Daily Papers

Scientific information extraction (SciIE), which aims to automatically extract information from scientific literature, is becoming more important than ever. However, there are no existing SciIE datasets for polymer materials, which is an important class of materials used ubiquitously in our daily lives. To bridge this gap, we introduce POLYIE, a new SciIE dataset for polymer materials. POLYIE is curated from 146 full-length polymer scholarly articles, which are annotated with different named entities (i.e., materials, properties, values, conditions) as well as their N-ary relations by domain experts. POLYIE presents several unique challenges due to diverse lexical formats of entities, ambiguity between entities, and variable-length relations. We evaluate state-of-the-art named entity extraction and relation extraction models on POLYIE, analyze their strengths and weaknesses, and highlight some difficult cases for these models. To the best of our knowledge, POLYIE is the first SciIE benchmark for polymer materials, and we hope it will lead to more research efforts from the community on this challenging task. Our code and data are available on: https://github.com/jerry3027/PolyIE.

Extracting key information from scientific papers has the potential to help researchers work more efficiently and accelerate the pace of scientific progress. Over the last few years, research on Scientific Information Extraction (SciIE) witnessed the release of several new systems and benchmarks. However, existing paper-focused datasets mostly focus only on specific parts of a manuscript (e.g., abstracts) and are single-modality (i.e., text- or table-only), due to complex processing and expensive annotations. Moreover, core information can be present in either text or tables or across both. To close this gap in data availability and enable cross-modality IE, while alleviating labeling costs, we propose a semi-supervised pipeline for annotating entities in text, as well as entities and relations in tables, in an iterative procedure. Based on this pipeline, we release novel resources for the scientific community, including a high-quality benchmark, a large-scale corpus, and a semi-supervised annotation pipeline. We further report the performance of state-of-the-art IE models on the proposed benchmark dataset, as a baseline. Lastly, we explore the potential capability of large language models such as ChatGPT for the current task. Our new dataset, results, and analysis validate the effectiveness and efficiency of our semi-supervised pipeline, and we discuss its remaining limitations.

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

We explore the ability of GPT-4 to perform ad-hoc schema based information extraction from scientific literature. We assess specifically whether it can, with a basic prompting approach, replicate two existing material science datasets, given the manuscripts from which they were originally manually extracted. We employ materials scientists to perform a detailed manual error analysis to assess where the model struggles to faithfully extract the desired information, and draw on their insights to suggest research directions to address this broadly important task.

In this paper, we champion the use of structured and semantic content representation of discourse-based scholarly communication, inspired by tools like Wikipedia infoboxes or structured Amazon product descriptions. These representations provide users with a concise overview, aiding scientists in navigating the dense academic landscape. Our novel automated approach leverages the robust text generation capabilities of LLMs to produce structured scholarly contribution summaries, offering both a practical solution and insights into LLMs' emergent abilities. For LLMs, the prime focus is on improving their general intelligence as conversational agents. We argue that these models can also be applied effectively in information extraction (IE), specifically in complex IE tasks within terse domains like Science. This paradigm shift replaces the traditional modular, pipelined machine learning approach with a simpler objective expressed through instructions. Our results show that finetuned FLAN-T5 with 1000x fewer parameters than the state-of-the-art GPT-davinci is competitive for the task.

Scientific information extraction (SciIE) is critical for converting unstructured knowledge from scholarly articles into structured data (entities and relations). Several datasets have been proposed for training and validating SciIE models. However, due to the high complexity and cost of annotating scientific texts, those datasets restrict their annotations to specific parts of paper, such as abstracts, resulting in the loss of diverse entity mentions and relations in context. In this paper, we release a new entity and relation extraction dataset for entities related to datasets, methods, and tasks in scientific articles. Our dataset contains 106 manually annotated full-text scientific publications with over 24k entities and 12k relations. To capture the intricate use and interactions among entities in full texts, our dataset contains a fine-grained tag set for relations. Additionally, we provide an out-of-distribution test set to offer a more realistic evaluation. We conduct comprehensive experiments, including state-of-the-art supervised models and our proposed LLM-based baselines, and highlight the challenges presented by our dataset, encouraging the development of innovative models to further the field of SciIE.

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

Whether the media faithfully communicate scientific information has long been a core issue to the science community. Automatically identifying paraphrased scientific findings could enable large-scale tracking and analysis of information changes in the science communication process, but this requires systems to understand the similarity between scientific information across multiple domains. To this end, we present the SCIENTIFIC PARAPHRASE AND INFORMATION CHANGE DATASET (SPICED), the first paraphrase dataset of scientific findings annotated for degree of information change. SPICED contains 6,000 scientific finding pairs extracted from news stories, social media discussions, and full texts of original papers. We demonstrate that SPICED poses a challenging task and that models trained on SPICED improve downstream performance on evidence retrieval for fact checking of real-world scientific claims. Finally, we show that models trained on SPICED can reveal large-scale trends in the degrees to which people and organizations faithfully communicate new scientific findings. Data, code, and pre-trained models are available at http://www.copenlu.com/publication/2022_emnlp_wright/.

The Scielo database is an important source of scientific information in Latin America, containing articles from several research domains. A striking characteristic of Scielo is that many of its full-text contents are presented in more than one language, thus being a potential source of parallel corpora. In this article, we present the development of a parallel corpus from Scielo in three languages: English, Portuguese, and Spanish. Sentences were automatically aligned using the Hunalign algorithm for all language pairs, and for a subset of trilingual articles also. We demonstrate the capabilities of our corpus by training a Statistical Machine Translation system (Moses) for each language pair, which outperformed related works on scientific articles. Sentence alignment was also manually evaluated, presenting an average of 98.8% correctly aligned sentences across all languages. Our parallel corpus is freely available in the TMX format, with complementary information regarding article metadata.

We introduce a multi-task setup of identifying and classifying entities, relations, and coreference clusters in scientific articles. We create SciERC, a dataset that includes annotations for all three tasks and develop a unified framework called Scientific Information Extractor (SciIE) for with shared span representations. The multi-task setup reduces cascading errors between tasks and leverages cross-sentence relations through coreference links. Experiments show that our multi-task model outperforms previous models in scientific information extraction without using any domain-specific features. We further show that the framework supports construction of a scientific knowledge graph, which we use to analyze information in scientific literature.

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.

Recent advancements in artificial intelligence have sparked interest in scientific assistants that could support researchers across the full spectrum of scientific workflows, from literature review to experimental design and data analysis. A key capability for such systems is the ability to process and reason about scientific information in both visual and textual forms - from interpreting spectroscopic data to understanding laboratory setups. Here, we introduce MaCBench, a comprehensive benchmark for evaluating how vision-language models handle real-world chemistry and materials science tasks across three core aspects: data extraction, experimental understanding, and results interpretation. Through a systematic evaluation of leading models, we find that while these systems show promising capabilities in basic perception tasks - achieving near-perfect performance in equipment identification and standardized data extraction - they exhibit fundamental limitations in spatial reasoning, cross-modal information synthesis, and multi-step logical inference. Our insights have important implications beyond chemistry and materials science, suggesting that developing reliable multimodal AI scientific assistants may require advances in curating suitable training data and approaches to training those models.

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

This paper describes the KnowledgeHub tool, a scientific literature Information Extraction (IE) and Question Answering (QA) pipeline. This is achieved by supporting the ingestion of PDF documents that are converted to text and structured representations. An ontology can then be constructed where a user defines the types of entities and relationships they want to capture. A browser-based annotation tool enables annotating the contents of the PDF documents according to the ontology. Named Entity Recognition (NER) and Relation Classification (RC) models can be trained on the resulting annotations and can be used to annotate the unannotated portion of the documents. A knowledge graph is constructed from these entity and relation triples which can be queried to obtain insights from the data. Furthermore, we integrate a suite of Large Language Models (LLMs) that can be used for QA and summarisation that is grounded in the included documents via a retrieval component. KnowledgeHub is a unique tool that supports annotation, IE and QA, which gives the user full insight into the knowledge discovery pipeline.

Since language models (LMs) now outperform average humans on many challenging tasks, it has become increasingly difficult to develop challenging, high-quality, and realistic evaluations. We address this issue by examining LMs' capabilities to generate code for solving real scientific research problems. Incorporating input from scientists and AI researchers in 16 diverse natural science sub-fields, including mathematics, physics, chemistry, biology, and materials science, we created a scientist-curated coding benchmark, SciCode. The problems in SciCode naturally factorize into multiple subproblems, each involving knowledge recall, reasoning, and code synthesis. In total, SciCode contains 338 subproblems decomposed from 80 challenging main problems. It offers optional descriptions specifying useful scientific background information and scientist-annotated gold-standard solutions and test cases for evaluation. Claude3.5-Sonnet, the best-performing model among those tested, can solve only 4.6% of the problems in the most realistic setting. We believe that SciCode demonstrates both contemporary LMs' progress towards becoming helpful scientific assistants and sheds light on the development and evaluation of scientific AI in the future.

Multi-modal information retrieval (MMIR) is a rapidly evolving field, where significant progress, particularly in image-text pairing, has been made through advanced representation learning and cross-modality alignment research. However, current benchmarks for evaluating MMIR performance in image-text pairing within the scientific domain show a notable gap, where chart and table images described in scholarly language usually do not play a significant role. To bridge this gap, we develop a specialised scientific MMIR (SciMMIR) benchmark by leveraging open-access paper collections to extract data relevant to the scientific domain. This benchmark comprises 530K meticulously curated image-text pairs, extracted from figures and tables with detailed captions in scientific documents. We further annotate the image-text pairs with two-level subset-subcategory hierarchy annotations to facilitate a more comprehensive evaluation of the baselines. We conducted zero-shot and fine-tuning evaluations on prominent multi-modal image-captioning and visual language models, such as CLIP and BLIP. Our analysis offers critical insights for MMIR in the scientific domain, including the impact of pre-training and fine-tuning settings and the influence of the visual and textual encoders. All our data and checkpoints are publicly available at https://github.com/Wusiwei0410/SciMMIR.

Researchers use figures to communicate rich, complex information in scientific papers. The captions of these figures are critical to conveying effective messages. However, low-quality figure captions commonly occur in scientific articles and may decrease understanding. In this paper, we propose an end-to-end neural framework to automatically generate informative, high-quality captions for scientific figures. To this end, we introduce SCICAP, a large-scale figure-caption dataset based on computer science arXiv papers published between 2010 and 2020. After pre-processing - including figure-type classification, sub-figure identification, text normalization, and caption text selection - SCICAP contained more than two million figures extracted from over 290,000 papers. We then established baseline models that caption graph plots, the dominant (19.2%) figure type. The experimental results showed both opportunities and steep challenges of generating captions for scientific figures.

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

Fully comprehending scientific papers by machines reflects a high level of Artificial General Intelligence, requiring the ability to reason across fragmented and heterogeneous sources of information, presenting a complex and practically significant challenge. While Vision-Language Models (VLMs) have made remarkable strides in various tasks, particularly those involving reasoning with evidence source from single image or text page, their ability to use cross-source information for reasoning remains an open problem. This work presents MMCR, a high-difficulty benchmark designed to evaluate VLMs' capacity for reasoning with cross-source information from scientific papers. The benchmark comprises 276 high-quality questions, meticulously annotated by humans across 7 subjects and 10 task types. Experiments with 18 VLMs demonstrate that cross-source reasoning presents a substantial challenge for existing models. Notably, even the top-performing model, GPT-4o, achieved only 48.55% overall accuracy, with only 20% accuracy in multi-table comprehension tasks, while the second-best model, Qwen2.5-VL-72B, reached 39.86% overall accuracy. Furthermore, we investigated the impact of the Chain-of-Thought (CoT) technique on cross-source reasoning and observed a detrimental effect on small models, whereas larger models demonstrated substantially enhanced performance. These results highlight the pressing need to develop VLMs capable of effectively utilizing cross-source information for reasoning.

Errors in understanding visual information in images (i.e., visual perception errors) remain a major source of mistakes in Large Vision Language Models (LVLMs). While further analysis is essential, there is a deficiency in datasets for evaluating the visual perception of LVLMs. In this work, we introduce VisOnlyQA, a new dataset designed to directly evaluate the visual perception capabilities of LVLMs on questions about geometric and numerical information in scientific figures. Our dataset enables us to analyze the visual perception of LVLMs for fine-grained visual information, independent of other capabilities such as reasoning. The evaluation set of VisOnlyQA includes 1,200 multiple-choice questions in 12 tasks on four categories of figures. We also provide synthetic training data consisting of 70k instances. Our experiments on VisOnlyQA highlight the following findings: (i) 20 LVLMs we evaluate, including GPT-4o and Gemini 1.5 Pro, work poorly on the visual perception tasks in VisOnlyQA, while human performance is nearly perfect. (ii) Fine-tuning on synthetic training data demonstrates the potential for enhancing the visual perception of LVLMs, but observed improvements are limited to certain tasks and specific models. (iii) Stronger language models improve the visual perception of LVLMs. In summary, our experiments suggest that both training data and model architectures should be improved to enhance the visual perception capabilities of LVLMs. The datasets, code, and model responses are provided at https://github.com/psunlpgroup/VisOnlyQA.

Scientific discoveries increasingly rely on complex multimodal reasoning based on information-intensive scientific data and domain-specific expertise. Empowered by expert-level scientific benchmarks, scientific Multimodal Large Language Models (MLLMs) hold the potential to significantly enhance this discovery process in realistic workflows. However, current scientific benchmarks mostly focus on evaluating the knowledge understanding capabilities of MLLMs, leading to an inadequate assessment of their perception and reasoning abilities. To address this gap, we present the Scientists' First Exam (SFE) benchmark, designed to evaluate the scientific cognitive capacities of MLLMs through three interconnected levels: scientific signal perception, scientific attribute understanding, scientific comparative reasoning. Specifically, SFE comprises 830 expert-verified VQA pairs across three question types, spanning 66 multimodal tasks across five high-value disciplines. Extensive experiments reveal that current state-of-the-art GPT-o3 and InternVL-3 achieve only 34.08% and 26.52% on SFE, highlighting significant room for MLLMs to improve in scientific realms. We hope the insights obtained in SFE will facilitate further developments in AI-enhanced scientific discoveries.

Tables are widely used in documents because of their compact and structured representation of information. In particular, in scientific papers, tables can sum up novel discoveries and summarize experimental results, making the research comparable and easily understandable by scholars. Since the layout of tables is highly variable, it would be useful to interpret their content and classify them into categories. This could be helpful to directly extract information from scientific papers, for instance comparing performance of some models given their paper result tables. In this work, we address the classification of tables using a Graph Neural Network, exploiting the table structure for the message passing algorithm in use. We evaluate our model on a subset of the Tab2Know dataset. Since it contains few examples manually annotated, we propose data augmentation techniques directly on the table graph structures. We achieve promising preliminary results, proposing a data augmentation method suitable for graph-based table representation.

Previous studies have shown that automated text-mining tools are becoming increasingly important for successfully unlocking variant information in scientific literature at large scale. Despite multiple attempts in the past, existing tools are still of limited recognition scope and precision. We propose tmVar 3.0: an improved variant recognition and normalization tool. Compared to its predecessors, tmVar 3.0 is able to recognize a wide spectrum of variant related entities (e.g., allele and copy number variants), and to group different variant mentions belonging to the same concept in an article for improved accuracy. Moreover, tmVar3 provides additional variant normalization options such as allele-specific identifiers from the ClinGen Allele Registry. tmVar3 exhibits a state-of-the-art performance with over 90% accuracy in F-measure in variant recognition and normalization, when evaluated on three independent benchmarking datasets. tmVar3 is freely available for download. We have also processed the entire PubMed and PMC with tmVar3 and released its annotations on our FTP. Availability: ftp://ftp.ncbi.nlm.nih.gov/pub/lu/tmVar3

This study is dedicated to assessing the capabilities of large language models (LLMs) such as GPT-3.5-Turbo, GPT-4, and GPT-4-Turbo in extracting structured information from scientific documents in materials science. To this end, we primarily focus on two critical tasks of information extraction: (i) a named entity recognition (NER) of studied materials and physical properties and (ii) a relation extraction (RE) between these entities. Due to the evident lack of datasets within Materials Informatics (MI), we evaluated using SuperMat, based on superconductor research, and MeasEval, a generic measurement evaluation corpus. The performance of LLMs in executing these tasks is benchmarked against traditional models based on the BERT architecture and rule-based approaches (baseline). We introduce a novel methodology for the comparative analysis of intricate material expressions, emphasising the standardisation of chemical formulas to tackle the complexities inherent in materials science information assessment. For NER, LLMs fail to outperform the baseline with zero-shot prompting and exhibit only limited improvement with few-shot prompting. However, a GPT-3.5-Turbo fine-tuned with the appropriate strategy for RE outperforms all models, including the baseline. Without any fine-tuning, GPT-4 and GPT-4-Turbo display remarkable reasoning and relationship extraction capabilities after being provided with merely a couple of examples, surpassing the baseline. Overall, the results suggest that although LLMs demonstrate relevant reasoning skills in connecting concepts, specialised models are currently a better choice for tasks requiring extracting complex domain-specific entities like materials. These insights provide initial guidance applicable to other materials science sub-domains in future work.

Cross-lingual information retrieval (CLIR) consists in finding relevant documents in a language that differs from the language of the queries. This paper presents CLIRudit, a new dataset created to evaluate cross-lingual academic search, focusing on English queries and French documents. The dataset is built using bilingual article metadata from \'Erudit, a Canadian publishing platform, and is designed to represent scenarios in which researchers search for scholarly content in languages other than English. We perform a comprehensive benchmarking of different zero-shot first-stage retrieval methods on the dataset, including dense and sparse retrievers, query and document machine translation, and state-of-the-art multilingual retrievers. Our results show that large dense retrievers, not necessarily trained for the cross-lingual retrieval task, can achieve zero-shot performance comparable to using ground truth human translations, without the need for machine translation. Sparse retrievers, such as BM25 or SPLADE, combined with document translation, show competitive results, providing an efficient alternative to large dense models. This research advances the understanding of cross-lingual academic information retrieval and provides a framework that others can use to build comparable datasets across different languages and disciplines. By making the dataset and code publicly available, we aim to facilitate further research that will help make scientific knowledge more accessible across language barriers.

Abstractive summarization of scientific papers has always been a research focus, yet existing methods face two main challenges. First, most summarization models rely on Encoder-Decoder architectures that treat papers as sequences of words, thus fail to fully capture the structured information inherent in scientific papers. Second, existing research often use keyword mapping or feature engineering to identify the structural information, but these methods struggle with the structural flexibility of scientific papers and lack robustness across different disciplines. To address these challenges, we propose a two-stage abstractive summarization framework that leverages automatic recognition of structural functions within scientific papers. In the first stage, we standardize chapter titles from numerous scientific papers and construct a large-scale dataset for structural function recognition. A classifier is then trained to automatically identify the key structural components (e.g., Background, Methods, Results, Discussion), which provides a foundation for generating more balanced summaries. In the second stage, we employ Longformer to capture rich contextual relationships across sections and generating context-aware summaries. Experiments conducted on two domain-specific scientific paper summarization datasets demonstrate that our method outperforms advanced baselines, and generates more comprehensive summaries. The code and dataset can be accessed at https://github.com/tongbao96/code-for-SFR-AS.

This paper introduces MISS-QA, the first benchmark specifically designed to evaluate the ability of models to interpret schematic diagrams within scientific literature. MISS-QA comprises 1,500 expert-annotated examples over 465 scientific papers. In this benchmark, models are tasked with interpreting schematic diagrams that illustrate research overviews and answering corresponding information-seeking questions based on the broader context of the paper. We assess the performance of 18 frontier multimodal foundation models, including o4-mini, Gemini-2.5-Flash, and Qwen2.5-VL. We reveal a significant performance gap between these models and human experts on MISS-QA. Our analysis of model performance on unanswerable questions and our detailed error analysis further highlight the strengths and limitations of current models, offering key insights to enhance models in comprehending multimodal scientific literature.

Scientific problem-solving involves synthesizing information while applying expert knowledge. We introduce CURIE, a scientific long-Context Understanding,Reasoning and Information Extraction benchmark to measure the potential of Large Language Models (LLMs) in scientific problem-solving and assisting scientists in realistic workflows. This benchmark introduces ten challenging tasks with a total of 580 problems and solution pairs curated by experts in six disciplines - materials science, condensed matter physics, quantum computing, geospatial analysis, biodiversity, and proteins - covering both experimental and theoretical work-flows in science. We evaluate a range of closed and open LLMs on tasks in CURIE which requires domain expertise, comprehension of long in-context information,and multi-step reasoning. While Gemini Flash 2.0 and Claude-3 show consistent high comprehension across domains, the popular GPT-4o and command-R+ fail dramatically on protein sequencing tasks. With the best performance at 32% there is much room for improvement for all models. We hope that insights gained from CURIE can guide the future development of LLMs in sciences. Evaluation code and data are in https://github.com/google/curie

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

Scientific literature understanding is crucial for extracting targeted information and garnering insights, thereby significantly advancing scientific discovery. Despite the remarkable success of Large Language Models (LLMs), they face challenges in scientific literature understanding, primarily due to (1) a lack of scientific knowledge and (2) unfamiliarity with specialized scientific tasks. To develop an LLM specialized in scientific literature understanding, we propose a hybrid strategy that integrates continual pre-training (CPT) and supervised fine-tuning (SFT), to simultaneously infuse scientific domain knowledge and enhance instruction-following capabilities for domain-specific tasks.cIn this process, we identify two key challenges: (1) constructing high-quality CPT corpora, and (2) generating diverse SFT instructions. We address these challenges through a meticulous pipeline, including PDF text extraction, parsing content error correction, quality filtering, and synthetic instruction creation. Applying this strategy, we present a suite of LLMs: SciLitLLM, specialized in scientific literature understanding. These models demonstrate promising performance on scientific literature understanding benchmarks. Our contributions are threefold: (1) We present an effective framework that integrates CPT and SFT to adapt LLMs to scientific literature understanding, which can also be easily adapted to other domains. (2) We propose an LLM-based synthesis method to generate diverse and high-quality scientific instructions, resulting in a new instruction set -- SciLitIns -- for supervised fine-tuning in less-represented scientific domains. (3) SciLitLLM achieves promising performance improvements on scientific literature understanding benchmarks.

Thousands of new scientific papers are published each month. Such information overload complicates researcher efforts to stay current with the state-of-the-art as well as to verify and correctly attribute claims. We pose the following research question: Given a text excerpt referencing a paper, could an LM act as a research assistant to correctly identify the referenced paper? We advance efforts to answer this question by building a benchmark that evaluates the abilities of LMs in citation attribution. Our benchmark, CiteME, consists of text excerpts from recent machine learning papers, each referencing a single other paper. CiteME use reveals a large gap between frontier LMs and human performance, with LMs achieving only 4.2-18.5% accuracy and humans 69.7%. We close this gap by introducing CiteAgent, an autonomous system built on the GPT-4o LM that can also search and read papers, which achieves an accuracy of 35.3\% on CiteME. Overall, CiteME serves as a challenging testbed for open-ended claim attribution, driving the research community towards a future where any claim made by an LM can be automatically verified and discarded if found to be incorrect.

Large language models (LLMs) often need to incorporate external knowledge to solve theme-specific problems. Retrieval-augmented generation (RAG) has shown its high promise, empowering LLMs to generate more qualified responses with retrieved external data and knowledge. However, most RAG methods retrieve relevant documents based on either sparse or dense retrieval methods or their combinations, which overlooks the essential, multi-dimensional, and structured semantic information present in documents. This structured information plays a critical role in finding concise yet highly relevant information for domain knowledge-intensive tasks, such as scientific question-answering (QA). In this work, we introduce a multi-dimensional (cube) structure, Hypercube, which can index and allocate documents in a pre-defined multi-dimensional space. Built on the hypercube, we further propose Hypercube-RAG, a novel RAG framework for precise and efficient retrieval. Given a query, Hypercube-RAG first decomposes it based on its entities, phrases, and topics along with pre-defined hypercube dimensions, and then retrieves relevant documents from cubes by aligning these decomposed components with corresponding dimensions. Experiments on three datasets across different domains demonstrate that our method improves response accuracy by 3.7% and retrieval accuracy by 5.3% over the strongest RAG baseline. It also boosts retrieval efficiency (speed) by one or two magnitudes faster than graph-based RAG. Notably, our Hypercube-RAG inherently offers explainability by revealing those underlying dimensions used for retrieval. The code and data are available at https://github.com/JimengShi/Hypercube-RAG.

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

Extracting structured information from unstructured text is crucial for modeling real-world processes, but traditional schema mining relies on semi-structured data, limiting scalability. This paper introduces schema-miner, a novel tool that combines large language models with human feedback to automate and refine schema extraction. Through an iterative workflow, it organizes properties from text, incorporates expert input, and integrates domain-specific ontologies for semantic depth. Applied to materials science--specifically atomic layer deposition--schema-miner demonstrates that expert-guided LLMs generate semantically rich schemas suitable for diverse real-world applications.

In this paper, we present the current progress of the project Verif.ai, an open-source scientific generative question-answering system with referenced and verified answers. The components of the system are (1) an information retrieval system combining semantic and lexical search techniques over scientific papers (PubMed), (2) a fine-tuned generative model (Mistral 7B) taking top answers and generating answers with references to the papers from which the claim was derived, and (3) a verification engine that cross-checks the generated claim and the abstract or paper from which the claim was derived, verifying whether there may have been any hallucinations in generating the claim. We are reinforcing the generative model by providing the abstract in context, but in addition, an independent set of methods and models are verifying the answer and checking for hallucinations. Therefore, we believe that by using our method, we can make scientists more productive, while building trust in the use of generative language models in scientific environments, where hallucinations and misinformation cannot be tolerated.

It is desirable to coarsely classify short scientific texts, such as grant or publication abstracts, for strategic insight or research portfolio management. These texts efficiently transmit dense information to experts possessing a rich body of knowledge to aid interpretation. Yet this task is remarkably difficult to automate because of brevity and the absence of context. To address this gap, we have developed a novel approach to generate and appropriately assign coarse domain-specific labels. We show that a Large Language Model (LLM) can provide metadata essential to the task, in a process akin to the augmentation of supplemental knowledge representing human intuition, and propose a workflow. As a pilot study, we use a corpus of award abstracts from the National Aeronautics and Space Administration (NASA). We develop new assessment tools in concert with established performance metrics.

The analysis of scientific data and complex multivariate systems requires information quantities that capture relationships among multiple random variables. Recently, new information-theoretic measures have been developed to overcome the shortcomings of classical ones, such as mutual information, that are restricted to considering pairwise interactions. Among them, the concept of information synergy and redundancy is crucial for understanding the high-order dependencies between variables. One of the most prominent and versatile measures based on this concept is O-information, which provides a clear and scalable way to quantify the synergy-redundancy balance in multivariate systems. However, its practical application is limited to simplified cases. In this work, we introduce SOmegaI, which allows for the first time to compute O-information without restrictive assumptions about the system. Our experiments validate our approach on synthetic data, and demonstrate the effectiveness of SOmegaI in the context of a real-world use case.

Recent advances in LLMs have made automated scientific research the next frontline in the path to artificial superintelligence. However, these systems are bound either to tasks of narrow scope or the limited creative capabilities of LLMs. We propose Spacer, a scientific discovery system that develops creative and factually grounded concepts without external intervention. Spacer attempts to achieve this via 'deliberate decontextualization,' an approach that disassembles information into atomic units - keywords - and draws creativity from unexplored connections between them. Spacer consists of (i) Nuri, an inspiration engine that builds keyword sets, and (ii) the Manifesting Pipeline that refines these sets into elaborate scientific statements. Nuri extracts novel, high-potential keyword sets from a keyword graph built with 180,000 academic publications in biological fields. The Manifesting Pipeline finds links between keywords, analyzes their logical structure, validates their plausibility, and ultimately drafts original scientific concepts. According to our experiments, the evaluation metric of Nuri accurately classifies high-impact publications with an AUROC score of 0.737. Our Manifesting Pipeline also successfully reconstructs core concepts from the latest top-journal articles solely from their keyword sets. An LLM-based scoring system estimates that this reconstruction was sound for over 85% of the cases. Finally, our embedding space analysis shows that outputs from Spacer are significantly more similar to leading publications compared with those from SOTA LLMs.

Seeking answers to questions within long scientific research articles is a crucial area of study that aids readers in quickly addressing their inquiries. However, existing question-answering (QA) datasets based on scientific papers are limited in scale and focus solely on textual content. To address this limitation, we introduce SPIQA (Scientific Paper Image Question Answering), the first large-scale QA dataset specifically designed to interpret complex figures and tables within the context of scientific research articles across various domains of computer science. Leveraging the breadth of expertise and ability of multimodal large language models (MLLMs) to understand figures, we employ automatic and manual curation to create the dataset. We craft an information-seeking task involving multiple images that cover a wide variety of plots, charts, tables, schematic diagrams, and result visualizations. SPIQA comprises 270K questions divided into training, validation, and three different evaluation splits. Through extensive experiments with 12 prominent foundational models, we evaluate the ability of current multimodal systems to comprehend the nuanced aspects of research articles. Additionally, we propose a Chain-of-Thought (CoT) evaluation strategy with in-context retrieval that allows fine-grained, step-by-step assessment and improves model performance. We further explore the upper bounds of performance enhancement with additional textual information, highlighting its promising potential for future research and the dataset's impact on revolutionizing how we interact with scientific literature.

Table extraction from document images is a challenging AI problem, and labelled data for many content domains is difficult to come by. Existing table extraction datasets often focus on scientific tables due to the vast amount of academic articles that are readily available, along with their source code. However, there are significant layout and typographical differences between tables found across scientific, financial, and other domains. Current datasets often lack the words, and their positions, contained within the tables, instead relying on unreliable OCR to extract these features for training modern machine learning models on natural language processing tasks. Therefore, there is a need for a more general method of obtaining labelled data. We present SynFinTabs, a large-scale, labelled dataset of synthetic financial tables. Our hope is that our method of generating these synthetic tables is transferable to other domains. To demonstrate the effectiveness of our dataset in training models to extract information from table images, we create FinTabQA, a layout large language model trained on an extractive question-answering task. We test our model using real-world financial tables and compare it to a state-of-the-art generative model and discuss the results. We make the dataset, model, and dataset generation code publicly available.

Large Language Model (LLM)-based multi-agent systems (MAS) demonstrate remarkable potential for scientific discovery. Existing approaches, however, often automate scientific discovery using predefined workflows that lack rationality constraints. This often leads to aimless hypothesizing and a failure to consistently link hypotheses with evidence, thereby hindering systematic uncertainty reduction. Overcoming these limitations fundamentally requires systematic uncertainty reduction. We introduce PiFlow, an information-theoretical framework, treating automated scientific discovery as a structured uncertainty reduction problem guided by principles (e.g., scientific laws). In evaluations across three distinct scientific domains -- discovering nanomaterial structures, bio-molecules, and superconductor candidates with targeted properties -- our method significantly improves discovery efficiency, reflected by a 73.55\% increase in the Area Under the Curve (AUC) of property values versus exploration steps, and enhances solution quality by 94.06\% compared to a vanilla agent system. Overall, PiFlow serves as a Plug-and-Play method, establishing a novel paradigm shift in highly efficient automated scientific discovery, paving the way for more robust and accelerated AI-driven research. Code is publicly available at our https://github.com/amair-lab/PiFlow{GitHub}.

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.

The automatic extraction of materials and related properties from the scientific literature is gaining attention in data-driven materials science (Materials Informatics). In this paper, we discuss Grobid-superconductors, our solution for automatically extracting superconductor material names and respective properties from text. Built as a Grobid module, it combines machine learning and heuristic approaches in a multi-step architecture that supports input data as raw text or PDF documents. Using Grobid-superconductors, we built SuperCon2, a database of 40324 materials and properties records from 37700 papers. The material (or sample) information is represented by name, chemical formula, and material class, and is characterized by shape, doping, substitution variables for components, and substrate as adjoined information. The properties include the Tc superconducting critical temperature and, when available, applied pressure with the Tc measurement method.

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.

Scientific data visualization plays a crucial role in research by enabling the direct display of complex information and assisting researchers in identifying implicit patterns. Despite its importance, the use of Large Language Models (LLMs) for scientific data visualization remains rather unexplored. In this study, we introduce MatPlotAgent, an efficient model-agnostic LLM agent framework designed to automate scientific data visualization tasks. Leveraging the capabilities of both code LLMs and multi-modal LLMs, MatPlotAgent consists of three core modules: query understanding, code generation with iterative debugging, and a visual feedback mechanism for error correction. To address the lack of benchmarks in this field, we present MatPlotBench, a high-quality benchmark consisting of 100 human-verified test cases. Additionally, we introduce a scoring approach that utilizes GPT-4V for automatic evaluation. Experimental results demonstrate that MatPlotAgent can improve the performance of various LLMs, including both commercial and open-source models. Furthermore, the proposed evaluation method shows a strong correlation with human-annotated scores.

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.

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.

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.

Hypertension, defined as blood pressure (BP) that is above normal, holds paramount significance in the realm of public health, as it serves as a critical precursor to various cardiovascular diseases (CVDs) and significantly contributes to elevated mortality rates worldwide. However, many existing BP measurement technologies and standards might be biased because they do not consider clinical outcomes, comorbidities, or demographic factors, making them inconclusive for diagnostic purposes. There is limited data-driven research focused on studying the variance in BP measurements across these variables. In this work, we employed GPT-35-turbo, a large language model (LLM), to automatically extract the mean and standard deviation values of BP for both males and females from a dataset comprising 25 million abstracts sourced from PubMed. 993 article abstracts met our predefined inclusion criteria (i.e., presence of references to blood pressure, units of blood pressure such as mmHg, and mention of biological sex). Based on the automatically-extracted information from these articles, we conducted an analysis of the variations of BP values across biological sex. Our results showed the viability of utilizing LLMs to study the BP variations across different demographic factors.

Decisions in agriculture are increasingly data-driven; however, valuable agricultural knowledge is often locked away in free-text reports, manuals and journal articles. Specialised search systems are needed that can mine agricultural information to provide relevant answers to users' questions. This paper presents AgAsk -- an agent able to answer natural language agriculture questions by mining scientific documents. We carefully survey and analyse farmers' information needs. On the basis of these needs we release an information retrieval test collection comprising real questions, a large collection of scientific documents split in passages, and ground truth relevance assessments indicating which passages are relevant to each question. We implement and evaluate a number of information retrieval models to answer farmers questions, including two state-of-the-art neural ranking models. We show that neural rankers are highly effective at matching passages to questions in this context. Finally, we propose a deployment architecture for AgAsk that includes a client based on the Telegram messaging platform and retrieval model deployed on commodity hardware. The test collection we provide is intended to stimulate more research in methods to match natural language to answers in scientific documents. While the retrieval models were evaluated in the agriculture domain, they are generalisable and of interest to others working on similar problems. The test collection is available at: https://github.com/ielab/agvaluate.

Scientific innovation is undergoing a paradigm shift driven by the rapid advancement of Large Language Models (LLMs). As science faces mounting challenges including information overload, disciplinary silos, and diminishing returns on conventional research methods, LLMs are emerging as powerful agents capable not only of enhancing scientific workflows but also of participating in and potentially leading the innovation process. Existing surveys mainly focus on different perspectives, phrases, and tasks in scientific research and discovery, while they have limitations in understanding the transformative potential and role differentiation of LLM. This survey proposes a comprehensive framework to categorize the evolving roles of LLMs in scientific innovation across three hierarchical levels: Evaluator, Collaborator, and Scientist. We distinguish between LLMs' contributions to structured scientific research processes and open-ended scientific discovery, thereby offering a unified taxonomy that clarifies capability boundaries, evaluation criteria, and human-AI interaction patterns at each level. Through an extensive analysis of current methodologies, benchmarks, systems, and evaluation metrics, this survey delivers an in-depth and systematic synthesis on LLM-driven scientific innovation. We present LLMs not only as tools for automating existing processes, but also as catalysts capable of reshaping the epistemological foundations of science itself. This survey offers conceptual clarity, practical guidance, and theoretical foundations for future research, while also highlighting open challenges and ethical considerations in the pursuit of increasingly autonomous AI-driven science. Resources related to this survey can be accessed on GitHub at: https://github.com/haoxuan-unt2024/llm4innovation.

Language barriers in scientific documents hinder the diffusion and development of science and technologies. However, prior efforts in translating such documents largely overlooked the information in layouts. To bridge the gap, we introduce PDFMathTranslate, the world's first open-source software for translating scientific documents while preserving layouts. Leveraging the most recent advances in large language models and precise layout detection, we contribute to the community with key improvements in precision, flexibility, and efficiency. The work has been open-sourced at https://github.com/byaidu/pdfmathtranslate with more than 222k downloads.

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.

Literature review requires researchers to synthesize a large amount of information and is increasingly challenging as the scientific literature expands. In this work, we investigate the potential of LLMs for producing hierarchical organizations of scientific studies to assist researchers with literature review. We define hierarchical organizations as tree structures where nodes refer to topical categories and every node is linked to the studies assigned to that category. Our naive LLM-based pipeline for hierarchy generation from a set of studies produces promising yet imperfect hierarchies, motivating us to collect CHIME, an expert-curated dataset for this task focused on biomedicine. Given the challenging and time-consuming nature of building hierarchies from scratch, we use a human-in-the-loop process in which experts correct errors (both links between categories and study assignment) in LLM-generated hierarchies. CHIME contains 2,174 LLM-generated hierarchies covering 472 topics, and expert-corrected hierarchies for a subset of 100 topics. Expert corrections allow us to quantify LLM performance, and we find that while they are quite good at generating and organizing categories, their assignment of studies to categories could be improved. We attempt to train a corrector model with human feedback which improves study assignment by 12.6 F1 points. We release our dataset and models to encourage research on developing better assistive tools for literature review.

Advancements in machine learning and artificial intelligence are transforming materials discovery. Yet, the availability of structured experimental data remains a bottleneck. The vast corpus of scientific literature presents a valuable and rich resource of such data. However, manual dataset creation from these resources is challenging due to issues in maintaining quality and consistency, scalability limitations, and the risk of human error and bias. Therefore, in this work, we develop a chemist AI agent, powered by large language models (LLMs), to overcome these challenges by autonomously creating structured datasets from natural language text, ranging from sentences and paragraphs to extensive scientific research articles. Our chemist AI agent, Eunomia, can plan and execute actions by leveraging the existing knowledge from decades of scientific research articles, scientists, the Internet and other tools altogether. We benchmark the performance of our approach in three different information extraction tasks with various levels of complexity, including solid-state impurity doping, metal-organic framework (MOF) chemical formula, and property relations. Our results demonstrate that our zero-shot agent, with the appropriate tools, is capable of attaining performance that is either superior or comparable to the state-of-the-art fine-tuned materials information extraction methods. This approach simplifies compilation of machine learning-ready datasets for various materials discovery applications, and significantly ease the accessibility of advanced natural language processing tools for novice users in natural language. The methodology in this work is developed as an open-source software on https://github.com/AI4ChemS/Eunomia.

Modern machine learning systems use models trained on ever-growing corpora. Typically, metadata such as ownership, access control, or licensing information is ignored during training. Instead, to mitigate privacy risks, we rely on generic techniques such as dataset sanitization and differentially private model training, with inherent privacy/utility trade-offs that hurt model performance. Moreover, these techniques have limitations in scenarios where sensitive information is shared across multiple participants and fine-grained access control is required. By ignoring metadata, we therefore miss an opportunity to better address security, privacy, and confidentiality challenges. In this paper, we take an information flow control perspective to describe machine learning systems, which allows us to leverage metadata such as access control policies and define clear-cut privacy and confidentiality guarantees with interpretable information flows. Under this perspective, we contrast two different approaches to achieve user-level non-interference: 1) fine-tuning per-user models, and 2) retrieval augmented models that access user-specific datasets at inference time. We compare these two approaches to a trivially non-interfering zero-shot baseline using a public model and to a baseline that fine-tunes this model on the whole corpus. We evaluate trained models on two datasets of scientific articles and demonstrate that retrieval augmented architectures deliver the best utility, scalability, and flexibility while satisfying strict non-interference guarantees.

With the explosive growth of scientific publications, making the synthesis of scientific knowledge and fact checking becomes an increasingly complex task. In this paper, we propose a multi-task approach for verifying the scientific questions based on a joint reasoning from facts and evidence in research articles. We propose an intelligent combination of (1) an automatic information summarization and (2) a Boolean Question Answering which allows to generate an answer to a scientific question from only extracts obtained after summarization. Thus on a given topic, our proposed approach conducts structured content modeling based on paper abstracts to answer a scientific question while highlighting texts from paper that discuss the topic. We based our final system on an end-to-end Extractive Question Answering (EQA) combined with a three outputs classification model to perform in-depth semantic understanding of a question to illustrate the aggregation of multiple responses. With our light and fast proposed architecture, we achieved an average error rate of 4% and a F1-score of 95.6%. Our results are supported via experiments with two QA models (BERT, RoBERTa) over 3 Million Open Access (OA) articles in the medical and health domains on Europe PMC.

The scientific claim verification task requires an NLP system to label scientific documents which Support or Refute an input claim, and to select evidentiary sentences (or rationales) justifying each predicted label. In this work, we present MultiVerS, which predicts a fact-checking label and identifies rationales in a multitask fashion based on a shared encoding of the claim and full document context. This approach accomplishes two key modeling goals. First, it ensures that all relevant contextual information is incorporated into each labeling decision. Second, it enables the model to learn from instances annotated with a document-level fact-checking label, but lacking sentence-level rationales. This allows MultiVerS to perform weakly-supervised domain adaptation by training on scientific documents labeled using high-precision heuristics. Our approach outperforms two competitive baselines on three scientific claim verification datasets, with particularly strong performance in zero / few-shot domain adaptation experiments. Our code and data are available at https://github.com/dwadden/multivers.

Prevalent models based on artificial neural network (ANN) for sentence classification often classify sentences in isolation without considering the context in which sentences appear. This hampers the traditional sentence classification approaches to the problem of sequential sentence classification, where structured prediction is needed for better overall classification performance. In this work, we present a hierarchical sequential labeling network to make use of the contextual information within surrounding sentences to help classify the current sentence. Our model outperforms the state-of-the-art results by 2%-3% on two benchmarking datasets for sequential sentence classification in medical scientific abstracts.

Neural information retrieval systems excel in high-resource languages but remain underexplored for morphologically rich, lower-resource languages such as Turkish. Dense bi-encoders currently dominate Turkish IR, yet late-interaction models -- which retain token-level representations for fine-grained matching -- have not been systematically evaluated. We introduce TurkColBERT, the first comprehensive benchmark comparing dense encoders and late-interaction models for Turkish retrieval. Our two-stage adaptation pipeline fine-tunes English and multilingual encoders on Turkish NLI/STS tasks, then converts them into ColBERT-style retrievers using PyLate trained on MS MARCO-TR. We evaluate 10 models across five Turkish BEIR datasets covering scientific, financial, and argumentative domains. Results show strong parameter efficiency: the 1.0M-parameter colbert-hash-nano-tr is 600times smaller than the 600M turkish-e5-large dense encoder while preserving over 71\% of its average mAP. Late-interaction models that are 3--5times smaller than dense encoders significantly outperform them; ColmmBERT-base-TR yields up to +13.8\% mAP on domain-specific tasks. For production-readiness, we compare indexing algorithms: MUVERA+Rerank is 3.33times faster than PLAID and offers +1.7\% relative mAP gain. This enables low-latency retrieval, with ColmmBERT-base-TR achieving 0.54 ms query times under MUVERA. We release all checkpoints, configs, and evaluation scripts. Limitations include reliance on moderately sized datasets (leq50K documents) and translated benchmarks, which may not fully reflect real-world Turkish retrieval conditions; larger-scale MUVERA evaluations remain necessary.

"An idea is nothing more nor less than a new combination of old elements" (Young, J.W.). The widespread adoption of Large Language Models (LLMs) and publicly available ChatGPT have marked a significant turning point in the integration of Artificial Intelligence (AI) into people's everyday lives. This study explores the capability of LLMs in generating novel research ideas based on information from research papers. We conduct a thorough examination of 4 LLMs in five domains (e.g., Chemistry, Computer, Economics, Medical, and Physics). We found that the future research ideas generated by Claude-2 and GPT-4 are more aligned with the author's perspective than GPT-3.5 and Gemini. We also found that Claude-2 generates more diverse future research ideas than GPT-4, GPT-3.5, and Gemini 1.0. We further performed a human evaluation of the novelty, relevancy, and feasibility of the generated future research ideas. This investigation offers insights into the evolving role of LLMs in idea generation, highlighting both its capability and limitations. Our work contributes to the ongoing efforts in evaluating and utilizing language models for generating future research ideas. We make our datasets and codes publicly available.

Prompt-based fine-tuning has become an essential method for eliciting information encoded in pre-trained language models for a variety of tasks, including text classification. For multi-class classification tasks, prompt-based fine-tuning under low-resource scenarios has resulted in performance levels comparable to those of fully fine-tuning methods. Previous studies have used crafted prompt templates and verbalizers, mapping from the label terms space to the class space, to solve the classification problem as a masked language modeling task. However, cross-domain and fine-grained prompt-based fine-tuning with an automatically enriched verbalizer remains unexplored, mainly due to the difficulty and costs of manually selecting domain label terms for the verbalizer, which requires humans with domain expertise. To address this challenge, we introduce SciPrompt, a framework designed to automatically retrieve scientific topic-related terms for low-resource text classification tasks. To this end, we select semantically correlated and domain-specific label terms within the context of scientific literature for verbalizer augmentation. Furthermore, we propose a new verbalization strategy that uses correlation scores as additional weights to enhance the prediction performance of the language model during model tuning. Our method outperforms state-of-the-art, prompt-based fine-tuning methods on scientific text classification tasks under few and zero-shot settings, especially in classifying fine-grained and emerging scientific topics.

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.

We present a novel training-free framework, PosterForest, for automated scientific poster generation. Unlike prior approaches, which largely neglect the hierarchical structure of scientific documents and the semantic integration of textual and visual elements, our method addresses both challenges directly. We introduce the Poster Tree, a hierarchical intermediate representation that jointly encodes document structure and visual-textual relationships at multiple levels. Our framework employs a multi-agent collaboration strategy, where agents specializing in content summarization and layout planning iteratively coordinate and provide mutual feedback. This approach enables the joint optimization of logical consistency, content fidelity, and visual coherence. Extensive experiments on multiple academic domains show that our method outperforms existing baselines in both qualitative and quantitative evaluations. The resulting posters achieve quality closest to expert-designed ground truth and deliver superior information preservation, structural clarity, and user preference.

Scientific texts often convey authority due to their technical language and complex data. However, this complexity can sometimes lead to the spread of misinformation. Non-experts are particularly susceptible to misleading claims based on scientific tables due to their high information density and perceived credibility. Existing table claim verification models, including state-of-the-art large language models (LLMs), often struggle with precise fine-grained reasoning, resulting in errors and a lack of precision in verifying scientific claims. Inspired by Cognitive Load Theory, we propose that enhancing a model's ability to interpret table-based claims involves reducing cognitive load by developing modular, reusable reasoning components (i.e., atomic skills). We introduce a skill-chaining schema that dynamically composes these skills to facilitate more accurate and generalizable reasoning with a reduced cognitive load. To evaluate this, we create SciAtomicBench, a cross-domain benchmark with fine-grained reasoning annotations. With only 350 fine-tuning examples, our model trained by atomic reasoning outperforms GPT-4o's chain-of-thought method, achieving state-of-the-art results with far less training data.

Assessing scientific claims requires identifying, extracting, and reasoning with multimodal data expressed in information-rich figures in scientific literature. Despite the large body of work in scientific QA, figure captioning, and other multimodal reasoning tasks over chart-based data, there are no readily usable multimodal benchmarks that directly test claim verification abilities. To remedy this gap, we introduce a new benchmark MuSciClaims accompanied by diagnostics tasks. We automatically extract supported claims from scientific articles, which we manually perturb to produce contradicted claims. The perturbations are designed to test for a specific set of claim verification capabilities. We also introduce a suite of diagnostic tasks that help understand model failures. Our results show most vision-language models are poor (~0.3-0.5 F1), with even the best model only achieving 0.72 F1. They are also biased towards judging claims as supported, likely misunderstanding nuanced perturbations within the claims. Our diagnostics show models are bad at localizing correct evidence within figures, struggle with aggregating information across modalities, and often fail to understand basic components of the figure.

High-quality training data has proven crucial for developing performant large language models (LLMs). However, commercial LLM providers disclose few, if any, details about the data used for training. This lack of transparency creates multiple challenges: it limits external oversight and inspection of LLMs for issues such as copyright infringement, it undermines the agency of data authors, and it hinders scientific research on critical issues such as data contamination and data selection. How can we recover what training data is known to LLMs? In this work, we demonstrate a new method to identify training data known to proprietary LLMs like GPT-4 without requiring any access to model weights or token probabilities, by using information-guided probes. Our work builds on a key observation: text passages with high surprisal are good search material for memorization probes. By evaluating a model's ability to successfully reconstruct high-surprisal tokens in text, we can identify a surprising number of texts memorized by LLMs.

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.

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.

Large language models (LLMs) have ushered in a new era for processing complex information in various fields, including science. The increasing amount of scientific literature allows these models to acquire and understand scientific knowledge effectively, thus improving their performance in a wide range of tasks. Due to the power of LLMs, they require extremely expensive computational resources, intense amounts of data, and training time. Therefore, in recent years, researchers have proposed various methodologies to make scientific LLMs more affordable. The most well-known approaches align in two directions. It can be either focusing on the size of the models or enhancing the quality of data. To date, a comprehensive review of these two families of methods has not yet been undertaken. In this paper, we (I) summarize the current advances in the emerging abilities of LLMs into more accessible AI solutions for science, and (II) investigate the challenges and opportunities of developing affordable solutions for scientific domains using LLMs.

This project investigates the efficacy of Large Language Models (LLMs) in understanding and extracting scientific knowledge across specific domains and to create a deep learning framework: Knowledge AI. As a part of this framework, we employ pre-trained models and fine-tune them on datasets in the scientific domain. The models are adapted for four key Natural Language Processing (NLP) tasks: summarization, text generation, question answering, and named entity recognition. Our results indicate that domain-specific fine-tuning significantly enhances model performance in each of these tasks, thereby improving their applicability for scientific contexts. This adaptation enables non-experts to efficiently query and extract information within targeted scientific fields, demonstrating the potential of fine-tuned LLMs as a tool for knowledge discovery in the sciences.

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

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.

The use of artificial intelligence (AI) offers various possibilities to expand and support educational research. Specifically, the implementation of AI can be used to develop new frameworks to establish new research tools that accelerate and meaningfully expand the efficiency of data evaluation and interpretation (Buckingham Shum et al., 2023). This article presents the prototype of the FACTS-V1 (Filtering and Analysis of Content in Textual Sources) framework. With the help of the application, numerous scientific papers can be automatically extracted, analyzed and interpreted from open access document servers without having to rely on proprietary applications and their limitations. The FACTS-V1 prototype consists of three building blocks. The first part deals with the extraction of texts, the second with filtering and interpretation, and the last with the actual statistical evaluation (topic modeling) using an interactive overview. The aim of the framework is to provide recommendations for future scientific questions based on existing data. The functionality is illustrated by asking how the use of AI will change the education sector. The data used to answer the question comes from 82 scientific papers on the topic of AI from 2024. The papers are publicly available on the peDOCS document server of the Leibniz Institute for Educational Research and Educational Information.

Natural Language Processing (NLP) is widely used to supply summarization ability from long context to structured information. However, extracting structured knowledge from scientific text by NLP models remains a challenge because of its domain-specific nature to complex data preprocessing and the granularity of multi-layered device-level information. To address this, we introduce ByteScience, a non-profit cloud-based auto fine-tuned Large Language Model (LLM) platform, which is designed to extract structured scientific data and synthesize new scientific knowledge from vast scientific corpora. The platform capitalizes on DARWIN, an open-source, fine-tuned LLM dedicated to natural science. The platform was built on Amazon Web Services (AWS) and provides an automated, user-friendly workflow for custom model development and data extraction. The platform achieves remarkable accuracy with only a small amount of well-annotated articles. This innovative tool streamlines the transition from the science literature to structured knowledge and data and benefits the advancements in natural informatics.

Most existing large-scale academic search engines are built to retrieve text-based information. However, there are no large-scale retrieval services for scientific figures and tables. One challenge for such services is understanding scientific figures' semantics, such as their types and purposes. A key obstacle is the need for datasets containing annotated scientific figures and tables, which can then be used for classification, question-answering, and auto-captioning. Here, we develop a pipeline that extracts figures and tables from the scientific literature and a deep-learning-based framework that classifies scientific figures using visual features. Using this pipeline, we built the first large-scale automatically annotated corpus, ACL-Fig, consisting of 112,052 scientific figures extracted from ~56K research papers in the ACL Anthology. The ACL-Fig-Pilot dataset contains 1,671 manually labeled scientific figures belonging to 19 categories. The dataset is accessible at https://huggingface.co/datasets/citeseerx/ACL-fig under a CC BY-NC license.

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

The rapid growth of scientific literature imposes significant challenges for researchers endeavoring to stay updated with the latest advancements in their fields and delve into new areas. We introduce OpenResearcher, an innovative platform that leverages Artificial Intelligence (AI) techniques to accelerate the research process by answering diverse questions from researchers. OpenResearcher is built based on Retrieval-Augmented Generation (RAG) to integrate Large Language Models (LLMs) with up-to-date, domain-specific knowledge. Moreover, we develop various tools for OpenResearcher to understand researchers' queries, search from the scientific literature, filter retrieved information, provide accurate and comprehensive answers, and self-refine these answers. OpenResearcher can flexibly use these tools to balance efficiency and effectiveness. As a result, OpenResearcher enables researchers to save time and increase their potential to discover new insights and drive scientific breakthroughs. Demo, video, and code are available at: https://github.com/GAIR-NLP/OpenResearcher.

Existing benchmarks for evaluating foundation models mainly focus on single-document, text-only tasks. However, they often fail to fully capture the complexity of research workflows, which typically involve interpreting non-textual data and gathering information across multiple documents. To address this gap, we introduce M3SciQA, a multi-modal, multi-document scientific question answering benchmark designed for a more comprehensive evaluation of foundation models. M3SciQA consists of 1,452 expert-annotated questions spanning 70 natural language processing paper clusters, where each cluster represents a primary paper along with all its cited documents, mirroring the workflow of comprehending a single paper by requiring multi-modal and multi-document data. With M3SciQA, we conduct a comprehensive evaluation of 18 foundation models. Our results indicate that current foundation models still significantly underperform compared to human experts in multi-modal information retrieval and in reasoning across multiple scientific documents. Additionally, we explore the implications of these findings for the future advancement of applying foundation models in multi-modal scientific literature analysis.

A hallmark of human innovation is the process of recombination -- creating original ideas by integrating elements of existing mechanisms and concepts. In this work, we automatically mine the scientific literature and build CHIMERA: a large-scale knowledge base (KB) of recombination examples. CHIMERA can be used to empirically explore at scale how scientists recombine concepts and take inspiration from different areas, or to train supervised machine learning models that learn to predict new creative cross-domain directions. To build this KB, we present a novel information extraction task of extracting recombination from scientific paper abstracts, collect a high-quality corpus of hundreds of manually annotated abstracts, and use it to train an LLM-based extraction model. The model is applied to a large corpus of papers in the AI domain, yielding a KB of over 28K recombination examples. We analyze CHIMERA to explore the properties of recombination in different subareas of AI. Finally, we train a scientific hypothesis generation model using the KB, which predicts new recombination directions that real-world researchers find inspiring. Our data and code are available at https://github.cs.huji.ac.il/tomhope-lab/CHIMERA

Creating high-quality scientific figures can be time-consuming and challenging, even though sketching ideas on paper is relatively easy. Furthermore, recreating existing figures that are not stored in formats preserving semantic information is equally complex. To tackle this problem, we introduce DeTikZify, a novel multimodal language model that automatically synthesizes scientific figures as semantics-preserving TikZ graphics programs based on sketches and existing figures. To achieve this, we create three new datasets: DaTikZv2, the largest TikZ dataset to date, containing over 360k human-created TikZ graphics; SketchFig, a dataset that pairs hand-drawn sketches with their corresponding scientific figures; and SciCap++, a collection of diverse scientific figures and associated metadata. We train DeTikZify on SciCap++ and DaTikZv2, along with synthetically generated sketches learned from SketchFig. We also introduce an MCTS-based inference algorithm that enables DeTikZify to iteratively refine its outputs without the need for additional training. Through both automatic and human evaluation, we demonstrate that DeTikZify outperforms commercial Claude 3 and GPT-4V in synthesizing TikZ programs, with the MCTS algorithm effectively boosting its performance. We make our code, models, and datasets publicly available.

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

We investigated the evolution and transformation of scientific knowledge in the early modern period, analyzing more than 350 different editions of textbooks used for teaching astronomy in European universities from the late fifteenth century to mid-seventeenth century. These historical sources constitute the Sphaera Corpus. By examining different semantic relations among individual parts of each edition on record, we built a multiplex network consisting of six layers, as well as the aggregated network built from the superposition of all the layers. The network analysis reveals the emergence of five different communities. The contribution of each layer in shaping the communities and the properties of each community are studied. The most influential books in the corpus are found by calculating the average age of all the out-going and in-coming links for each book. A small group of editions is identified as a transmitter of knowledge as they bridge past knowledge to the future through a long temporal interval. Our analysis, moreover, identifies the most disruptive books. These books introduce new knowledge that is then adopted by almost all the books published afterwards until the end of the whole period of study. The historical research on the content of the identified books, as an empirical test, finally corroborates the results of all our analyses.

Keyphrase extraction (KPE) is an important task in Natural Language Processing for many scenarios, which aims to extract keyphrases that are present in a given document. Many existing supervised methods treat KPE as sequential labeling, span-level classification, or generative tasks. However, these methods lack the ability to utilize keyphrase information, which may result in biased results. In this study, we propose Diff-KPE, which leverages the supervised Variational Information Bottleneck (VIB) to guide the text diffusion process for generating enhanced keyphrase representations. Diff-KPE first generates the desired keyphrase embeddings conditioned on the entire document and then injects the generated keyphrase embeddings into each phrase representation. A ranking network and VIB are then optimized together with rank loss and classification loss, respectively. This design of Diff-KPE allows us to rank each candidate phrase by utilizing both the information of keyphrases and the document. Experiments show that Diff-KPE outperforms existing KPE methods on a large open domain keyphrase extraction benchmark, OpenKP, and a scientific domain dataset, KP20K.

Hypothesis generation is a fundamental step in scientific discovery, yet it is increasingly challenged by information overload and disciplinary fragmentation. Recent advances in Large Language Models (LLMs) have sparked growing interest in their potential to enhance and automate this process. This paper presents a comprehensive survey of hypothesis generation with LLMs by (i) reviewing existing methods, from simple prompting techniques to more complex frameworks, and proposing a taxonomy that categorizes these approaches; (ii) analyzing techniques for improving hypothesis quality, such as novelty boosting and structured reasoning; (iii) providing an overview of evaluation strategies; and (iv) discussing key challenges and future directions, including multimodal integration and human-AI collaboration. Our survey aims to serve as a reference for researchers exploring LLMs for hypothesis generation.

Scientific figure captioning is a complex task that requires generating contextually appropriate descriptions of visual content. However, existing methods often fall short by utilizing incomplete information, treating the task solely as either an image-to-text or text summarization problem. This limitation hinders the generation of high-quality captions that fully capture the necessary details. Moreover, existing data sourced from arXiv papers contain low-quality captions, posing significant challenges for training large language models (LLMs). In this paper, we introduce a framework called Multi-LLM Collaborative Figure Caption Generation (MLBCAP) to address these challenges by leveraging specialized LLMs for distinct sub-tasks. Our approach unfolds in three key modules: (Quality Assessment) We utilize multimodal LLMs to assess the quality of training data, enabling the filtration of low-quality captions. (Diverse Caption Generation) We then employ a strategy of fine-tuning/prompting multiple LLMs on the captioning task to generate candidate captions. (Judgment) Lastly, we prompt a prominent LLM to select the highest quality caption from the candidates, followed by refining any remaining inaccuracies. Human evaluations demonstrate that informative captions produced by our approach rank better than human-written captions, highlighting its effectiveness. Our code is available at https://github.com/teamreboott/MLBCAP

Identifying keyphrases (KPs) from text documents is a fundamental task in natural language processing and information retrieval. Vast majority of the benchmark datasets for this task are from the scientific domain containing only the document title and abstract information. This limits keyphrase extraction (KPE) and keyphrase generation (KPG) algorithms to identify keyphrases from human-written summaries that are often very short (approx 8 sentences). This presents three challenges for real-world applications: human-written summaries are unavailable for most documents, the documents are almost always long, and a high percentage of KPs are directly found beyond the limited context of title and abstract. Therefore, we release two extensive corpora mapping KPs of ~1.3M and ~100K scientific articles with their fully extracted text and additional metadata including publication venue, year, author, field of study, and citations for facilitating research on this real-world problem.

This paper presents a new challenging information extraction task in the domain of materials science. We develop an annotation scheme for marking information on experiments related to solid oxide fuel cells in scientific publications, such as involved materials and measurement conditions. With this paper, we publish our annotation guidelines, as well as our SOFC-Exp corpus consisting of 45 open-access scholarly articles annotated by domain experts. A corpus and an inter-annotator agreement study demonstrate the complexity of the suggested named entity recognition and slot filling tasks as well as high annotation quality. We also present strong neural-network based models for a variety of tasks that can be addressed on the basis of our new data set. On all tasks, using BERT embeddings leads to large performance gains, but with increasing task complexity, adding a recurrent neural network on top seems beneficial. Our models will serve as competitive baselines in future work, and analysis of their performance highlights difficult cases when modeling the data and suggests promising research directions.

While Large Language Models (LLMs) have demonstrated remarkable capabilities in scientific tasks, existing evaluation frameworks primarily assess their performance using rich contextual inputs, overlooking their ability to generate novel ideas from minimal information. We introduce LiveIdeaBench, a comprehensive benchmark that evaluates LLMs' scientific creativity and divergent thinking capabilities using single-keyword prompts. Drawing from Guilford's creativity theory, our framework employs a dynamic panel of state-of-the-art LLMs to assess generated ideas across four key dimensions: originality, feasibility, fluency, and flexibility. Through extensive experimentation with 20 leading models across 1,180 keywords spanning 18 scientific domains, we reveal that scientific creative ability shows distinct patterns from general intelligence metrics. Notably, our results demonstrate that models like QwQ-32B-preview achieve comparable creative performance to top-tier models like o1-preview, despite significant gaps in their general intelligence scores. These findings highlight the importance of specialized evaluation frameworks for scientific creativity and suggest that the development of creative capabilities in LLMs may follow different trajectories than traditional problem-solving abilities.

Large multimodal models (LMMs) have proven flexible and generalisable across many tasks and fields. Although they have strong potential to aid scientific research, their capabilities in this domain are not well characterised. A key aspect of scientific research is the ability to understand and interpret figures, which serve as a rich, compressed source of complex information. In this work, we present SciFIBench, a scientific figure interpretation benchmark. Our main benchmark consists of a 1000-question gold set of multiple-choice questions split between two tasks across 12 categories. The questions are curated from CS arXiv paper figures and captions, using adversarial filtering to find hard negatives and human verification for quality control. We evaluate 26 LMMs on SciFIBench, finding it to be a challenging benchmark. Finally, we investigate the alignment and reasoning faithfulness of the LMMs on augmented question sets from our benchmark. We release SciFIBench to encourage progress in this domain.

Academic presentation videos have become an essential medium for research communication, yet producing them remains highly labor-intensive, often requiring hours of slide design, recording, and editing for a short 2 to 10 minutes video. Unlike natural video, presentation video generation involves distinctive challenges: inputs from research papers, dense multi-modal information (text, figures, tables), and the need to coordinate multiple aligned channels such as slides, subtitles, speech, and human talker. To address these challenges, we introduce PaperTalker, the first benchmark of 101 research papers paired with author-created presentation videos, slides, and speaker metadata. We further design four tailored evaluation metrics--Meta Similarity, PresentArena, PresentQuiz, and IP Memory--to measure how videos convey the paper's information to the audience. Building on this foundation, we propose PaperTalker, the first multi-agent framework for academic presentation video generation. It integrates slide generation with effective layout refinement by a novel effective tree search visual choice, cursor grounding, subtitling, speech synthesis, and talking-head rendering, while parallelizing slide-wise generation for efficiency. Experiments on Paper2Video demonstrate that the presentation videos produced by our approach are more faithful and informative than existing baselines, establishing a practical step toward automated and ready-to-use academic video generation. Our dataset, agent, and code are available at https://github.com/showlab/Paper2Video.

Large language models (LLMs) trained on general domain corpora showed remarkable results on natural language processing (NLP) tasks. However, previous research demonstrated LLMs trained using domain-focused corpora perform better on specialized tasks. Inspired by this pivotal insight, we developed INDUS, a comprehensive suite of LLMs tailored for the Earth science, biology, physics, heliophysics, planetary sciences and astrophysics domains and trained using curated scientific corpora drawn from diverse data sources. The suite of models include: (1) an encoder model trained using domain-specific vocabulary and corpora to address natural language understanding tasks, (2) a contrastive-learning-based general text embedding model trained using a diverse set of datasets drawn from multiple sources to address information retrieval tasks and (3) smaller versions of these models created using knowledge distillation techniques to address applications which have latency or resource constraints. We also created three new scientific benchmark datasets namely, CLIMATE-CHANGE-NER (entity-recognition), NASA-QA (extractive QA) and NASA-IR (IR) to accelerate research in these multi-disciplinary fields. Finally, we show that our models outperform both general-purpose encoders (RoBERTa) and existing domain-specific encoders (SciBERT) on these new tasks as well as existing benchmark tasks in the domains of interest.

Large Language Models (LLMs) demonstrate promising capabilities in solving simple scientific problems but often produce hallucinations for complex ones. While integrating LLMs with tools can increase reliability, this approach typically results in over-reliance on tools, diminishing the model's ability to solve simple problems through basic reasoning. In contrast, human experts first assess problem complexity using domain knowledge before choosing an appropriate solution approach. Inspired by this human problem-solving process, we propose a novel two-component fine-tuning method. In the first component World Knowledge Distillation (WKD), LLMs learn directly from solutions generated using tool's information to internalize domain knowledge. In the second component Tool Usage Adaptation (TUA), we partition problems into easy and hard categories based on the model's direct answering accuracy. While maintaining the same alignment target for easy problems as in WKD, we train the model to intelligently switch to tool usage for more challenging problems. We validate our method on six scientific benchmark datasets, spanning mathematics, climate science and epidemiology. On average, our models demonstrate a 28.18% improvement in answer accuracy and a 13.89% increase in tool usage precision across all datasets, surpassing state-of-the-art models including GPT-4o and Claude-3.5.

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.

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at https://github.com/opendatalab-raiser/CoKE.

Scientific Research, vital for improving human life, is hindered by its inherent complexity, slow pace, and the need for specialized experts. To enhance its productivity, we propose a ResearchAgent, a large language model-powered research idea writing agent, which automatically generates problems, methods, and experiment designs while iteratively refining them based on scientific literature. Specifically, starting with a core paper as the primary focus to generate ideas, our ResearchAgent is augmented not only with relevant publications through connecting information over an academic graph but also entities retrieved from an entity-centric knowledge store based on their underlying concepts, mined and shared across numerous papers. In addition, mirroring the human approach to iteratively improving ideas with peer discussions, we leverage multiple ReviewingAgents that provide reviews and feedback iteratively. Further, they are instantiated with human preference-aligned large language models whose criteria for evaluation are derived from actual human judgments. We experimentally validate our ResearchAgent on scientific publications across multiple disciplines, showcasing its effectiveness in generating novel, clear, and valid research ideas based on human and model-based evaluation results.

The rapid advancement of unsupervised representation learning and large-scale pre-trained vision-language models has significantly improved cross-modal retrieval tasks. However, existing multi-modal information retrieval (MMIR) studies lack a comprehensive exploration of document-level retrieval and suffer from the absence of cross-domain datasets at this granularity. To address this limitation, we introduce DocMMIR, a novel multi-modal document retrieval framework designed explicitly to unify diverse document formats and domains, including Wikipedia articles, scientific papers (arXiv), and presentation slides, within a comprehensive retrieval scenario. We construct a large-scale cross-domain multimodal benchmark, comprising 450K samples, which systematically integrates textual and visual information. Our comprehensive experimental analysis reveals substantial limitations in current state-of-the-art MLLMs (CLIP, BLIP2, SigLIP-2, ALIGN) when applied to our tasks, with only CLIP demonstrating reasonable zero-shot performance. Furthermore, we conduct a systematic investigation of training strategies, including cross-modal fusion methods and loss functions, and develop a tailored approach to train CLIP on our benchmark. This results in a +31% improvement in MRR@10 compared to the zero-shot baseline. All our data and code are released in https://github.com/J1mL1/DocMMIR.

The detection and extraction of abbreviations from unstructured texts can help to improve the performance of Natural Language Processing tasks, such as machine translation and information retrieval. However, in terms of publicly available datasets, there is not enough data for training deep-neural-networks-based models to the point of generalising well over data. This paper presents PLOD, a large-scale dataset for abbreviation detection and extraction that contains 160k+ segments automatically annotated with abbreviations and their long forms. We performed manual validation over a set of instances and a complete automatic validation for this dataset. We then used it to generate several baseline models for detecting abbreviations and long forms. The best models achieved an F1-score of 0.92 for abbreviations and 0.89 for detecting their corresponding long forms. We release this dataset along with our code and all the models publicly in https://github.com/surrey-nlp/PLOD-AbbreviationDetection

Large Vision-Language Models (LVLMs) show promise for scientific applications, yet open-source models still struggle with Scientific Visual Question Answering (SVQA), namely answering questions about figures from scientific papers. A key bottleneck lies in the lack of public, large-scale, high-quality SVQA datasets. Although recent work uses LVLMs to synthesize data at scale, we identify systematic errors in their resulting QA pairs, stemming from LVLMs' inherent limitations and information asymmetry between figures and text. To address these challenges, we propose a verification-centric Generate-then-Verify framework that first generates QA pairs with figure-associated textual context, then applies cross-modal consistency checks against figures along with auxiliary filters to eliminate erroneous pairs. We instantiate this framework to curate VeriSciQA, a dataset of 20,351 QA pairs spanning 20 scientific domains and 12 figure types. VeriSciQA poses a challenging benchmark for open-source models, with a substantial accuracy gap between the leading open-source models (64%) and a proprietary model (82%). Moreover, models fine-tuned on VeriSciQA achieve consistent improvements on SVQA benchmarks, with performance gains that scale with data size and surpass models trained on existing datasets. Human evaluation further validates the superior correctness of VeriSciQA. Together, these evidences demonstrate that continued data expansion by our scalable framework can further advance SVQA capability in the open-source community.

Synthesis procedures play a critical role in materials research, as they directly affect material properties. With data-driven approaches increasingly accelerating materials discovery, there is growing interest in extracting synthesis procedures from scientific literature as structured data. However, existing studies often rely on rigid, domain-specific schemas with predefined fields for structuring synthesis procedures or assume that synthesis procedures are linear sequences of operations, which limits their ability to capture the structural complexity of real-world procedures. To address these limitations, we adopt PROV-DM, an international standard for provenance information, which supports flexible, graph-based modeling of procedures. We present MatPROV, a dataset of PROV-DM-compliant synthesis procedures extracted from scientific literature using large language models. MatPROV captures structural complexities and causal relationships among materials, operations, and conditions through visually intuitive directed graphs. This representation enables machine-interpretable synthesis knowledge, opening opportunities for future research such as automated synthesis planning and optimization.

Verifying scientific claims presents a significantly greater challenge than verifying political or news-related claims. Unlike the relatively broad audience for political claims, the users of scientific claim verification systems can vary widely, ranging from researchers testing specific hypotheses to everyday users seeking information on a medication. Additionally, the evidence for scientific claims is often highly complex, involving technical terminology and intricate domain-specific concepts that require specialized models for accurate verification. Despite considerable interest from the research community, there is a noticeable lack of large-scale scientific claim verification datasets to benchmark and train effective models. To bridge this gap, we introduce two large-scale datasets, SciClaimHunt and SciClaimHunt_Num, derived from scientific research papers. We propose several baseline models tailored for scientific claim verification to assess the effectiveness of these datasets. Additionally, we evaluate models trained on SciClaimHunt and SciClaimHunt_Num against existing scientific claim verification datasets to gauge their quality and reliability. Furthermore, we conduct human evaluations of the claims in proposed datasets and perform error analysis to assess the effectiveness of the proposed baseline models. Our findings indicate that SciClaimHunt and SciClaimHunt_Num serve as highly reliable resources for training models in scientific claim verification.

Multi-modal large language models (MLLMs) have demonstrated promising capabilities across various tasks by integrating textual and visual information to achieve visual understanding in complex scenarios. Despite the availability of several benchmarks aims to evaluating MLLMs in tasks from visual question answering to complex problem-solving, most focus predominantly on mathematics or general visual understanding tasks. This reveals a critical gap in current benchmarks, which often overlook the inclusion of other key scientific disciplines such as physics and chemistry. To address this gap, we meticulously construct a comprehensive benchmark, named VisScience, which is utilized to assess the multi-modal scientific reasoning across the three disciplines of mathematics, physics, and chemistry. This benchmark comprises 3,000 questions drawn from K12 education - spanning elementary school through high school - equally distributed across three disciplines, with 1,000 questions per discipline. The questions within VisScience span 21 distinct subjects and are categorized into five difficulty levels, offering a broad spectrum of topics within each discipline. With VisScience, we present a detailed evaluation of the performance of 25 representative MLLMs in scientific reasoning. Experimental results demonstrate that closed-source MLLMs generally outperform open-source models. The best performance observed include a 53.4\% accuracy in mathematics by Claude3.5-Sonnet, 38.2\% in physics by GPT-4o, and 47.0\% in chemistry by Gemini-1.5-Pro. These results underscore the strengths and limitations of MLLMs, suggesting areas for future improvement and highlighting the importance of developing models that can effectively handle the diverse demands of multi-modal scientific reasoning.

Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement. Conclusions: SourceData-NLP's scale highlights the value of integrating curation into publishing. Models trained with SourceData-NLP will furthermore enable the development of tools able to extract causal hypotheses from the literature and assemble them into knowledge graphs.

As the number of open and shared scientific datasets on the Internet increases under the open science movement, efficiently retrieving these datasets is a crucial task in information retrieval (IR) research. In recent years, the development of large models, particularly the pre-training and fine-tuning paradigm, which involves pre-training on large models and fine-tuning on downstream tasks, has provided new solutions for IR match tasks. In this study, we use the original BERT token in the embedding layer, improve the Sentence-BERT model structure in the model layer by introducing the SimCSE and K-Nearest Neighbors method, and use the cosent loss function in the optimization phase to optimize the target output. Our experimental results show that our model outperforms other competing models on both public and self-built datasets through comparative experiments and ablation implementations. This study explores and validates the feasibility and efficiency of pre-training techniques for semantic retrieval of Chinese scientific datasets.

An overwhelmingly large amount of knowledge in the materials domain is generated and stored as text published in peer-reviewed scientific literature. Recent developments in natural language processing, such as bidirectional encoder representations from transformers (BERT) models, provide promising tools to extract information from these texts. However, direct application of these models in the materials domain may yield suboptimal results as the models themselves may not be trained on notations and jargon that are specific to the domain. Here, we present a materials-aware language model, namely, MatSciBERT, which is trained on a large corpus of scientific literature published in the materials domain. We further evaluate the performance of MatSciBERT on three downstream tasks, namely, abstract classification, named entity recognition, and relation extraction, on different materials datasets. We show that MatSciBERT outperforms SciBERT, a language model trained on science corpus, on all the tasks. Further, we discuss some of the applications of MatSciBERT in the materials domain for extracting information, which can, in turn, contribute to materials discovery or optimization. Finally, to make the work accessible to the larger materials community, we make the pretrained and finetuned weights and the models of MatSciBERT freely accessible.

Acronyms are the short forms of longer phrases and they are frequently used in writing, especially scholarly writing, to save space and facilitate the communication of information. As such, every text understanding tool should be capable of recognizing acronyms in text (i.e., acronym identification) and also finding their correct meaning (i.e., acronym disambiguation). As most of the prior works on these tasks are restricted to the biomedical domain and use unsupervised methods or models trained on limited datasets, they fail to perform well for scientific document understanding. To push forward research in this direction, we have organized two shared task for acronym identification and acronym disambiguation in scientific documents, named AI@SDU and AD@SDU, respectively. The two shared tasks have attracted 52 and 43 participants, respectively. While the submitted systems make substantial improvements compared to the existing baselines, there are still far from the human-level performance. This paper reviews the two shared tasks and the prominent participating systems for each of them.

Scientific posters play a vital role in academic communication by presenting ideas through visual summaries. Analyzing reading order and parent-child relations of posters is essential for building structure-aware interfaces that facilitate clear and accurate understanding of research content. Despite their prevalence in academic communication, posters remain underexplored in structural analysis research, which has primarily focused on papers. To address this gap, we constructed SciPostLayoutTree, a dataset of approximately 8,000 posters annotated with reading order and parent-child relations. Compared to an existing structural analysis dataset, SciPostLayoutTree contains more instances of spatially challenging relations, including upward, horizontal, and long-distance relations. As a solution to these challenges, we develop Layout Tree Decoder, which incorporates visual features as well as bounding box features including position and category information. The model also uses beam search to predict relations while capturing sequence-level plausibility. Experimental results demonstrate that our model improves the prediction accuracy for spatially challenging relations and establishes a solid baseline for poster structure analysis. The dataset is publicly available at https://huggingface.co/datasets/omron-sinicx/scipostlayouttree. The code is also publicly available at https://github.com/omron-sinicx/scipostlayouttree.

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

We describe the SemEval task of extracting keyphrases and relations between them from scientific documents, which is crucial for understanding which publications describe which processes, tasks and materials. Although this was a new task, we had a total of 26 submissions across 3 evaluation scenarios. We expect the task and the findings reported in this paper to be relevant for researchers working on understanding scientific content, as well as the broader knowledge base population and information extraction communities.

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.

We introduce InterChart, a diagnostic benchmark that evaluates how well vision-language models (VLMs) reason across multiple related charts, a task central to real-world applications such as scientific reporting, financial analysis, and public policy dashboards. Unlike prior benchmarks focusing on isolated, visually uniform charts, InterChart challenges models with diverse question types ranging from entity inference and trend correlation to numerical estimation and abstract multi-step reasoning grounded in 2-3 thematically or structurally related charts. We organize the benchmark into three tiers of increasing difficulty: (1) factual reasoning over individual charts, (2) integrative analysis across synthetically aligned chart sets, and (3) semantic inference over visually complex, real-world chart pairs. Our evaluation of state-of-the-art open and closed-source VLMs reveals consistent and steep accuracy declines as chart complexity increases. We find that models perform better when we decompose multi-entity charts into simpler visual units, underscoring their struggles with cross-chart integration. By exposing these systematic limitations, InterChart provides a rigorous framework for advancing multimodal reasoning in complex, multi-visual environments.

Citations in scientific papers not only help us trace the intellectual lineage but also are a useful indicator of the scientific significance of the work. Citation intents prove beneficial as they specify the role of the citation in a given context. In this paper, we present CitePrompt, a framework which uses the hitherto unexplored approach of prompt-based learning for citation intent classification. We argue that with the proper choice of the pretrained language model, the prompt template, and the prompt verbalizer, we can not only get results that are better than or comparable to those obtained with the state-of-the-art methods but also do it with much less exterior information about the scientific document. We report state-of-the-art results on the ACL-ARC dataset, and also show significant improvement on the SciCite dataset over all baseline models except one. As suitably large labelled datasets for citation intent classification can be quite hard to find, in a first, we propose the conversion of this task to the few-shot and zero-shot settings. For the ACL-ARC dataset, we report a 53.86% F1 score for the zero-shot setting, which improves to 63.61% and 66.99% for the 5-shot and 10-shot settings, respectively.

Academic poster generation is a crucial yet challenging task in scientific communication, requiring the compression of long-context interleaved documents into a single, visually coherent page. To address this challenge, we introduce the first benchmark and metric suite for poster generation, which pairs recent conference papers with author-designed posters and evaluates outputs on (i)Visual Quality-semantic alignment with human posters, (ii)Textual Coherence-language fluency, (iii)Holistic Assessment-six fine-grained aesthetic and informational criteria scored by a VLM-as-judge, and notably (iv)PaperQuiz-the poster's ability to convey core paper content as measured by VLMs answering generated quizzes. Building on this benchmark, we propose PosterAgent, a top-down, visual-in-the-loop multi-agent pipeline: the (a)Parser distills the paper into a structured asset library; the (b)Planner aligns text-visual pairs into a binary-tree layout that preserves reading order and spatial balance; and the (c)Painter-Commenter loop refines each panel by executing rendering code and using VLM feedback to eliminate overflow and ensure alignment. In our comprehensive evaluation, we find that GPT-4o outputs-though visually appealing at first glance-often exhibit noisy text and poor PaperQuiz scores, and we find that reader engagement is the primary aesthetic bottleneck, as human-designed posters rely largely on visual semantics to convey meaning. Our fully open-source variants (e.g. based on the Qwen-2.5 series) outperform existing 4o-driven multi-agent systems across nearly all metrics, while using 87% fewer tokens. It transforms a 22-page paper into a finalized yet editable .pptx poster - all for just $0.005. These findings chart clear directions for the next generation of fully automated poster-generation models. The code and datasets are available at https://github.com/Paper2Poster/Paper2Poster.

Recent advances in large language models have catalyzed the development of multimodal LLMs (MLLMs) that integrate text, speech, and vision within unified frameworks. As MLLMs evolve from narrow, monolingual, task-specific systems to general-purpose instruction-following models, a key frontier lies in evaluating their multilingual and multimodal capabilities over both long and short contexts. However, existing benchmarks fall short in evaluating these dimensions jointly: they are often limited to English, mostly focus on one single modality at a time, rely on short-form contexts, or lack human annotations -- hindering comprehensive assessment of model performance across languages, modalities, and task complexity. To address these gaps, we introduce MCIF (Multimodal Crosslingual Instruction Following), the first multilingual human-annotated benchmark based on scientific talks that is designed to evaluate instruction-following in crosslingual, multimodal settings over both short- and long-form inputs. MCIF spans three core modalities -- speech, vision, and text -- and four diverse languages (English, German, Italian, and Chinese), enabling a comprehensive evaluation of MLLMs' abilities to interpret instructions across languages and combine them with multimodal contextual information. MCIF is released under a CC-BY 4.0 license to encourage open research and progress in MLLMs development.

Information overload is a major obstacle to scientific progress. The explosive growth in scientific literature and data has made it ever harder to discover useful insights in a large mass of information. Today scientific knowledge is accessed through search engines, but they are unable to organize scientific knowledge alone. In this paper we introduce Galactica: a large language model that can store, combine and reason about scientific knowledge. We train on a large scientific corpus of papers, reference material, knowledge bases and many other sources. We outperform existing models on a range of scientific tasks. On technical knowledge probes such as LaTeX equations, Galactica outperforms the latest GPT-3 by 68.2% versus 49.0%. Galactica also performs well on reasoning, outperforming Chinchilla on mathematical MMLU by 41.3% to 35.7%, and PaLM 540B on MATH with a score of 20.4% versus 8.8%. It also sets a new state-of-the-art on downstream tasks such as PubMedQA and MedMCQA dev of 77.6% and 52.9%. And despite not being trained on a general corpus, Galactica outperforms BLOOM and OPT-175B on BIG-bench. We believe these results demonstrate the potential for language models as a new interface for science. We open source the model for the benefit of the scientific community.

Scientific literature review generation aims to extract and organize important information from an abundant collection of reference papers and produces corresponding reviews while lacking a clear and logical hierarchy. We observe that a high-quality catalogue-guided generation process can effectively alleviate this problem. Therefore, we present an atomic and challenging task named Hierarchical Catalogue Generation for Literature Review as the first step for review generation, which aims to produce a hierarchical catalogue of a review paper given various references. We construct a novel English Hierarchical Catalogues of Literature Reviews Dataset with 7.6k literature review catalogues and 389k reference papers. To accurately assess the model performance, we design two evaluation metrics for informativeness and similarity to ground truth from semantics and structure.Our extensive analyses verify the high quality of our dataset and the effectiveness of our evaluation metrics. We further benchmark diverse experiments on state-of-the-art summarization models like BART and large language models like ChatGPT to evaluate their capabilities. We further discuss potential directions for this task to motivate future research.

Wheat varieties show a large diversity of traits and phenotypes. Linking them to genetic variability is essential for shorter and more efficient wheat breeding programs. Newly desirable wheat variety traits include disease resistance to reduce pesticide use, adaptation to climate change, resistance to heat and drought stresses, or low gluten content of grains. Wheat breeding experiments are documented by a large body of scientific literature and observational data obtained in-field and under controlled conditions. The cross-referencing of complementary information from the literature and observational data is essential to the study of the genotype-phenotype relationship and to the improvement of wheat selection. The scientific literature on genetic marker-assisted selection describes much information about the genotype-phenotype relationship. However, the variety of expressions used to refer to traits and phenotype values in scientific articles is a hinder to finding information and cross-referencing it. When trained adequately by annotated examples, recent text mining methods perform highly in named entity recognition and linking in the scientific domain. While several corpora contain annotations of human and animal phenotypes, currently, no corpus is available for training and evaluating named entity recognition and entity-linking methods in plant phenotype literature. The Triticum aestivum trait Corpus is a new gold standard for traits and phenotypes of wheat. It consists of 540 PubMed references fully annotated for trait, phenotype, and species named entities using the Wheat Trait and Phenotype Ontology and the species taxonomy of the National Center for Biotechnology Information. A study of the performance of tools trained on the Triticum aestivum trait Corpus shows that the corpus is suitable for the training and evaluation of named entity recognition and linking.

Scientific discoveries often hinge on synthesizing decades of research, a task that potentially outstrips human information processing capacities. Large language models (LLMs) offer a solution. LLMs trained on the vast scientific literature could potentially integrate noisy yet interrelated findings to forecast novel results better than human experts. To evaluate this possibility, we created BrainBench, a forward-looking benchmark for predicting neuroscience results. We find that LLMs surpass experts in predicting experimental outcomes. BrainGPT, an LLM we tuned on the neuroscience literature, performed better yet. Like human experts, when LLMs were confident in their predictions, they were more likely to be correct, which presages a future where humans and LLMs team together to make discoveries. Our approach is not neuroscience-specific and is transferable to other knowledge-intensive endeavors.

The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the molecule structures. However, automatically parsing the exact chemical structure is a formidable challenge, due to the amount of detailed information, the diversity of drawing styles, and the need for training data. In this work, we introduce MolGrapher to recognize chemical structures visually. First, a deep keypoint detector detects the atoms. Second, we treat all candidate atoms and bonds as nodes and put them in a graph. This construct allows a natural graph representation of the molecule. Last, we classify atom and bond nodes in the graph with a Graph Neural Network. To address the lack of real training data, we propose a synthetic data generation pipeline producing diverse and realistic results. In addition, we introduce a large-scale benchmark of annotated real molecule images, USPTO-30K, to spur research on this critical topic. Extensive experiments on five datasets show that our approach significantly outperforms classical and learning-based methods in most settings. Code, models, and datasets are available.

Recent work in scientific machine learning (SciML) has focused on incorporating partial differential equation (PDE) information into the learning process. Much of this work has focused on relatively ``easy'' PDE operators (e.g., elliptic and parabolic), with less emphasis on relatively ``hard'' PDE operators (e.g., hyperbolic). Within numerical PDEs, the latter problem class requires control of a type of volume element or conservation constraint, which is known to be challenging. Delivering on the promise of SciML requires seamlessly incorporating both types of problems into the learning process. To address this issue, we propose ProbConserv, a framework for incorporating conservation constraints into a generic SciML architecture. To do so, ProbConserv combines the integral form of a conservation law with a Bayesian update. We provide a detailed analysis of ProbConserv on learning with the Generalized Porous Medium Equation (GPME), a widely-applicable parameterized family of PDEs that illustrates the qualitative properties of both easier and harder PDEs. ProbConserv is effective for easy GPME variants, performing well with state-of-the-art competitors; and for harder GPME variants it outperforms other approaches that do not guarantee volume conservation. ProbConserv seamlessly enforces physical conservation constraints, maintains probabilistic uncertainty quantification (UQ), and deals well with shocks and heteroscedasticities. In each case, it achieves superior predictive performance on downstream tasks.