents are segmented and represented -- remain underexplored in domain-specific contexts. This study presents the first large-scale, systematic evaluation of chunking strategies and embedding models tailored to chemistry-focused RAG systems. We investigate 25 chunking configurations across five method families and evaluate 48 embedding models on three chemistry-specific benchmarks, including the newly introduced QuestChemRetrieval dataset. Our results reveal that recursive token-based chunking (specifically R100-0) consistently outperforms other approaches, offering strong performance with minimal resource overhead. We also find that retrieval-optimized embeddings -- such as Nomic and Intfloat E5 variants -- substantially outperform domain-specialized models like SciBERT. By releasing our datasets, evaluation framework, and empirical benchmarks, we provide actionable guidelines for building effective and efficient chemistry-aware RAG systems.

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

Medical information retrieval (MIR) is essential for retrieving relevant medical knowledge from diverse sources, including electronic health records, scientific literature, and medical databases. However, achieving effective zero-shot dense retrieval in the medical domain poses substantial challenges due to the lack of relevance-labeled data. In this paper, we introduce a novel approach called Self-Learning Hypothetical Document Embeddings (SL-HyDE) to tackle this issue. SL-HyDE leverages large language models (LLMs) as generators to generate hypothetical documents based on a given query. These generated documents encapsulate key medical context, guiding a dense retriever in identifying the most relevant documents. The self-learning framework progressively refines both pseudo-document generation and retrieval, utilizing unlabeled medical corpora without requiring any relevance-labeled data. Additionally, we present the Chinese Medical Information Retrieval Benchmark (CMIRB), a comprehensive evaluation framework grounded in real-world medical scenarios, encompassing five tasks and ten datasets. By benchmarking ten models on CMIRB, we establish a rigorous standard for evaluating medical information retrieval systems. Experimental results demonstrate that SL-HyDE significantly surpasses existing methods in retrieval accuracy while showcasing strong generalization and scalability across various LLM and retriever configurations. CMIRB data and evaluation code are publicly available at: https://github.com/CMIRB-benchmark/CMIRB.

In the field of language modeling, models augmented with retrieval components have emerged as a promising solution to address several challenges faced in the natural language processing (NLP) field, including knowledge grounding, interpretability, and scalability. Despite the primary focus on NLP, we posit that the paradigm of retrieval-enhancement can be extended to a broader spectrum of machine learning (ML) such as computer vision, time series prediction, and computational biology. Therefore, this work introduces a formal framework of this paradigm, Retrieval-Enhanced Machine Learning (REML), by synthesizing the literature in various domains in ML with consistent notations which is missing from the current literature. Also, we found that while a number of studies employ retrieval components to augment their models, there is a lack of integration with foundational Information Retrieval (IR) research. We bridge this gap between the seminal IR research and contemporary REML studies by investigating each component that comprises the REML framework. Ultimately, the goal of this work is to equip researchers across various disciplines with a comprehensive, formally structured framework of retrieval-enhanced models, thereby fostering interdisciplinary future research.

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.

Learned sparse text embeddings have gained popularity due to their effectiveness in top-k retrieval and inherent interpretability. Their distributional idiosyncrasies, however, have long hindered their use in real-world retrieval systems. That changed with the recent development of approximate algorithms that leverage the distributional properties of sparse embeddings to speed up retrieval. Nonetheless, in much of the existing literature, evaluation has been limited to datasets with only a few million documents such as MSMARCO. It remains unclear how these systems behave on much larger datasets and what challenges lurk in larger scales. To bridge that gap, we investigate the behavior of state-of-the-art retrieval algorithms on massive datasets. We compare and contrast the recently-proposed Seismic and graph-based solutions adapted from dense retrieval. We extensively evaluate Splade embeddings of 138M passages from MsMarco-v2 and report indexing time and other efficiency and effectiveness metrics.

Ranking models lie at the heart of research on information retrieval (IR). During the past decades, different techniques have been proposed for constructing ranking models, from traditional heuristic methods, probabilistic methods, to modern machine learning methods. Recently, with the advance of deep learning technology, we have witnessed a growing body of work in applying shallow or deep neural networks to the ranking problem in IR, referred to as neural ranking models in this paper. The power of neural ranking models lies in the ability to learn from the raw text inputs for the ranking problem to avoid many limitations of hand-crafted features. Neural networks have sufficient capacity to model complicated tasks, which is needed to handle the complexity of relevance estimation in ranking. Since there have been a large variety of neural ranking models proposed, we believe it is the right time to summarize the current status, learn from existing methodologies, and gain some insights for future development. In contrast to existing reviews, in this survey, we will take a deep look into the neural ranking models from different dimensions to analyze their underlying assumptions, major design principles, and learning strategies. We compare these models through benchmark tasks to obtain a comprehensive empirical understanding of the existing techniques. We will also discuss what is missing in the current literature and what are the promising and desired future directions.

In the era of Large Language Models (LLMs), given their remarkable text understanding and generation abilities, there is an unprecedented opportunity to develop new, LLM-based methods for trustworthy medical knowledge synthesis, extraction and summarization. This paper focuses on the problem of Pharmacovigilance (PhV), where the significance and challenges lie in identifying Adverse Drug Events (ADEs) from diverse text sources, such as medical literature, clinical notes, and drug labels. Unfortunately, this task is hindered by factors including variations in the terminologies of drugs and outcomes, and ADE descriptions often being buried in large amounts of narrative text. We present MALADE, the first effective collaborative multi-agent system powered by LLM with Retrieval Augmented Generation for ADE extraction from drug label data. This technique involves augmenting a query to an LLM with relevant information extracted from text resources, and instructing the LLM to compose a response consistent with the augmented data. MALADE is a general LLM-agnostic architecture, and its unique capabilities are: (1) leveraging a variety of external sources, such as medical literature, drug labels, and FDA tools (e.g., OpenFDA drug information API), (2) extracting drug-outcome association in a structured format along with the strength of the association, and (3) providing explanations for established associations. Instantiated with GPT-4 Turbo or GPT-4o, and FDA drug label data, MALADE demonstrates its efficacy with an Area Under ROC Curve of 0.90 against the OMOP Ground Truth table of ADEs. Our implementation leverages the Langroid multi-agent LLM framework and can be found at https://github.com/jihyechoi77/malade.

The specialized language and complex concepts in physics pose significant challenges for information extraction through Natural Language Processing (NLP). Central to effective NLP applications is the text embedding model, which converts text into dense vector representations for efficient information retrieval and semantic analysis. In this work, we introduce PhysBERT, the first physics-specific text embedding model. Pre-trained on a curated corpus of 1.2 million arXiv physics papers and fine-tuned with supervised data, PhysBERT outperforms leading general-purpose models on physics-specific tasks including the effectiveness in fine-tuning for specific physics subdomains.

Understanding and reasoning on the web-scale scientific literature is a crucial touchstone for large language model (LLM) based agents designed to support complex knowledge-intensive tasks. However, existing works are mainly restricted to tool-free tasks within isolated papers, largely due to the lack of a benchmark for cross-paper reasoning and multi-tool orchestration in real research scenarios. In this work, we propose PaperArena, an evaluation benchmark for agents to address real-world research questions that typically require integrating information across multiple papers with the assistance of external tools. Given a research question, agents should integrate diverse formats across multiple papers through reasoning and interacting with appropriate tools, thereby producing a well-grounded answer. To support standardized evaluation, we provide a modular and extensible platform for agent execution, offering tools such as multimodal parsing, context retrieval, and programmatic computation. Experimental results reveal that even the most advanced LLM powering a well-established agent system achieves merely 38.78% average accuracy. On the hard subset, accuracy drops to only 18.47%, highlighting great potential for improvement. We also present several empirical findings, including that all agents tested exhibit inefficient tool usage, often invoking more tools than necessary to solve a task. We invite the community to adopt PaperArena to develop and evaluate more capable agents for scientific discovery. Our code and data are available https://github.com/Melmaphother/PaperArena.

Despite the rapid advancement of large language models (LLMs), low-resource languages remain largely excluded from the NLP landscape. We present PunGPT2, the first fully open-source suite of Punjabi large language models, trained from scratch on a 35GB domain-diverse corpus encompassing literature, religious texts, news, and social discourse. Unlike prior multilingual approaches, PunGPT2 captures rich syntactic and morphological features unique to Punjabi through a tokenizer optimised with byte pair encoding and linguistically aligned pretraining objectives. To improve factual grounding and domain recall, we introduce Pun-RAG, a retrieval-augmented generation framework combining PunGPT2 with a dense FAISS retriever over a curated Punjabi knowledge base. We further develop Pun-Instruct, a parameter-efficient, instruction-tuned variant using QLoRA, enabling robust zero-shot and instruction-following performance with significantly reduced compute needs. As a key innovation, we propose Quantum-RAG, a novel hybrid retrieval system that fuses sparse (BM25) and dense methods with quantum-inspired semantic matching. By encoding queries using amplitude-based embeddings and retrieving via quantum kernel similarity, Quantum-RAG achieves improved contextual relevance with minimal memory overhead marking the first practical integration of quantum representations in low-resource language generation. Our models significantly outperform strong multilingual baselines (mBERT, mT5, MuRIL) in perplexity, factuality, and fluency. This work provides a scalable, reproducible blueprint for extending LLM capabilities to underrepresented languages and pioneers quantum-aware retrieval in low-resource NLP

Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences where reproducibility is crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. Here we introduce LLaMP, a multimodal retrieval-augmented generation (RAG) framework of multiple data-aware reasoning-and-acting (ReAct) agents that dynamically interact with computational and experimental data on Materials Project (MP). Without fine-tuning, LLaMP demonstrates an ability to comprehend and integrate various modalities of materials science concepts, fetch relevant data stores on the fly, process higher-order data (such as crystal structures and elastic tensors), and summarize multi-step procedures for solid-state synthesis. We show that LLaMP effectively corrects errors in GPT-3.5's intrinsic knowledge, reducing a 5.21% MAPE on frequently-documented bandgaps and a significant 1103.54% MAPE on formation energies -- errors that GPT-3.5 seems to derive from mixed data sources. Additionally, LLaMP substantially reduces the hallucinated volumetric strain in a diamond cubic silicon structure from 66.3% to 0. The proposed framework offers an intuitive and nearly hallucination-free approach to exploring materials informatics and establishes a pathway for knowledge distillation and fine-tuning other language models. We envision the framework as a valuable component for scientific hypotheses and a foundation for future autonomous laboratories where multiple LLM agents communicate and cooperate with robotics to drive material synthesis and chemical reactions without hard-coded human logic and intervention.

Search engines often follow a two-phase paradigm where in the first stage (the retrieval stage) an initial set of documents is retrieved and in the second stage (the re-ranking stage) the documents are re-ranked to obtain the final result list. While deep neural networks were shown to improve the performance of the re-ranking stage in previous works, there is little literature about using deep neural networks to improve the retrieval stage. In this paper, we study the merits of combining deep neural network models and lexical models for the retrieval stage. A hybrid approach, which leverages both semantic (deep neural network-based) and lexical (keyword matching-based) retrieval models, is proposed. We perform an empirical study, using a publicly available TREC collection, which demonstrates the effectiveness of our approach and sheds light on the different characteristics of the semantic approach, the lexical approach, and their combination.

Systematic literature reviews (SLRs) play an essential role in summarising, synthesising and validating scientific evidence. In recent years, there has been a growing interest in using machine learning techniques to automate the identification of relevant studies for SLRs. However, the lack of standardised evaluation datasets makes comparing the performance of such automated literature screening systems difficult. In this paper, we analyse the citation screening evaluation datasets, revealing that many of the available datasets are either too small, suffer from data leakage or have limited applicability to systems treating automated literature screening as a classification task, as opposed to, for example, a retrieval or question-answering task. To address these challenges, we introduce CSMeD, a meta-dataset consolidating nine publicly released collections, providing unified access to 325 SLRs from the fields of medicine and computer science. CSMeD serves as a comprehensive resource for training and evaluating the performance of automated citation screening models. Additionally, we introduce CSMeD-FT, a new dataset designed explicitly for evaluating the full text publication screening task. To demonstrate the utility of CSMeD, we conduct experiments and establish baselines on new datasets.

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

A plethora of sentence embedding models makes it challenging to choose one, especially for domains such as telecom, rich with specialized vocabulary. We evaluate multiple embeddings obtained from publicly available models and their domain-adapted variants, on both point retrieval accuracies as well as their (95\%) confidence intervals. We establish a systematic method to obtain thresholds for similarity scores for different embeddings. We observe that fine-tuning improves mean bootstrapped accuracies as well as tightens confidence intervals. The pre-training combined with fine-tuning makes confidence intervals even tighter. To understand these variations, we analyse and report significant correlations between the distributional overlap between top-K, correct and random sentence similarities with retrieval accuracies and similarity thresholds. Following current literature, we analyze if retrieval accuracy variations can be attributed to isotropy of embeddings. Our conclusions are that isotropy of embeddings (as measured by two independent state-of-the-art isotropy metric definitions) cannot be attributed to better retrieval performance. However, domain adaptation which improves retrieval accuracies also improves isotropy. We establish that domain adaptation moves domain specific embeddings further away from general domain embeddings.

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 rapid expansion of scientific literature in computer science presents challenges in tracking research trends and extracting key insights. Existing datasets provide metadata but lack structured summaries that capture core contributions and methodologies. We introduce CS-PaperSum, a large-scale dataset of 91,919 papers from 31 top-tier computer science conferences, enriched with AI-generated structured summaries using ChatGPT. To assess summary quality, we conduct embedding alignment analysis and keyword overlap analysis, demonstrating strong preservation of key concepts. We further present a case study on AI research trends, highlighting shifts in methodologies and interdisciplinary crossovers, including the rise of self-supervised learning, retrieval-augmented generation, and multimodal AI. Our dataset enables automated literature analysis, research trend forecasting, and AI-driven scientific discovery, providing a valuable resource for researchers, policymakers, and scientific information retrieval systems.

We present a Conversational Chain-of-Action (Conv-CoA) framework for Open-domain Conversational Question Answering (OCQA). Compared with literature, Conv-CoA addresses three major challenges: (i) unfaithful hallucination that is inconsistent with real-time or domain facts, (ii) weak reasoning performance in conversational scenarios, and (iii) unsatisfying performance in conversational information retrieval. Our key contribution is a dynamic reasoning-retrieval mechanism that extracts the intent of the question and decomposes it into a reasoning chain to be solved via systematic prompting, pre-designed actions, updating the Contextual Knowledge Set (CKS), and a novel Hopfield-based retriever. Methodologically, we propose a resource-efficiency Hopfield retriever to enhance the efficiency and accuracy of conversational information retrieval within our actions. Additionally, we propose a conversational-multi-reference faith score (Conv-MRFS) to verify and resolve conflicts between retrieved knowledge and answers in conversations. Empirically, we conduct comparisons between our framework and 23 state-of-the-art methods across five different research directions and two public benchmarks. These comparisons demonstrate that our Conv-CoA outperforms other methods in both the accuracy and efficiency dimensions.

We introduce SciVer, the first benchmark specifically designed to evaluate the ability of foundation models to verify claims within a multimodal scientific context. SciVer consists of 3,000 expert-annotated examples over 1,113 scientific papers, covering four subsets, each representing a common reasoning type in multimodal scientific claim verification. To enable fine-grained evaluation, each example includes expert-annotated supporting evidence. We assess the performance of 21 state-of-the-art multimodal foundation models, including o4-mini, Gemini-2.5-Flash, Llama-3.2-Vision, and Qwen2.5-VL. Our experiment reveals a substantial performance gap between these models and human experts on SciVer. Through an in-depth analysis of retrieval-augmented generation (RAG), and human-conducted error evaluations, we identify critical limitations in current open-source models, offering key insights to advance models' comprehension and reasoning in multimodal scientific literature tasks.

For centuries, researchers have sought out ways to connect disparate areas of knowledge. While early scholars (Galileo, da Vinci, etc.) were experts across fields, specialization has taken hold later. With the advent of Artificial Intelligence, we can now explore relationships across areas (e.g., mechanics-biology) or disparate domains (e.g., failure mechanics-art). To achieve this, we use a fine-tuned Large Language Model (LLM), here for a subset of knowledge in multiscale materials failure. The approach includes the use of a general-purpose LLM to distill question-answer pairs from raw sources followed by LLM fine-tuning. The resulting MechGPT LLM foundation model is used in a series of computational experiments to explore its capacity for knowledge retrieval, various language tasks, hypothesis generation, and connecting knowledge across disparate areas. While the model has some ability to recall knowledge from training, we find that LLMs are particularly useful to extract structural insights through Ontological Knowledge Graphs. These interpretable graph structures provide explanatory insights, frameworks for new research questions, and visual representations of knowledge that also can be used in retrieval-augmented generation. Three versions of MechGPT are discussed, featuring different sizes from 13 billion to 70 billion parameters, and reaching context lengths of more than 10,000 tokens. This provides ample capacity for sophisticated retrieval augmented strategies, as well as agent-based modeling where multiple LLMs interact collaboratively and/or adversarially, the incorporation of new data from the literature or web searches, as well as multimodality.

The rapid advancement of perovskite solar cells (PSCs) has led to an exponential growth in research publications, creating an urgent need for efficient knowledge management and reasoning systems in this domain. We present a comprehensive knowledge-enhanced system for PSCs that integrates three key components. First, we develop Perovskite-KG, a domain-specific knowledge graph constructed from 1,517 research papers, containing 23,789 entities and 22,272 relationships. Second, we create two complementary datasets: Perovskite-Chat, comprising 55,101 high-quality question-answer pairs generated through a novel multi-agent framework, and Perovskite-Reasoning, containing 2,217 carefully curated materials science problems. Third, we introduce two specialized large language models: Perovskite-Chat-LLM for domain-specific knowledge assistance and Perovskite-Reasoning-LLM for scientific reasoning tasks. Experimental results demonstrate that our system significantly outperforms existing models in both domain-specific knowledge retrieval and scientific reasoning tasks, providing researchers with effective tools for literature review, experimental design, and complex problem-solving in PSC research.

Language models are known to hallucinate incorrect information, and it is unclear if they are sufficiently accurate and reliable for use in scientific research. We developed a rigorous human-AI comparison methodology to evaluate language model agents on real-world literature search tasks covering information retrieval, summarization, and contradiction detection tasks. We show that PaperQA2, a frontier language model agent optimized for improved factuality, matches or exceeds subject matter expert performance on three realistic literature research tasks without any restrictions on humans (i.e., full access to internet, search tools, and time). PaperQA2 writes cited, Wikipedia-style summaries of scientific topics that are significantly more accurate than existing, human-written Wikipedia articles. We also introduce a hard benchmark for scientific literature research called LitQA2 that guided design of PaperQA2, leading to it exceeding human performance. Finally, we apply PaperQA2 to identify contradictions within the scientific literature, an important scientific task that is challenging for humans. PaperQA2 identifies 2.34 +/- 1.99 contradictions per paper in a random subset of biology papers, of which 70% are validated by human experts. These results demonstrate that language model agents are now capable of exceeding domain experts across meaningful tasks on scientific literature.

Learning semantically meaningful representations from scientific documents can facilitate academic literature search and improve performance of recommendation systems. Pre-trained language models have been shown to learn rich textual representations, yet they cannot provide powerful document-level representations for scientific articles. We propose MIReAD, a simple method that learns high-quality representations of scientific papers by fine-tuning transformer model to predict the target journal class based on the abstract. We train MIReAD on more than 500,000 PubMed and arXiv abstracts across over 2,000 journal classes. We show that MIReAD produces representations that can be used for similar papers retrieval, topic categorization and literature search. Our proposed approach outperforms six existing models for representation learning on scientific documents across four evaluation standards.

We present an overview of the TREC-COVID Challenge, an information retrieval (IR) shared task to evaluate search on scientific literature related to COVID-19. The goals of TREC-COVID include the construction of a pandemic search test collection and the evaluation of IR methods for COVID-19. The challenge was conducted over five rounds from April to July, 2020, with participation from 92 unique teams and 556 individual submissions. A total of 50 topics (sets of related queries) were used in the evaluation, starting at 30 topics for Round 1 and adding 5 new topics per round to target emerging topics at that state of the still-emerging pandemic. This paper provides a comprehensive overview of the structure and results of TREC-COVID. Specifically, the paper provides details on the background, task structure, topic structure, corpus, participation, pooling, assessment, judgments, results, top-performing systems, lessons learned, and benchmark datasets.

Clinical evidence, derived from rigorous research and data analysis, provides healthcare professionals with reliable scientific foundations for informed decision-making. Integrating clinical evidence into real-time practice is challenging due to the enormous workload, complex professional processes, and time constraints. This highlights the need for tools that automate evidence synthesis to support more efficient and accurate decision making in clinical settings. This study introduces Quicker, an evidence-based clinical decision support system powered by large language models (LLMs), designed to automate evidence synthesis and generate clinical recommendations modeled after standard clinical guideline development processes. Quicker implements a fully automated chain that covers all phases, from questions to clinical recommendations, and further enables customized decision-making through integrated tools and interactive user interfaces. To evaluate Quicker's capabilities, we developed the Q2CRBench-3 benchmark dataset, based on clinical guideline development records for three different diseases. Experimental results highlighted Quicker's strong performance, with fine-grained question decomposition tailored to user preferences, retrieval sensitivities comparable to human experts, and literature screening performance approaching comprehensive inclusion of relevant studies. In addition, Quicker-assisted evidence assessment effectively supported human reviewers, while Quicker's recommendations were more comprehensive and logically coherent than those of clinicians. In system-level testing, collaboration between a single reviewer and Quicker reduced the time required for recommendation development to 20-40 minutes. In general, our findings affirm the potential of Quicker to help physicians make quicker and more reliable evidence-based clinical decisions.

Identifying reliable synthesis pathways in materials chemistry is a complex task, particularly in polymer science, due to the intricate and often non-unique nomenclature of macromolecules. To address this challenge, we propose an agent system that integrates large language models (LLMs) and knowledge graphs (KGs). By leveraging LLMs' powerful capabilities for extracting and recognizing chemical substance names, and storing the extracted data in a structured knowledge graph, our system fully automates the retrieval of relevant literatures, extraction of reaction data, database querying, construction of retrosynthetic pathway trees, further expansion through the retrieval of additional literature and recommendation of optimal reaction pathways. A novel Multi-branched Reaction Pathway Search (MBRPS) algorithm enables the exploration of all pathways, with a particular focus on multi-branched ones, helping LLMs overcome weak reasoning in multi-branched paths. This work represents the first attempt to develop a fully automated retrosynthesis planning agent tailored specially for macromolecules powered by LLMs. Applied to polyimide synthesis, our new approach constructs a retrosynthetic pathway tree with hundreds of pathways and recommends optimized routes, including both known and novel pathways, demonstrating its effectiveness and potential for broader applications.

Research question answering requires accurate retrieval and contextual understanding of scientific literature. However, current Retrieval-Augmented Generation (RAG) methods often struggle to balance complex document relationships with precise information retrieval. In this paper, we introduce Contextualized Graph Retrieval-Augmented Generation (CG-RAG), a novel framework that integrates sparse and dense retrieval signals within graph structures to enhance retrieval efficiency and subsequently improve generation quality for research question answering. First, we propose a contextual graph representation for citation graphs, effectively capturing both explicit and implicit connections within and across documents. Next, we introduce Lexical-Semantic Graph Retrieval (LeSeGR), which seamlessly integrates sparse and dense retrieval signals with graph encoding. It bridges the gap between lexical precision and semantic understanding in citation graph retrieval, demonstrating generalizability to existing graph retrieval and hybrid retrieval methods. Finally, we present a context-aware generation strategy that utilizes the retrieved graph-structured information to generate precise and contextually enriched responses using large language models (LLMs). Extensive experiments on research question answering benchmarks across multiple domains demonstrate that our CG-RAG framework significantly outperforms RAG methods combined with various state-of-the-art retrieval approaches, delivering superior retrieval accuracy and generation quality.

Video generation is experiencing rapid growth, driven by advances in diffusion models and the development of better and larger datasets. However, producing high-quality videos remains challenging due to the high-dimensional data and the complexity of the task. Recent efforts have primarily focused on enhancing visual quality and addressing temporal inconsistencies, such as flickering. Despite progress in these areas, the generated videos often fall short in terms of motion complexity and physical plausibility, with many outputs either appearing static or exhibiting unrealistic motion. In this work, we propose a framework to improve the realism of motion in generated videos, exploring a complementary direction to much of the existing literature. Specifically, we advocate for the incorporation of a retrieval mechanism during the generation phase. The retrieved videos act as grounding signals, providing the model with demonstrations of how the objects move. Our pipeline is designed to apply to any text-to-video diffusion model, conditioning a pretrained model on the retrieved samples with minimal fine-tuning. We demonstrate the superiority of our approach through established metrics, recently proposed benchmarks, and qualitative results, and we highlight additional applications of the framework.

The Airbnb search system grapples with many unique challenges as it continues to evolve. We oversee a marketplace that is nuanced by geography, diversity of homes, and guests with a variety of preferences. Crafting an efficient search system that can accommodate diverse guest needs, while showcasing relevant homes lies at the heart of Airbnb's success. Airbnb search has many challenges that parallel other recommendation and search systems but it has a unique information retrieval problem, upstream of ranking, called location retrieval. It requires defining a topological map area that is relevant to the searched query for homes listing retrieval. The purpose of this paper is to demonstrate the methodology, challenges, and impact of building a machine learning based location retrieval product from the ground up. Despite the lack of suitable, prevalent machine learning based approaches, we tackle cold start, generalization, differentiation and algorithmic bias. We detail the efficacy of heuristics, statistics, machine learning, and reinforcement learning approaches to solve these challenges, particularly for systems that are often unexplored by current literature.

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.

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

We introduce IFIR, the first comprehensive benchmark designed to evaluate instruction-following information retrieval (IR) in expert domains. IFIR includes 2,426 high-quality examples and covers eight subsets across four specialized domains: finance, law, healthcare, and science literature. Each subset addresses one or more domain-specific retrieval tasks, replicating real-world scenarios where customized instructions are critical. IFIR enables a detailed analysis of instruction-following retrieval capabilities by incorporating instructions at different levels of complexity. We also propose a novel LLM-based evaluation method to provide a more precise and reliable assessment of model performance in following instructions. Through extensive experiments on 15 frontier retrieval models, including those based on LLMs, our results reveal that current models face significant challenges in effectively following complex, domain-specific instructions. We further provide in-depth analyses to highlight these limitations, offering valuable insights to guide future advancements in retriever development.

Machine learning is now used in many areas of astrophysics, from detecting exoplanets in Kepler transit signals to removing telescope systematics. Recent work demonstrated the potential of using machine learning algorithms for atmospheric retrieval by implementing a random forest to perform retrievals in seconds that are consistent with the traditional, computationally-expensive nested-sampling retrieval method. We expand upon their approach by presenting a new machine learning model, plan-net, based on an ensemble of Bayesian neural networks that yields more accurate inferences than the random forest for the same data set of synthetic transmission spectra. We demonstrate that an ensemble provides greater accuracy and more robust uncertainties than a single model. In addition to being the first to use Bayesian neural networks for atmospheric retrieval, we also introduce a new loss function for Bayesian neural networks that learns correlations between the model outputs. Importantly, we show that designing machine learning models to explicitly incorporate domain-specific knowledge both improves performance and provides additional insight by inferring the covariance of the retrieved atmospheric parameters. We apply plan-net to the Hubble Space Telescope Wide Field Camera 3 transmission spectrum for WASP-12b and retrieve an isothermal temperature and water abundance consistent with the literature. We highlight that our method is flexible and can be expanded to higher-resolution spectra and a larger number of atmospheric parameters.

Contrastive learning has emerged as a powerful technique in audio-visual representation learning, leveraging the natural co-occurrence of audio and visual modalities in extensive web-scale video datasets to achieve significant advancements. However, conventional contrastive audio-visual learning methodologies often rely on aggregated representations derived through temporal aggregation, which neglects the intrinsic sequential nature of the data. This oversight raises concerns regarding the ability of standard approaches to capture and utilize fine-grained information within sequences, information that is vital for distinguishing between semantically similar yet distinct examples. In response to this limitation, we propose sequential contrastive audio-visual learning (SCAV), which contrasts examples based on their non-aggregated representation space using sequential distances. Retrieval experiments with the VGGSound and Music datasets demonstrate the effectiveness of SCAV, showing 2-3x relative improvements against traditional aggregation-based contrastive learning and other methods from the literature. We also show that models trained with SCAV exhibit a high degree of flexibility regarding the metric employed for retrieval, allowing them to operate on a spectrum of efficiency-accuracy trade-offs, potentially making them applicable in multiple scenarios, from small- to large-scale retrieval.

This research explores the integration of large language models (LLMs) into scientific data assimilation, focusing on combustion science as a case study. Leveraging foundational models integrated with Retrieval-Augmented Generation (RAG) framework, the study introduces an approach to process diverse combustion research data, spanning experimental studies, simulations, and literature. The multifaceted nature of combustion research emphasizes the critical role of knowledge processing in navigating and extracting valuable information from a vast and diverse pool of sources. The developed approach minimizes computational and economic expenses while optimizing data privacy and accuracy. It incorporates prompt engineering and offline open-source LLMs, offering user autonomy in selecting base models. The study provides a thorough examination of text segmentation strategies, conducts comparative studies between LLMs, and explores various optimized prompts to demonstrate the effectiveness of the framework. By incorporating an external database, the framework outperforms a conventional LLM in generating accurate responses and constructing robust arguments. Additionally, the study delves into the investigation of optimized prompt templates for the purpose of efficient extraction of scientific literature. The research addresses concerns related to hallucinations and false research articles by introducing a custom workflow developed with a detection algorithm to filter out inaccuracies. Despite identified areas for improvement, the framework consistently delivers accurate domain-specific responses with minimal human oversight. The prompt-agnostic approach introduced holds promise for future deliberations. The study underscores the significance of integrating LLMs and knowledge processing techniques in scientific research, providing a foundation for advancements in data assimilation and utilization.