Daily Papers

Evaluating long-form responses to research queries heavily relies on expert annotators, restricting attention to areas like AI where researchers can conveniently enlist colleagues. Yet, research expertise is widespread: survey articles synthesize knowledge distributed across the literature. We introduce ResearchQA, a resource for evaluating LLM systems by distilling survey articles from 75 research fields into 21K queries and 160K rubric items. Each rubric, derived jointly with queries from survey sections, lists query-specific answer evaluation criteria, i.e., citing papers, making explanations, and describing limitations. Assessments by 31 Ph.D. annotators in 8 fields indicate 96% of queries support Ph.D. information needs and 87% of rubric items should be addressed in system responses by a sentence or more. Using our rubrics, we are able to construct an automatic pairwise judge obtaining 74% agreement with expert judgments. We leverage ResearchQA to analyze competency gaps in 18 systems in over 7.6K pairwise evaluations. No parametric or retrieval-augmented system we evaluate exceeds 70% on covering rubric items, and the highest-ranking agentic system shows 75% coverage. Error analysis reveals that the highest-ranking system fully addresses less than 11% of citation rubric items, 48% of limitation items, and 49% of comparison items. We release our data to facilitate more comprehensive multi-field evaluations.

Solving complex classification tasks using deep neural networks typically requires large amounts of annotated data. However, corresponding class labels are noisy when provided by error-prone annotators, e.g., crowd workers. Training standard deep neural networks leads to subpar performances in such multi-annotator supervised learning settings. We address this issue by presenting a probabilistic training framework named multi-annotator deep learning (MaDL). A ground truth and an annotator performance model are jointly trained in an end-to-end learning approach. The ground truth model learns to predict instances' true class labels, while the annotator performance model infers probabilistic estimates of annotators' performances. A modular network architecture enables us to make varying assumptions regarding annotators' performances, e.g., an optional class or instance dependency. Further, we learn annotator embeddings to estimate annotators' densities within a latent space as proxies of their potentially correlated annotations. Together with a weighted loss function, we improve the learning from correlated annotation patterns. In a comprehensive evaluation, we examine three research questions about multi-annotator supervised learning. Our findings indicate MaDL's state-of-the-art performance and robustness against many correlated, spamming annotators.

Human annotation is the empirical foundation of much NLP research, from dataset construction to model evaluation, but papers often leave unclear who produced the annotations and how the annotation process was controlled. We provide the first large-scale, task-level audit of human annotation reporting across major NLP venues, asking which annotation details are documented, which are missing, and how reporting varies across time, topic, venue, and intended use of human judgment. We introduce a unified taxonomy of annotation-reporting practices and validate an LLM-assisted extraction pipeline against Annotated-gold, a human-adjudicated gold standard of 41 papers and 72 annotation tasks, where the best model reaches human-comparable agreement with adjudicated labels, with Krippendorff's alpha of 0.606 versus 0.585 for human-human agreement. Using this pipeline, we construct Annotated-llm, a dataset covering ACL-venue papers from 2018-2025, with 2,667 extracted annotation tasks from 1,603 papers, and find that papers frequently report operational details such as recruitment strategies, annotator expertise, and annotation volume, but often omit details needed to assess annotation validity, including training, language proficiency, compensation, socio-demographics, adjudication, and agreement values, especially in model-evaluation studies. Our results show that annotation reporting in NLP has improved over time but remains uneven, and they establish a scalable framework and bare-minimum reporting recommendations for making human annotation more reliable, reproducible, and interpretable.

In large organisations, identifying experts on a given topic is crucial in leveraging the internal knowledge spread across teams and departments. So-called enterprise expert retrieval systems automatically discover and structure employees' expertise based on the vast amount of heterogeneous data available about them and the work they perform. Evaluating these systems requires comprehensive ground truth expert annotations, which are hard to obtain. Therefore, the annotation process typically relies on automated recommendations of knowledge areas to validate. This case study provides an analysis of how these recommendations can impact the evaluation of expert finding systems. We demonstrate on a popular benchmark that system-validated annotations lead to overestimated performance of traditional term-based retrieval models and even invalidate comparisons with more recent neural methods. We also augment knowledge areas with synonyms to uncover a strong bias towards literal mentions of their constituent words. Finally, we propose constraints to the annotation process to prevent these biased evaluations, and show that this still allows annotation suggestions of high utility. These findings should inform benchmark creation or selection for expert finding, to guarantee meaningful comparison of methods.

Academic researchers need efficient and reliable methods for collecting high-quality information from trusted sources, but modern tools for AI-assisted research still suffer from the tendency of Large Language Models (LLMs) to produce factually inaccurate or nonsensical output, commonly referred to as hallucinations. We apply the extractive question answering system VerbatimRAG to research papers in the ACL Anthology, directly mapping user queries to verbatim text spans in retrieved documents. We contribute a novel ground truth dataset for the task of mapping user queries to relevant text spans in research papers, and use it to train and evaluate a variety of extractive models. Human annotation is performed by NLP researchers and is based on synthetic user queries generated using a custom pipeline based on the ScIRGen methodology, paired with chunks of research papers retrieved by VerbatimRAG. On this benchmark, a 150M-parameter ModernBERT token classifier trained on silver supervision from our pipeline achieves the best word-level F1 (53.6), ahead of the strongest evaluated LLM extractor (48.7).

Frontier LLMs can navigate complex websites, but their cost and reliance on third-party APIs make local deployment impractical. We introduce Agent-as-Annotators, a framework that structures synthetic trajectory generation for web agents by analogy to human annotation roles, replacing the Task Designer, Annotator, and Supervisor with modular LLM components. Using Gemini 3 Pro as teacher, we generate 3,000 trajectories across six web environments and fine-tune a 9B-parameter student with pure supervised learning on the 2,322 that pass quality filtering. The resulting model achieves 41.5% on WebArena, surpassing closed-source models such as Claude 3.5 Sonnet (36.0%) and GPT-4o (31.5%) under the same evaluation protocol, and nearly doubling the previous best open-weight result (Go-Browse, 21.7%). Capabilities transfer to unseen environments, with an 18.2 percentage point gain on WorkArena L1 (an enterprise platform never seen during training) and consistent improvements across three additional benchmarks. Ablations confirm that each pipeline component contributes meaningfully, with Judge filtering, evaluation hints, and reasoning traces each accounting for measurable gains. These results demonstrate that structured trajectory synthesis from a single frontier teacher is sufficient to produce competitive, locally deployable web agents. Project page: https://agent-as-annotators.github.io

Data annotation is the labeling or tagging of raw data with relevant information, essential for improving the efficacy of machine learning models. The process, however, is labor-intensive and expensive. The emergence of advanced Large Language Models (LLMs), exemplified by GPT-4, presents an unprecedented opportunity to revolutionize and automate the intricate process of data annotation. While existing surveys have extensively covered LLM architecture, training, and general applications, this paper uniquely focuses on their specific utility for data annotation. This survey contributes to three core aspects: LLM-Based Data Annotation, Assessing LLM-generated Annotations, and Learning with LLM-generated annotations. Furthermore, the paper includes an in-depth taxonomy of methodologies employing LLMs for data annotation, a comprehensive review of learning strategies for models incorporating LLM-generated annotations, and a detailed discussion on primary challenges and limitations associated with using LLMs for data annotation. As a key guide, this survey aims to direct researchers and practitioners in exploring the potential of the latest LLMs for data annotation, fostering future advancements in this critical domain. We provide a comprehensive papers list at https://github.com/Zhen-Tan-dmml/LLM4Annotation.git.

Lectures are a learning experience for both students and teachers. Students learn from teachers about the subject material, while teachers learn from students about how to refine their instruction. However, online student feedback is unstructured and abundant, making it challenging for teachers to learn and improve. We take a step towards tackling this challenge. First, we contribute a dataset for studying this problem: SIGHT is a large dataset of 288 math lecture transcripts and 15,784 comments collected from the Massachusetts Institute of Technology OpenCourseWare (MIT OCW) YouTube channel. Second, we develop a rubric for categorizing feedback types using qualitative analysis. Qualitative analysis methods are powerful in uncovering domain-specific insights, however they are costly to apply to large data sources. To overcome this challenge, we propose a set of best practices for using large language models (LLMs) to cheaply classify the comments at scale. We observe a striking correlation between the model's and humans' annotation: Categories with consistent human annotations (>0.9 inter-rater reliability, IRR) also display higher human-model agreement (>0.7), while categories with less consistent human annotations (0.7-0.8 IRR) correspondingly demonstrate lower human-model agreement (0.3-0.5). These techniques uncover useful student feedback from thousands of comments, costing around 0.002$ per comment. We conclude by discussing exciting future directions on using online student feedback and improving automated annotation techniques for qualitative research.

Data annotation remains a significant bottleneck in the Humanities and Social Sciences, particularly for complex semantic tasks such as metaphor identification. While Large Language Models (LLMs) show promise, a significant gap remains between the theoretical capability of LLMs and their practical utility for researchers. This paper introduces LinguistAgent, an integrated, user-friendly platform that leverages a reflective multi-model architecture to automate linguistic annotation. The system implements a dual-agent workflow, comprising an Annotator and a Reviewer, to simulate a professional peer-review process. LinguistAgent supports comparative experiments across three paradigms: Prompt Engineering (Zero/Few-shot), Retrieval-Augmented Generation, and Fine-tuning. We demonstrate LinguistAgent's efficacy using the task of metaphor identification as an example, providing real-time token-level evaluation (Precision, Recall, and F_1 score) against human gold standards. The application and codes are released on https://github.com/Bingru-Li/LinguistAgent.

Large Language Models provide significant new opportunities for the generation of high-quality written works. However, their employment in the research community is inhibited by their tendency to hallucinate invalid sources and lack of direct access to a knowledge base of relevant scientific articles. In this work, we present Citegeist: An application pipeline using dynamic Retrieval Augmented Generation (RAG) on the arXiv Corpus to generate a related work section and other citation-backed outputs. For this purpose, we employ a mixture of embedding-based similarity matching, summarization, and multi-stage filtering. To adapt to the continuous growth of the document base, we also present an optimized way of incorporating new and modified papers. To enable easy utilization in the scientific community, we release both, a website (https://citegeist.org), as well as an implementation harness that works with several different LLM implementations.

Active learning algorithms automatically identify the most informative samples from large amounts of unlabeled data and tremendously reduce human annotation effort in inducing a machine learning model. In a conventional active learning setup, the labeling oracles are assumed to be infallible, that is, they always provide correct answers (in terms of class labels) to the queried unlabeled instances, which cannot be guaranteed in real-world applications. To this end, a body of research has focused on the development of active learning algorithms in the presence of imperfect / noisy oracles. Existing research on active learning with noisy oracles typically simulate the oracles using machine learning models; however, real-world situations are much more challenging, and using ML models to simulate the annotation patterns may not appropriately capture the nuances of real-world annotation challenges. In this research, we first collect annotations of text samples (from 3 benchmark text classification datasets) from crowd-sourced workers through a crowd-sourcing platform. We then conduct extensive empirical studies of 8 commonly used active learning techniques (in conjunction with deep neural networks) using the obtained annotations. Our analyses sheds light on the performance of these techniques under real-world challenges, where annotators can provide incorrect labels, and can also refuse to provide labels. We hope this research will provide valuable insights that will be useful for the deployment of deep active learning systems in real-world applications. The obtained annotations can be accessed at https://github.com/varuntotakura/al_rcta/.

This paper presents a hybrid framework for literature reviews that augments traditional bibliometric methods with large language models (LLMs). By fine-tuning open-source LLMs, our approach enables scalable extraction of qualitative insights from large volumes of research content, enhancing both the breadth and depth of knowledge synthesis. To improve annotation efficiency and consistency, we introduce an error-focused validation process in which LLMs generate initial labels and human reviewers correct misclassifications. Applying this framework to over 20000 scientific articles about human migration, we demonstrate that a domain-adapted LLM can serve as a "specialist" model - capable of accurately selecting relevant studies, detecting emerging trends, and identifying critical research gaps. Notably, the LLM-assisted review reveals a growing scholarly interest in climate-induced migration. However, existing literature disproportionately centers on a narrow set of environmental hazards (e.g., floods, droughts, sea-level rise, and land degradation), while overlooking others that more directly affect human health and well-being, such as air and water pollution or infectious diseases. This imbalance highlights the need for more comprehensive research that goes beyond physical environmental changes to examine their ecological and societal consequences, particularly in shaping migration as an adaptive response. Overall, our proposed framework demonstrates the potential of fine-tuned LLMs to conduct more efficient, consistent, and insightful literature reviews across disciplines, ultimately accelerating knowledge synthesis and scientific discovery.

Active Learning (AL) addresses the high costs of collecting human annotations by strategically annotating the most informative samples. However, for subjective NLP tasks, incorporating a wide range of perspectives in the annotation process is crucial to capture the variability in human judgments. We introduce Annotator-Centric Active Learning (ACAL), which incorporates an annotator selection strategy following data sampling. Our objective is two-fold: (1) to efficiently approximate the full diversity of human judgments, and (2) to assess model performance using annotator-centric metrics, which emphasize minority perspectives over a majority. We experiment with multiple annotator selection strategies across seven subjective NLP tasks, employing both traditional and novel, human-centered evaluation metrics. Our findings indicate that ACAL improves data efficiency and excels in annotator-centric performance evaluations. However, its success depends on the availability of a sufficiently large and diverse pool of annotators to sample from.

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.

Recently, Large Language Models (LLMs) have demonstrated significant potential for data annotation, markedly reducing the labor costs associated with downstream applications. However, existing methods mostly adopt an aggressive strategy by prompting LLM to determine a single gold label for each unlabeled sample. Due to the inherent uncertainty within LLMs, they often produce incorrect labels for difficult samples, severely compromising the data quality for downstream applications. Motivated by ambiguity aversion in human behaviors, we propose a novel candidate annotation paradigm wherein large language models are encouraged to output all possible labels when incurring uncertainty. To ensure unique labels are provided for downstream tasks, we develop a teacher-student framework CanDist that distills candidate annotations with a Small Language Model (SLM). We further provide a rigorous justification demonstrating that distilling candidate annotations from the teacher LLM offers superior theoretical guarantees compared to directly using single annotations. Extensive experiments across six text classification tasks validate the effectiveness of our proposed method. The source code is available at https://github.com/MingxuanXia/CanDist.

NLP benchmarks rely on standardized datasets for training and evaluating models and are crucial for advancing the field. Traditionally, expert annotations ensure high-quality labels; however, the cost of expert annotation does not scale well with the growing demand for larger datasets required by modern models. While crowd-sourcing provides a more scalable solution, it often comes at the expense of annotation precision and consistency. Recent advancements in large language models (LLMs) offer new opportunities to enhance the annotation process, particularly for detecting label errors in existing datasets. In this work, we consider the recent approach of LLM-as-a-judge, leveraging an ensemble of LLMs to flag potentially mislabeled examples. Through a case study of four datasets from the TRUE benchmark, covering different tasks and domains, we empirically analyze the labeling quality of existing datasets, and compare expert, crowd-sourced, and our LLM-based annotations in terms of agreement, label quality, and efficiency, demonstrating the strengths and limitations of each annotation method. Our findings reveal a substantial number of label errors, which, when corrected, induce a significant upward shift in reported model performance. This suggests that many of the LLMs so-called mistakes are due to label errors rather than genuine model failures. Additionally, we discuss the implications of mislabeled data and propose methods to mitigate them in training to improve model performance.

Identifying significant references within the complex interrelations of a citation knowledge graph is challenging, which encompasses connections through citations, authorship, keywords, and other relational attributes. The Paper Source Tracing (PST) task seeks to automate the identification of pivotal references for given scholarly articles utilizing advanced data mining techniques. In the KDD CUP 2024, we design a recommendation-based framework tailored for the PST task. This framework employs the Neural Collaborative Filtering (NCF) model to generate final predictions. To process the textual attributes of the papers and extract input features for the model, we utilize SciBERT, a pre-trained language model. According to the experimental results, our method achieved a score of 0.37814 on the Mean Average Precision (MAP) metric, outperforming baseline models and ranking 11th among all participating teams. The source code is publicly available at https://github.com/MyLove-XAB/KDDCupFinal.

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.

Peer review in grant evaluation informs funding decisions, but the contents of peer review reports are rarely analyzed. In this work, we develop a thoroughly tested pipeline to analyze the texts of grant peer review reports using methods from applied Natural Language Processing (NLP) and machine learning. We start by developing twelve categories reflecting content of grant peer review reports that are of interest to research funders. This is followed by multiple human annotators' iterative annotation of these categories in a novel text corpus of grant peer review reports submitted to the Swiss National Science Foundation. After validating the human annotation, we use the annotated texts to fine-tune pre-trained transformer models to classify these categories at scale, while conducting several robustness and validation checks. Our results show that many categories can be reliably identified by human annotators and machine learning approaches. However, the choice of text classification approach considerably influences the classification performance. We also find a high correspondence between out-of-sample classification performance and human annotators' perceived difficulty in identifying categories. Our results and publicly available fine-tuned transformer models will allow researchers and research funders and anybody interested in peer review to examine and report on the contents of these reports in a structured manner. Ultimately, we hope our approach can contribute to ensuring the quality and trustworthiness of grant peer review.

Peer review relies on substantive, evidence-based questions, yet current LLMs generate surface-level queries that perform worse than human reviewer questions in expert evaluation. To address this gap, we curate a high-quality dataset of reviewer questions from OpenReview and conduct a human preference study where expert annotators evaluate question-paper pairs across three dimensions: effort, evidence, and grounding. From these annotations, we train IntelliReward, a reward model built from a frozen autoregressive LLM with trainable multi-head transformers. Validated against expert judgments, IntelliReward predicts reviewer-question quality better than API-based SFT baselines and provides scalable evaluation. We apply Decoupled Clip and Dynamic Sampling Policy Optimization (DAPO) with IntelliReward to train IntelliAsk, a question-generation model aligned with human standards of effortful, evidence-based critique. Human evaluations show IntelliAsk generates more grounded, substantive and effortful questions than strong baselines and reduces reliance on first-page content. We also find improvements on reasoning and writing benchmarks, suggesting reviewer-question quality correlates with broader capabilities. Compared to Qwen3-32B, IntelliAsk improves MuSR (68.3 vs 64.7 Acc) and WritingBench (8.31 vs 8.07). We release our code, filtered review dataset, expert annotations, IntelliAsk and IntelliReward to support automatic evaluation of grounding, effort, and evidence in LLM-generated review questions.

Large pretrained models can be used as annotators, helping replace or augment crowdworkers and enabling distilling generalist models into smaller specialist models. Unfortunately, this comes at a cost: employing top-of-the-line models often requires paying thousands of dollars for API calls, while the resulting datasets are static and challenging to audit. To address these challenges, we propose a simple alternative: rather than directly querying labels from pretrained models, we task models to generate programs that can produce labels. These programs can be stored and applied locally, re-used and extended, and cost orders of magnitude less. Our system, Alchemist, obtains comparable to or better performance than large language model-based annotation in a range of tasks for a fraction of the cost: on average, improvements amount to a 12.9% enhancement while the total labeling costs across all datasets are reduced by a factor of approximately 500x.

This paper presents a comprehensive study on resume classification to reduce the time and labor needed to screen an overwhelming number of applications significantly, while improving the selection of suitable candidates. A total of 6,492 resumes are extracted from 24,933 job applications for 252 positions designated into four levels of experience for Clinical Research Coordinators (CRC). Each resume is manually annotated to its most appropriate CRC position by experts through several rounds of triple annotation to establish guidelines. As a result, a high Kappa score of 61% is achieved for inter-annotator agreement. Given this dataset, novel transformer-based classification models are developed for two tasks: the first task takes a resume and classifies it to a CRC level (T1), and the second task takes both a resume and a job description to apply and predicts if the application is suited to the job T2. Our best models using section encoding and multi-head attention decoding give results of 73.3% to T1 and 79.2% to T2. Our analysis shows that the prediction errors are mostly made among adjacent CRC levels, which are hard for even experts to distinguish, implying the practical value of our models in real HR platforms.

Active learning, a label-efficient paradigm, empowers models to interactively query an oracle for labeling new data. In the realm of LiDAR semantic segmentation, the challenges stem from the sheer volume of point clouds, rendering annotation labor-intensive and cost-prohibitive. This paper presents Annotator, a general and efficient active learning baseline, in which a voxel-centric online selection strategy is tailored to efficiently probe and annotate the salient and exemplar voxel girds within each LiDAR scan, even under distribution shift. Concretely, we first execute an in-depth analysis of several common selection strategies such as Random, Entropy, Margin, and then develop voxel confusion degree (VCD) to exploit the local topology relations and structures of point clouds. Annotator excels in diverse settings, with a particular focus on active learning (AL), active source-free domain adaptation (ASFDA), and active domain adaptation (ADA). It consistently delivers exceptional performance across LiDAR semantic segmentation benchmarks, spanning both simulation-to-real and real-to-real scenarios. Surprisingly, Annotator exhibits remarkable efficiency, requiring significantly fewer annotations, e.g., just labeling five voxels per scan in the SynLiDAR-to-SemanticKITTI task. This results in impressive performance, achieving 87.8% fully-supervised performance under AL, 88.5% under ASFDA, and 94.4% under ADA. We envision that Annotator will offer a simple, general, and efficient solution for label-efficient 3D applications. Project page: https://binhuixie.github.io/annotator-web

The use of propagandistic techniques in online content has increased in recent years aiming to manipulate online audiences. Fine-grained propaganda detection and extraction of textual spans where propaganda techniques are used, are essential for more informed content consumption. Automatic systems targeting the task over lower resourced languages are limited, usually obstructed by lack of large scale training datasets. Our study investigates whether Large Language Models (LLMs), such as GPT-4, can effectively extract propagandistic spans. We further study the potential of employing the model to collect more cost-effective annotations. Finally, we examine the effectiveness of labels provided by GPT-4 in training smaller language models for the task. The experiments are performed over a large-scale in-house manually annotated dataset. The results suggest that providing more annotation context to GPT-4 within prompts improves its performance compared to human annotators. Moreover, when serving as an expert annotator (consolidator), the model provides labels that have higher agreement with expert annotators, and lead to specialized models that achieve state-of-the-art over an unseen Arabic testing set. Finally, our work is the first to show the potential of utilizing LLMs to develop annotated datasets for propagandistic spans detection task prompting it with annotations from human annotators with limited expertise. All scripts and annotations will be shared with the community.

This paper explores the use of open generative Large Language Models (LLMs) for annotation tasks in the social sciences. The study highlights the challenges associated with proprietary models, such as limited reproducibility and privacy concerns, and advocates for the adoption of open (source) models that can be operated on independent devices. Two examples of annotation tasks, sentiment analysis in tweets and identification of leisure activities in childhood aspirational essays are provided. The study evaluates the performance of different prompting strategies and models (neural-chat-7b-v3-2, Starling-LM-7B-alpha, openchat_3.5, zephyr-7b-alpha and zephyr-7b-beta). The results indicate the need for careful validation and tailored prompt engineering. The study highlights the advantages of open models for data privacy and reproducibility.

We introduce Biomed-Enriched, a biomedical text dataset constructed from PubMed via a two-stage annotation process. In the first stage, a large language model annotates 400K paragraphs from PubMed scientific articles, assigning scores for their type (review, study, clinical case, other), domain (clinical, biomedical, other), and educational quality. The educational quality score (rated 1 to 5) estimates how useful a paragraph is for college-level learning. These annotations are then used to fine-tune a small language model, which propagates the labels across the full PMC-OA corpus. The resulting metadata allows us to extract refined subsets, including 2M clinical case paragraphs with over 450K high-quality ones from articles with commercial-use licenses, and to construct several variants via quality filtering and domain upsampling. Clinical text is typically difficult to access due to privacy constraints, as hospital records cannot be publicly shared. Hence, our dataset provides an alternative large-scale, openly available collection of clinical cases from PubMed, making it a valuable resource for biomedical and clinical NLP. Preliminary continual-pretraining experiments with OLMo2 suggest these curated subsets enable targeted improvements, with clinical upsampling boosting performance by ~5% on MMLU ProfMed and educational quality filtering improving MedQA and MedMCQA by ~1%. Combinations of these techniques led to faster convergence, reaching same performance with a third of training tokens, indicating potential for more efficient and effective biomedical pretraining strategies.

Human annotated data plays a crucial role in machine learning (ML) research and development. However, the ethical considerations around the processes and decisions that go into dataset annotation have not received nearly enough attention. In this paper, we survey an array of literature that provides insights into ethical considerations around crowdsourced dataset annotation. We synthesize these insights, and lay out the challenges in this space along two layers: (1) who the annotator is, and how the annotators' lived experiences can impact their annotations, and (2) the relationship between the annotators and the crowdsourcing platforms, and what that relationship affords them. Finally, we introduce a novel framework, CrowdWorkSheets, for dataset developers to facilitate transparent documentation of key decisions points at various stages of the data annotation pipeline: task formulation, selection of annotators, platform and infrastructure choices, dataset analysis and evaluation, and dataset release and maintenance.

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.

Large language models are increasingly used in scientific writing, yet they can fabricate citation-shaped references that appear plausible but fail bibliographic verification. Existing detectors often reduce verification to binary found/not-found decisions and rely on brittle parsing or incomplete retrieval, offering little field-level signal to auditors. We reframe citation hallucination detection as taxonomy-aligned field-level adjudication and introduce a 12-code taxonomy spanning Real, Potential, and Hallucinated citations. Based on this taxonomy, we build CiteTracer, a cascading multi-agent detector that extracts structured citations from PDF and BibTeX, retrieves evidence through cache lookup, URL fetch, scholar connectors, and web search, applies deterministic field matching, and routes ambiguous cases to class-specialist judgers. We release a benchmark of 2,450 synthetic citations built from real seeds with controlled LLM mutations, paired with 957 real-world fabricated citations drawn from ICLR 2026 and an anonymous conference desk-rejected submissions. CiteTracer reaches 97.1% accuracy on the synthetic benchmark, with class-level F1 scores of 97.0, 95.8, and 98.5 for Real, Potential, and Hallucinated, respectively, and detects 97.1% of fabrications on the real-world set without abstaining. Code: https://github.com/aaFrostnova/CiteTracer.

High-quality data annotation is an essential but laborious and costly aspect of developing machine learning-based software. We explore the inherent tradeoff between annotation accuracy and cost by detecting and removing minority reports -- instances where annotators provide incorrect responses -- that indicate unnecessary redundancy in task assignments. We propose an approach to prune potentially redundant annotation task assignments before they are executed by estimating the likelihood of an annotator disagreeing with the majority vote for a given task. Our approach is informed by an empirical analysis over computer vision datasets annotated by a professional data annotation platform, which reveals that the likelihood of a minority report event is dependent primarily on image ambiguity, worker variability, and worker fatigue. Simulations over these datasets show that we can reduce the number of annotations required by over 60% with a small compromise in label quality, saving approximately 6.6 days-equivalent of labor. Our approach provides annotation service platforms with a method to balance cost and dataset quality. Machine learning practitioners can tailor annotation accuracy levels according to specific application needs, thereby optimizing budget allocation while maintaining the data quality necessary for critical settings like autonomous driving technology.

The "LLM-as-a-judge" paradigm employs Large Language Models (LLMs) as annotators and evaluators in tasks traditionally performed by humans. LLM annotations are widely used, not only in NLP research but also in fields like medicine, psychology, and social science. Despite their role in shaping study results and insights, there is no standard or rigorous procedure to determine whether LLMs can replace human annotators. In this paper, we propose a novel statistical procedure -- the Alternative Annotator Test (alt-test) -- that requires only a modest subset of annotated examples to justify using LLM annotations. Additionally, we introduce a versatile and interpretable measure for comparing LLM judges. To demonstrate our procedure, we curated a diverse collection of ten datasets, consisting of language and vision-language tasks, and conducted experiments with six LLMs and four prompting techniques. Our results show that LLMs can sometimes replace humans with closed-source LLMs (such as GPT-4o), outperforming open-source LLMs, and that prompting techniques yield judges of varying quality. We hope this study encourages more rigorous and reliable practices.

Annotation noise is widespread in datasets, but manually revising a flawed corpus is time-consuming and error-prone. Hence, given the prior knowledge in Pre-trained Language Models and the expected uniformity across all annotations, we attempt to reduce annotation noise in the corpus through two tasks automatically: (1) Annotation Inconsistency Detection that indicates the credibility of annotations, and (2) Annotation Error Correction that rectifies the abnormal annotations. We investigate how to acquire semantic sensitive annotation representations from Pre-trained Language Models, expecting to embed the examples with identical annotations to the mutually adjacent positions even without fine-tuning. We proposed a novel credibility score to reveal the likelihood of annotation inconsistencies based on the neighbouring consistency. Then, we fine-tune the Pre-trained Language Models based classifier with cross-validation for annotation correction. The annotation corrector is further elaborated with two approaches: (1) soft labelling by Kernel Density Estimation and (2) a novel distant-peer contrastive loss. We study the re-annotation in relation extraction and create a new manually revised dataset, Re-DocRED, for evaluating document-level re-annotation. The proposed credibility scores show promising agreement with human revisions, achieving a Binary F1 of 93.4 and 72.5 in detecting inconsistencies on TACRED and DocRED respectively. Moreover, the neighbour-aware classifiers based on distant-peer contrastive learning and uncertain labels achieve Macro F1 up to 66.2 and 57.8 in correcting annotations on TACRED and DocRED respectively. These improvements are not merely theoretical: Rather, automatically denoised training sets demonstrate up to 3.6% performance improvement for state-of-the-art relation extraction models.

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

The task of annotating data into concise summaries poses a significant challenge across various domains, frequently requiring the allocation of significant time and specialized knowledge by human experts. Despite existing efforts to use large language models for annotation tasks, significant problems such as limited applicability to unlabeled data, the absence of self-supervised methods, and the lack of focus on complex structured data still persist. In this work, we propose a GPT self-supervision annotation method, which embodies a generating-recovering paradigm that leverages the one-shot learning capabilities of the Generative Pretrained Transformer (GPT). The proposed approach comprises a one-shot tuning phase followed by a generation phase. In the one-shot tuning phase, we sample a data from the support set as part of the prompt for GPT to generate a textual summary, which is then used to recover the original data. The alignment score between the recovered and original data serves as a self-supervision navigator to refine the process. In the generation stage, the optimally selected one-shot sample serves as a template in the prompt and is applied to generating summaries from challenging datasets. The annotation performance is evaluated by tuning several human feedback reward networks and by calculating alignment scores between original and recovered data at both sentence and structure levels. Our self-supervised annotation method consistently achieves competitive scores, convincingly demonstrating its robust strength in various data-to-summary annotation tasks.

Acknowledgments in scientific papers may give an insight into aspects of the scientific community, such as reward systems, collaboration patterns, and hidden research trends. The aim of the paper is to evaluate the performance of different embedding models for the task of automatic extraction and classification of acknowledged entities from the acknowledgment text in scientific papers. We trained and implemented a named entity recognition (NER) task using the Flair NLP framework. The training was conducted using three default Flair NER models with four differently-sized corpora and different versions of the Flair NLP framework. The Flair Embeddings model trained on the medium corpus with the latest FLAIR version showed the best accuracy of 0.79. Expanding the size of a training corpus from very small to medium size massively increased the accuracy of all training algorithms, but further expansion of the training corpus did not bring further improvement. Moreover, the performance of the model slightly deteriorated. Our model is able to recognize six entity types: funding agency, grant number, individuals, university, corporation, and miscellaneous. The model works more precisely for some entity types than for others; thus, individuals and grant numbers showed a very good F1-Score over 0.9. Most of the previous works on acknowledgment analysis were limited by the manual evaluation of data and therefore by the amount of processed data. This model can be applied for the comprehensive analysis of acknowledgment texts and may potentially make a great contribution to the field of automated acknowledgment analysis.

Large crowd-sourced datasets are often noisy and relation classification (RC) datasets are no exception. Reannotating the entire dataset is one probable solution however it is not always viable due to time and budget constraints. This paper addresses the problem of efficient reannotation of a large noisy dataset for the RC. Our goal is to catch more annotation errors in the dataset while reannotating fewer instances. Existing work on RC dataset reannotation lacks the flexibility about how much data to reannotate. We introduce the concept of a reannotation budget to overcome this limitation. The immediate follow-up problem is: Given a specific reannotation budget, which subset of the data should we reannotate? To address this problem, we present two strategies to selectively reannotate RC datasets. Our strategies utilize the taxonomic hierarchy of relation labels. The intuition of our work is to rely on the graph distance between actual and predicted relation labels in the label hierarchy graph. We evaluate our reannotation strategies on the well-known TACRED dataset. We design our experiments to answer three specific research questions. First, does our strategy select novel candidates for reannotation? Second, for a given reannotation budget is our reannotation strategy more efficient at catching annotation errors? Third, what is the impact of data reannotation on RC model performance measurement? Experimental results show that our both reannotation strategies are novel and efficient. Our analysis indicates that the current reported performance of RC models on noisy TACRED data is inflated.

High-quality and consistent annotations are fundamental to the successful development of robust machine learning models. Traditional data annotation methods are resource-intensive and inefficient, often leading to a reliance on third-party annotators who are not the domain experts. Hard samples, which are usually the most informative for model training, tend to be difficult to label accurately and consistently without business context. These can arise unpredictably during the annotation process, requiring a variable number of iterations and rounds of feedback, leading to unforeseen expenses and time commitments to guarantee quality. We posit that more direct involvement of domain experts, using a human-in-the-loop system, can resolve many of these practical challenges. We propose a novel framework we call Video Annotator (VA) for annotating, managing, and iterating on video classification datasets. Our approach offers a new paradigm for an end-user-centered model development process, enhancing the efficiency, usability, and effectiveness of video classifiers. Uniquely, VA allows for a continuous annotation process, seamlessly integrating data collection and model training. We leverage the zero-shot capabilities of vision-language foundation models combined with active learning techniques, and demonstrate that VA enables the efficient creation of high-quality models. VA achieves a median 6.8 point improvement in Average Precision relative to the most competitive baseline across a wide-ranging assortment of tasks. We release a dataset with 153k labels across 56 video understanding tasks annotated by three professional video editors using VA, and also release code to replicate our experiments at: http://github.com/netflix/videoannotator.

The Open Images Dataset contains approximately 9 million images and is a widely accepted dataset for computer vision research. As is common practice for large datasets, the annotations are not exhaustive, with bounding boxes and attribute labels for only a subset of the classes in each image. In this paper, we present a new set of annotations on a subset of the Open Images dataset called the MIAP (More Inclusive Annotations for People) subset, containing bounding boxes and attributes for all of the people visible in those images. The attributes and labeling methodology for the MIAP subset were designed to enable research into model fairness. In addition, we analyze the original annotation methodology for the person class and its subclasses, discussing the resulting patterns in order to inform future annotation efforts. By considering both the original and exhaustive annotation sets, researchers can also now study how systematic patterns in training annotations affect modeling.

We introduce AWED-FiNER, an open-source ecosystem designed to bridge the gap in Fine-grained Named Entity Recognition (FgNER) for 36 global languages spoken by more than 6.6 billion people. While Large Language Models (LLMs) dominate general Natural Language Processing (NLP) tasks, they often struggle with low-resource languages and fine-grained NLP tasks. AWED-FiNER provides a collection of agentic toolkits, web applications, and several state-of-the-art expert models that provides FgNER solutions across 36 languages. The agentic tools enable to route multilingual text to specialized expert models and fetch FgNER annotations within seconds. The web-based platforms provide ready-to-use FgNER annotation service for non-technical users. Moreover, the collection of language specific extremely small sized open-source state-of-the-art expert models facilitate offline deployment in resource contraint scenerios including edge devices. AWED-FiNER covers languages spoken by over 6.6 billion people, including a specific focus on vulnerable languages such as Bodo, Manipuri, Bishnupriya, and Mizo. The resources can be accessed here: Agentic Tool (https://github.com/PrachuryyaKaushik/AWED-FiNER), Web Application (https://hf.co/spaces/prachuryyaIITG/AWED-FiNER), and 49 Expert Detector Models (https://hf.co/collections/prachuryyaIITG/awed-finer).

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

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

Frontier scientific reasoning is rapidly emerging as a key foundation for advancing AI agents in automated scientific discovery. Deep research agents offer a promising approach to this challenge. These models develop robust problem-solving capabilities through post-training on information-seeking tasks, which are typically curated via knowledge graph construction or iterative web browsing. However, these strategies face inherent limitations in frontier science, where domain-specific knowledge is scattered across sparse and heterogeneous academic sources, and problem solving requires sophisticated computation and reasoning far beyond factual recall. To bridge this gap, we introduce SciResearcher, a fully automated agentic framework for frontier-science data construction. SciResearcher synthesizes diverse conceptual and computational tasks grounded in academic evidence, while eliciting information acquisition, tool-integrated reasoning, and long-horizon capabilities. Leveraging the curated data for supervised fine-tuning and agentic reinforcement learning, we develop SciResearcher-8B, an agent foundation model that achieves 19.46% on the HLE-Bio/Chem-Gold benchmark, establishing a new state of the art at its parameter scale and surpassing several larger proprietary agents. It further achieves 13-15% absolute gains on SuperGPQA-Hard-Biology and TRQA-Literature benchmarks. Overall, SciResearcher introduces a new paradigm for automated data construction for frontier scientific reasoning and offers a scalable path toward future scientific agents.

Recent advances in large language models (LLMs) have fueled the vision of automated scientific discovery, often called AI Co-Scientists. To date, prior work casts these systems as generative co-authors responsible for crafting hypotheses, synthesizing code, or drafting manuscripts. In this work, we explore a complementary application: using LLMs as verifiers to automate the academic verification of scientific manuscripts. To that end, we introduce SPOT, a dataset of 83 published papers paired with 91 errors significant enough to prompt errata or retraction, cross-validated with actual authors and human annotators. Evaluating state-of-the-art LLMs on SPOT, we find that none surpasses 21.1\% recall or 6.1\% precision (o3 achieves the best scores, with all others near zero). Furthermore, confidence estimates are uniformly low, and across eight independent runs, models rarely rediscover the same errors, undermining their reliability. Finally, qualitative analysis with domain experts reveals that even the strongest models make mistakes resembling student-level misconceptions derived from misunderstandings. These findings highlight the substantial gap between current LLM capabilities and the requirements for dependable AI-assisted academic verification.

The NLP community has long advocated for the construction of multi-annotator datasets to better capture the nuances of language interpretation, subjectivity, and ambiguity. This paper conducts a retrospective study to show how performance scores can vary when a dataset expands from a single annotation per instance to multiple annotations. We propose a novel multi-annotator simulation process to generate datasets with varying annotation budgets. We show that similar datasets with the same annotation budget can lead to varying performance gains. Our findings challenge the popular belief that models trained on multi-annotation examples always lead to better performance than models trained on single or few-annotation examples.

Cognitive psychologists have documented that humans use cognitive heuristics, or mental shortcuts, to make quick decisions while expending less effort. While performing annotation work on crowdsourcing platforms, we hypothesize that such heuristic use among annotators cascades on to data quality and model robustness. In this work, we study cognitive heuristic use in the context of annotating multiple-choice reading comprehension datasets. We propose tracking annotator heuristic traces, where we tangibly measure low-effort annotation strategies that could indicate usage of various cognitive heuristics. We find evidence that annotators might be using multiple such heuristics, based on correlations with a battery of psychological tests. Importantly, heuristic use among annotators determines data quality along several dimensions: (1) known biased models, such as partial input models, more easily solve examples authored by annotators that rate highly on heuristic use, (2) models trained on annotators scoring highly on heuristic use don't generalize as well, and (3) heuristic-seeking annotators tend to create qualitatively less challenging examples. Our findings suggest that tracking heuristic usage among annotators can potentially help with collecting challenging datasets and diagnosing model biases.

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.

Domain-specific named entity recognition (NER) on Computer Science (CS) scholarly articles is an information extraction task that is arguably more challenging for the various annotation aims that can beset the task and has been less studied than NER in the general domain. Given that significant progress has been made on NER, we believe that scholarly domain-specific NER will receive increasing attention in the years to come. Currently, progress on CS NER -- the focus of this work -- is hampered in part by its recency and the lack of a standardized annotation aim for scientific entities/terms. This work proposes a standardized task by defining a set of seven contribution-centric scholarly entities for CS NER viz., research problem, solution, resource, language, tool, method, and dataset. Following which, its main contributions are: combines existing CS NER resources that maintain their annotation focus on the set or subset of contribution-centric scholarly entities we consider; further, noting the need for big data to train neural NER models, this work additionally supplies thousands of contribution-centric entity annotations from article titles and abstracts, thus releasing a cumulative large novel resource for CS NER; and, finally, trains a sequence labeling CS NER model inspired after state-of-the-art neural architectures from the general domain NER task. Throughout the work, several practical considerations are made which can be useful to information technology designers of the digital libraries.

Annotating data is a time-consuming and costly task, but it is inherently required for supervised machine learning. Active Learning (AL) is an established method that minimizes human labeling effort by iteratively selecting the most informative unlabeled samples for expert annotation, thereby improving the overall classification performance. Even though AL has been known for decades, AL is still rarely used in real-world applications. As indicated in the two community web surveys among the NLP community about AL, two main reasons continue to hold practitioners back from using AL: first, the complexity of setting AL up, and second, a lack of trust in its effectiveness. We hypothesize that both reasons share the same culprit: the large hyperparameter space of AL. This mostly unexplored hyperparameter space often leads to misleading and irreproducible AL experiment results. In this study, we first compiled a large hyperparameter grid of over 4.6 million hyperparameter combinations, second, recorded the performance of all combinations in the so-far biggest conducted AL study, and third, analyzed the impact of each hyperparameter in the experiment results. In the end, we give recommendations about the influence of each hyperparameter, demonstrate the surprising influence of the concrete AL strategy implementation, and outline an experimental study design for reproducible AL experiments with minimal computational effort, thus contributing to more reproducible and trustworthy AL research in the future.

Pool-based active learning (AL) aims to optimize the annotation process (i.e., labeling) as the acquisition of annotations is often time-consuming and therefore expensive. For this purpose, an AL strategy queries annotations intelligently from annotators to train a high-performance classification model at a low annotation cost. Traditional AL strategies operate in an idealized framework. They assume a single, omniscient annotator who never gets tired and charges uniformly regardless of query difficulty. However, in real-world applications, we often face human annotators, e.g., crowd or in-house workers, who make annotation mistakes and can be reluctant to respond if tired or faced with complex queries. Recently, a wide range of novel AL strategies has been proposed to address these issues. They differ in at least one of the following three central aspects from traditional AL: (1) They explicitly consider (multiple) human annotators whose performances can be affected by various factors, such as missing expertise. (2) They generalize the interaction with human annotators by considering different query and annotation types, such as asking an annotator for feedback on an inferred classification rule. (3) They take more complex cost schemes regarding annotations and misclassifications into account. This survey provides an overview of these AL strategies and refers to them as real-world AL. Therefore, we introduce a general real-world AL strategy as part of a learning cycle and use its elements, e.g., the query and annotator selection algorithm, to categorize about 60 real-world AL strategies. Finally, we outline possible directions for future research in the field of AL.

Scientific article summarization is challenging: large, annotated corpora are not available, and the summary should ideally include the article's impacts on research community. This paper provides novel solutions to these two challenges. We 1) develop and release the first large-scale manually-annotated corpus for scientific papers (on computational linguistics) by enabling faster annotation, and 2) propose summarization methods that integrate the authors' original highlights (abstract) and the article's actual impacts on the community (citations), to create comprehensive, hybrid summaries. We conduct experiments to demonstrate the efficacy of our corpus in training data-driven models for scientific paper summarization and the advantage of our hybrid summaries over abstracts and traditional citation-based summaries. Our large annotated corpus and hybrid methods provide a new framework for scientific paper summarization research.

The application of Large Language Models (LLMs) in accelerating scientific discovery has garnered increasing attention, with a key focus on constructing research agents endowed with innovative capability, i.e., the ability to autonomously generate novel and significant research ideas. Existing approaches predominantly rely on sophisticated prompt engineering and lack a systematic training paradigm. To address this, we propose DeepInnovator, a training framework designed to trigger the innovative capability of LLMs. Our approach comprises two core components. (1) ``Standing on the shoulders of giants''. We construct an automated data extraction pipeline to extract and organize structured research knowledge from a vast corpus of unlabeled scientific literature. (2) ``Conjectures and refutations''. We introduce a ``Next Idea Prediction'' training paradigm, which models the generation of research ideas as an iterative process of continuously predicting, evaluating, and refining plausible and novel next idea. Both automatic and expert evaluations demonstrate that our DeepInnovator-14B significantly outperforms untrained baselines, achieving win rates of 80.53\%-93.81\%, and attains performance comparable to that of current leading LLMs. This work provides a scalable training pathway toward building research agents with genuine, originative innovative capability, and will open-source the dataset to foster community advancement. Source code and data are available at: https://github.com/HKUDS/DeepInnovator.

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

Many computer scientists use the aggregated answers of online workers to represent ground truth. Prior work has shown that aggregation methods such as majority voting are effective for measuring relatively objective features. For subjective features such as semantic connotation, online workers, known for optimizing their hourly earnings, tend to deteriorate in the quality of their responses as they work longer. In this paper, we aim to address this issue by proposing a quality-aware semantic data annotation system. We observe that with timely feedback on workers' performance quantified by quality scores, better informed online workers can maintain the quality of their labeling throughout an extended period of time. We validate the effectiveness of the proposed annotation system through i) evaluating performance based on an expert-labeled dataset, and ii) demonstrating machine learning tasks that can lead to consistent learning behavior with 70%-80% accuracy. Our results suggest that with our system, researchers can collect high-quality answers of subjective semantic features at a large scale.

The advancements of language language models (LLMs) have piqued growing interest in developing LLM-based language agents to automate scientific discovery end-to-end, which has sparked both excitement and skepticism about the true capabilities of such agents. In this work, we argue that for an agent to fully automate scientific discovery, it must be able to complete all essential tasks in the workflow. Thus, we call for rigorous assessment of agents on individual tasks in a scientific workflow before making bold claims on end-to-end automation. To this end, we present ScienceAgentBench, a new benchmark for evaluating language agents for data-driven scientific discovery. To ensure the scientific authenticity and real-world relevance of our benchmark, we extract 102 tasks from 44 peer-reviewed publications in four disciplines and engage nine subject matter experts to validate them. We unify the target output for every task to a self-contained Python program file and employ an array of evaluation metrics to examine the generated programs, execution results, and costs. Each task goes through multiple rounds of manual validation by annotators and subject matter experts to ensure its annotation quality and scientific plausibility. We also propose two effective strategies to mitigate data contamination concerns. Using our benchmark, we evaluate five open-weight and proprietary LLMs, each with three frameworks: direct prompting, OpenHands, and self-debug. Given three attempts for each task, the best-performing agent can only solve 32.4% of the tasks independently and 34.3% with expert-provided knowledge. These results underscore the limited capacities of current language agents in generating code for data-driven discovery, let alone end-to-end automation for scientific research.

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

We present SAINE, an Scientific Annotation and Inference ENgine based on a set of standard open-source software, such as Label Studio and MLflow. We show that our annotation engine can benefit the further development of a more accurate classification. Based on our previous work on hierarchical discipline classifications, we demonstrate its application using SAINE in understanding the space for scholarly publications. The user study of our annotation results shows that user input collected with the help of our system can help us better understand the classification process. We believe that our work will help to foster greater transparency and better understand scientific research. Our annotation and inference engine can further support the downstream meta-science projects. We welcome collaboration and feedback from the scientific community on these projects. The demonstration video can be accessed from https://youtu.be/yToO-G9YQK4. A live demo website is available at https://app.heartex.com/user/signup/?token=e2435a2f97449fa1 upon free registration.

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

The explosive growth in academic literature necessitates automated deep research (DR) agents, yet their evaluation remains a significant challenge. First, existing benchmarks often focus narrowly on retrieval while neglecting high-level planning and reasoning. Second, existing benchmarks favor general domains over the scientific domains that are the core application for DR agents. To address these gaps, we introduce Dr.Mi-Bench, a Modular-integrated benchmark for scientific DR agents. Grounded in academic literature, our benchmark uses a human-annotated dataset of 200 instances across 10 scientific domains, including both research and review papers. Besides, we also propose a Modular-integrated Evaluation Paradigm for DR Agents (Dr.Mi-Eval), a novel modular-integrated evaluation paradigm, which leverages the rich structure of academic papers to assess the core competencies of planning, retrieval, and reasoning through two complementary modes: an end-to-end evaluation for DR agents and an isolated evaluation for foundational LLMs as potential backbones. Experimental results reveal a fragmented performance landscape: agents exhibit specialized strengths but share critical weaknesses, most notably in performing the multi-source retrieval required for review-style tasks and performing consistently across diverse scientific fields. Moreover, improving high-level planning capability is the crucial factor for unlocking the reasoning potential of foundational LLMs as backbones. By exposing these actionable failure modes, Dr.Mi-Bench provides a diagnostic tool to guide the development of more reliable academic research assistants.

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

The rapid growth of scientific literature has made it increasingly difficult for researchers to efficiently discover, evaluate, and synthesize relevant work. Recent advances in multi-agent large language models (LLMs) have demonstrated strong potential for understanding user intent and are being trained to utilize various tools. In this paper, we introduce Paper Circle, a multi-agent research discovery and analysis system designed to reduce the effort required to find, assess, organize, and understand academic literature. The system comprises two complementary pipelines: (1) a Discovery Pipeline that integrates offline and online retrieval from multiple sources, multi-criteria scoring, diversity-aware ranking, and structured outputs; and (2) an Analysis Pipeline that transforms individual papers into structured knowledge graphs with typed nodes such as concepts, methods, experiments, and figures, enabling graph-aware question answering and coverage verification. Both pipelines are implemented within a coder LLM-based multi-agent orchestration framework and produce fully reproducible, synchronized outputs including JSON, CSV, BibTeX, Markdown, and HTML at each agent step. This paper describes the system architecture, agent roles, retrieval and scoring methods, knowledge graph schema, and evaluation interfaces that together form the Paper Circle research workflow. We benchmark Paper Circle on both paper retrieval and paper review generation, reporting hit rate, MRR, and Recall at K. Results show consistent improvements with stronger agent models. We have publicly released the website at https://papercircle.vercel.app/ and the code at https://github.com/MAXNORM8650/papercircle.

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.

The core challenge of de novo protein design lies in creating proteins with specific functions or properties, guided by certain conditions. Current models explore to generate protein using structural and evolutionary guidance, which only provide indirect conditions concerning functions and properties. However, textual annotations of proteins, especially the annotations for protein domains, which directly describe the protein's high-level functionalities, properties, and their correlation with target amino acid sequences, remain unexplored in the context of protein design tasks. In this paper, we propose Protein-Annotation Alignment Generation, PAAG, a multi-modality protein design framework that integrates the textual annotations extracted from protein database for controllable generation in sequence space. Specifically, within a multi-level alignment module, PAAG can explicitly generate proteins containing specific domains conditioned on the corresponding domain annotations, and can even design novel proteins with flexible combinations of different kinds of annotations. Our experimental results underscore the superiority of the aligned protein representations from PAAG over 7 prediction tasks. Furthermore, PAAG demonstrates a significant increase in generation success rate (24.7% vs 4.7% in zinc finger, and 54.3% vs 22.0% in the immunoglobulin domain) in comparison to the existing model. We anticipate that PAAG will broaden the horizons of protein design by leveraging the knowledge from between textual annotation and proteins.

Researchers have proposed numerous text-to-SQL techniques to streamline data analytics and accelerate the development of data-driven applications. To compare these techniques and select the best one for deployment, the community depends on public benchmarks and their leaderboards. Since these benchmarks heavily rely on human annotations during question construction and answer evaluation, the validity of the annotations is crucial. In this paper, we conduct an empirical study that (i) benchmarks annotation error rates for two widely used text-to-SQL benchmarks, BIRD and Spider 2.0-Snow, and (ii) corrects a subset of the BIRD development (Dev) set to measure the impact of annotation errors on text-to-SQL agent performance and leaderboard rankings. Through expert analysis, we show that BIRD Mini-Dev and Spider 2.0-Snow have error rates of 52.8% and 62.8%, respectively. We re-evaluate all 16 open-source agents from the BIRD leaderboard on both the original and the corrected BIRD Dev subsets. We show that performance changes range from -7% to 31% (in relative terms) and rank changes range from -9 to +9 positions. We further assess whether these impacts generalize to the full BIRD Dev set. We find that the rankings of agents on the uncorrected subset correlate strongly with those on the full Dev set (Spearman's r_s=0.85, p=3.26e-5), whereas they correlate weakly with those on the corrected subset (Spearman's r_s=0.32, p=0.23). These findings show that annotation errors can significantly distort reported performance and rankings, potentially misguiding research directions or deployment choices. Our code and data are available at https://github.com/uiuc-kang-lab/text_to_sql_benchmarks.

Machine learning models are commonly used to detect toxicity in online conversations. These models are trained on datasets annotated by human raters. We explore how raters' self-described identities impact how they annotate toxicity in online comments. We first define the concept of specialized rater pools: rater pools formed based on raters' self-described identities, rather than at random. We formed three such rater pools for this study--specialized rater pools of raters from the U.S. who identify as African American, LGBTQ, and those who identify as neither. Each of these rater pools annotated the same set of comments, which contains many references to these identity groups. We found that rater identity is a statistically significant factor in how raters will annotate toxicity for identity-related annotations. Using preliminary content analysis, we examined the comments with the most disagreement between rater pools and found nuanced differences in the toxicity annotations. Next, we trained models on the annotations from each of the different rater pools, and compared the scores of these models on comments from several test sets. Finally, we discuss how using raters that self-identify with the subjects of comments can create more inclusive machine learning models, and provide more nuanced ratings than those by random raters.

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

Data annotation, the practice of assigning descriptive labels to raw data, is pivotal in optimizing the performance of machine learning models. However, it is a resource-intensive process susceptible to biases introduced by annotators. The emergence of sophisticated Large Language Models (LLMs), like ChatGPT presents a unique opportunity to modernize and streamline this complex procedure. While existing research extensively evaluates the efficacy of LLMs, as annotators, this paper delves into the biases present in LLMs, specifically GPT 3.5 and GPT 4o when annotating hate speech data. Our research contributes to understanding biases in four key categories: gender, race, religion, and disability. Specifically targeting highly vulnerable groups within these categories, we analyze annotator biases. Furthermore, we conduct a comprehensive examination of potential factors contributing to these biases by scrutinizing the annotated data. We introduce our custom hate speech detection dataset, HateSpeechCorpus, to conduct this research. Additionally, we perform the same experiments on the ETHOS (Mollas et al., 2022) dataset also for comparative analysis. This paper serves as a crucial resource, guiding researchers and practitioners in harnessing the potential of LLMs for dataannotation, thereby fostering advancements in this critical field. The HateSpeechCorpus dataset is available here: https://github.com/AmitDasRup123/HateSpeechCorpus

While prior work has examined the generation capabilities of Agentic AI systems, little is known about how reviewers respond to AI-authored code in practice. In this paper, we present a large-scale empirical study of code review dynamics in agent-generated PRs. Using a curated subset of the AIDev dataset, we analyze 19,450 inline review comments spanning 3,177 agent-authored PRs from real-world GitHub repositories. We first derive a taxonomy of 12 review comment themes using topic modeling combined with large language model (LLM)-assisted semantic clustering and consolidation. According to this taxonomy, we then investigate whether zero-shot prompts to LLM can reliably annotate review comments. Our evaluation against human annotations shows that open-source LLM achieves reasonably high exact match (78.63%), macro F1 score (0.78), and substantial agreement with human annotators at the review comment level. At the PR level, the LLM also correctly identifies the dominant review theme with 78% Top-1 accuracy and achieves an average Jaccard similarity of 0.76, indicating strong alignment with human judgments. Applying this annotation pipeline at scale, we find that apart from functional correctness and logical changes, reviews of agent-authored PRs predominantly focus on documentation gaps, refactoring needs, styling and formatting issues, with testing and security-related concerns. These findings suggest that while AI agents can accelerate code production, there remain gaps requiring targeted human review oversight.

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.

In this paper, we study how well humans can detect text generated by commercial LLMs (GPT-4o, Claude, o1). We hire annotators to read 300 non-fiction English articles, label them as either human-written or AI-generated, and provide paragraph-length explanations for their decisions. Our experiments show that annotators who frequently use LLMs for writing tasks excel at detecting AI-generated text, even without any specialized training or feedback. In fact, the majority vote among five such "expert" annotators misclassifies only 1 of 300 articles, significantly outperforming most commercial and open-source detectors we evaluated even in the presence of evasion tactics like paraphrasing and humanization. Qualitative analysis of the experts' free-form explanations shows that while they rely heavily on specific lexical clues ('AI vocabulary'), they also pick up on more complex phenomena within the text (e.g., formality, originality, clarity) that are challenging to assess for automatic detectors. We release our annotated dataset and code to spur future research into both human and automated detection of AI-generated text.

We introduce the AnnoPage Dataset, a novel collection of 7550 pages from historical documents, primarily in Czech and German, spanning from 1485 to the present, focusing on the late 19th and early 20th centuries. The dataset is designed to support research in document layout analysis and object detection. Each page is annotated with axis-aligned bounding boxes (AABB) representing elements of 25 categories of non-textual elements, such as images, maps, decorative elements, or charts, following the Czech Methodology of image document processing. The annotations were created by expert librarians to ensure accuracy and consistency. The dataset also incorporates pages from multiple, mainly historical, document datasets to enhance variability and maintain continuity. The dataset is divided into development and test subsets, with the test set carefully selected to maintain the category distribution. We provide baseline results using YOLO and DETR object detectors, offering a reference point for future research. The AnnoPage Dataset is publicly available on Zenodo (https://doi.org/10.5281/zenodo.12788419), along with ground-truth annotations in YOLO format.

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.

Real-world data for classification is often labeled by multiple annotators. For analyzing such data, we introduce CROWDLAB, a straightforward approach to utilize any trained classifier to estimate: (1) A consensus label for each example that aggregates the available annotations; (2) A confidence score for how likely each consensus label is correct; (3) A rating for each annotator quantifying the overall correctness of their labels. Existing algorithms to estimate related quantities in crowdsourcing often rely on sophisticated generative models with iterative inference. CROWDLAB instead uses a straightforward weighted ensemble. Existing algorithms often rely solely on annotator statistics, ignoring the features of the examples from which the annotations derive. CROWDLAB utilizes any classifier model trained on these features, and can thus better generalize between examples with similar features. On real-world multi-annotator image data, our proposed method provides superior estimates for (1)-(3) than existing algorithms like Dawid-Skene/GLAD.

When training data are collected from human annotators, the design of the annotation instrument, the instructions given to annotators, the characteristics of the annotators, and their interactions can impact training data. This study demonstrates that design choices made when creating an annotation instrument also impact the models trained on the resulting annotations. We introduce the term annotation sensitivity to refer to the impact of annotation data collection methods on the annotations themselves and on downstream model performance and predictions. We collect annotations of hate speech and offensive language in five experimental conditions of an annotation instrument, randomly assigning annotators to conditions. We then fine-tune BERT models on each of the five resulting datasets and evaluate model performance on a holdout portion of each condition. We find considerable differences between the conditions for 1) the share of hate speech/offensive language annotations, 2) model performance, 3) model predictions, and 4) model learning curves. Our results emphasize the crucial role played by the annotation instrument which has received little attention in the machine learning literature. We call for additional research into how and why the instrument impacts the annotations to inform the development of best practices in instrument design.

Large language models (LLMs) offer an inexpensive yet powerful way to annotate text, but are often inconsistent when compared with experts. These errors can bias downstream estimates of population parameters such as regression coefficients and causal effects. To mitigate this bias, researchers have developed debiasing methods such as Design-based Supervised Learning (DSL) and Prediction-Powered Inference (PPI), which promise valid estimation by combining LLM annotations with a limited number of expensive expert annotations. Although these methods produce consistent estimates under theoretical assumptions, it is unknown how they compare in finite samples of sizes encountered in applied research. We make two contributions: First, we study how each method's performance scales with the number of expert annotations, highlighting regimes where LLM bias or limited expert labels significantly affect results. Second, we compare DSL and PPI across a range of tasks, finding that although both achieve low bias with large datasets, DSL often outperforms PPI on bias reduction and empirical efficiency, but its performance is less consistent across datasets. Our findings indicate that there is a bias-variance tradeoff at the level of debiasing methods, calling for more research on developing metrics for quantifying their efficiency in finite samples.

Since FineWeb-Edu, data curation for LLM pretraining has predominantly relied on single scalar quality scores produced by small classifiers. A single score conflates multiple quality dimensions, prevents flexible filtering, and offers no interpretability. We introduce propella-1, a family of small multilingual LLMs (0.6B, 1.7B, 4B parameters) that annotate text documents across 18 properties organized into six categories: core content, classification, quality and value, audience and purpose, safety and compliance, and geographic relevance. The models support 57 languages and produce structured JSON annotations conforming to a predefined schema. Evaluated against a frontier commercial LLM as a reference annotator, the 4B model achieves higher agreement than much larger general-purpose models. We release propella-annotations, a dataset of over three billion document annotations covering major pretraining corpora including data from FineWeb-2, FinePDFs, HPLT 3.0, and Nemotron-CC. Using these annotations, we present a multi-dimensional compositional analysis of widely used pretraining datasets, revealing substantial differences in quality, reasoning depth, and content composition that single-score approaches cannot capture. All model weights and annotations are released under permissive, commercial-use licenses.

Medical research generates a large number of publications with the PubMed database already containing >35 million research articles. Integration of the knowledge scattered across this large body of literature could provide key insights into physiological mechanisms and disease processes leading to novel medical interventions. However, it is a great challenge for researchers to utilize this information in full since the scale and complexity of the data greatly surpasses human processing abilities. This becomes especially problematic in cases of extreme urgency like the COVID-19 pandemic. Automated text mining can help extract and connect information from the large body of medical research articles. The first step in text mining is typically the identification of specific classes of keywords (e.g., all protein or disease names), so called Named Entity Recognition (NER). Here we present an end-to-end pipeline for NER of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.

The DocRED dataset is one of the most popular and widely used benchmarks for document-level relation extraction (RE). It adopts a recommend-revise annotation scheme so as to have a large-scale annotated dataset. However, we find that the annotation of DocRED is incomplete, i.e., false negative samples are prevalent. We analyze the causes and effects of the overwhelming false negative problem in the DocRED dataset. To address the shortcoming, we re-annotate 4,053 documents in the DocRED dataset by adding the missed relation triples back to the original DocRED. We name our revised DocRED dataset Re-DocRED. We conduct extensive experiments with state-of-the-art neural models on both datasets, and the experimental results show that the models trained and evaluated on our Re-DocRED achieve performance improvements of around 13 F1 points. Moreover, we conduct a comprehensive analysis to identify the potential areas for further improvement. Our dataset is publicly available at https://github.com/tonytan48/Re-DocRED.

Keyphrase generation is the task of predicting a set of lexical units that conveys the main content of a source text. Existing datasets for keyphrase generation are only readily available for the scholarly domain and include non-expert annotations. In this paper we present KPTimes, a large-scale dataset of news texts paired with editor-curated keyphrases. Exploring the dataset, we show how editors tag documents, and how their annotations differ from those found in existing datasets. We also train and evaluate state-of-the-art neural keyphrase generation models on KPTimes to gain insights on how well they perform on the news domain. The dataset is available online at https://github.com/ygorg/KPTimes .

The increasing diversity of languages used on the web introduces a new level of complexity to Information Retrieval (IR) systems. We can no longer assume that textual content is written in one language or even the same language family. In this paper, we demonstrate how to build massive multilingual annotators with minimal human expertise and intervention. We describe a system that builds Named Entity Recognition (NER) annotators for 40 major languages using Wikipedia and Freebase. Our approach does not require NER human annotated datasets or language specific resources like treebanks, parallel corpora, and orthographic rules. The novelty of approach lies therein - using only language agnostic techniques, while achieving competitive performance. Our method learns distributed word representations (word embeddings) which encode semantic and syntactic features of words in each language. Then, we automatically generate datasets from Wikipedia link structure and Freebase attributes. Finally, we apply two preprocessing stages (oversampling and exact surface form matching) which do not require any linguistic expertise. Our evaluation is two fold: First, we demonstrate the system performance on human annotated datasets. Second, for languages where no gold-standard benchmarks are available, we propose a new method, distant evaluation, based on statistical machine translation.

We introduce TLDR generation, a new form of extreme summarization, for scientific papers. TLDR generation involves high source compression and requires expert background knowledge and understanding of complex domain-specific language. To facilitate study on this task, we introduce SciTLDR, a new multi-target dataset of 5.4K TLDRs over 3.2K papers. SciTLDR contains both author-written and expert-derived TLDRs, where the latter are collected using a novel annotation protocol that produces high-quality summaries while minimizing annotation burden. We propose CATTS, a simple yet effective learning strategy for generating TLDRs that exploits titles as an auxiliary training signal. CATTS improves upon strong baselines under both automated metrics and human evaluations. Data and code are publicly available at https://github.com/allenai/scitldr.

Fine-tuning pre-trained language models (PLMs), e.g., SciBERT, generally requires large numbers of annotated data to achieve state-of-the-art performance on a range of NLP tasks in the scientific domain. However, obtaining the fine-tune data for scientific NLP task is still challenging and expensive. Inspired by recent advancement in prompt learning, in this paper, we propose the Mix Prompt Tuning (MPT), which is a semi-supervised method to alleviate the dependence on annotated data and improve the performance of multi-granularity academic function recognition tasks with a small number of labeled examples. Specifically, the proposed method provides multi-perspective representations by combining manual prompt templates with automatically learned continuous prompt templates to help the given academic function recognition task take full advantage of knowledge in PLMs. Based on these prompt templates and the fine-tuned PLM, a large number of pseudo labels are assigned to the unlabeled examples. Finally, we fine-tune the PLM using the pseudo training set. We evaluate our method on three academic function recognition tasks of different granularity including the citation function, the abstract sentence function, and the keyword function, with datasets from computer science domain and biomedical domain. Extensive experiments demonstrate the effectiveness of our method and statistically significant improvements against strong baselines. In particular, it achieves an average increase of 5% in Macro-F1 score compared with fine-tuning, and 6% in Macro-F1 score compared with other semi-supervised method under low-resource settings. In addition, MPT is a general method that can be easily applied to other low-resource scientific classification tasks.

With the rapid growth of Web-based academic publications, more and more papers are being published annually, making it increasingly difficult to find relevant prior work. Citation prediction aims to automatically suggest appropriate references, helping scholars navigate the expanding scientific literature. Here we present CiteRAG, the first comprehensive retrieval-augmented generation (RAG)-integrated benchmark for evaluating large language models on academic citation prediction, featuring a multi-level retrieval strategy, specialized retrievers, and generators. Our benchmark makes four core contributions: (1) We establish two instances of the citation prediction task with different granularity. Task 1 focuses on coarse-grained list-specific citation prediction, while Task 2 targets fine-grained position-specific citation prediction. To enhance these two tasks, we build a dataset containing 7,267 instances for Task 1 and 8,541 instances for Task 2, enabling comprehensive evaluation of both retrieval and generation. (2) We construct a three-level large-scale corpus with 554k papers spanning many major subfields, using an incremental pipeline. (3) We propose a multi-level hybrid RAG approach for citation prediction, fine-tuning embedding models with contrastive learning to capture complex citation relationships, paired with specialized generation models. (4) We conduct extensive experiments across state-of-the-art language models, including closed-source APIs, open-source models, and our fine-tuned generators, demonstrating the effectiveness of our framework. Our open-source toolkit enables reproducible evaluation and focuses on academic literature, providing the first comprehensive evaluation framework for citation prediction and serving as a methodological template for other scientific domains. Our source code and data are released at https://github.com/LQgdwind/CiteRAG.

Peer reviewing is a central process in modern research and essential for ensuring high quality and reliability of published work. At the same time, it is a time-consuming process and increasing interest in emerging fields often results in a high review workload, especially for senior researchers in this area. How to cope with this problem is an open question and it is vividly discussed across all major conferences. In this work, we propose an Argument Mining based approach for the assistance of editors, meta-reviewers, and reviewers. We demonstrate that the decision process in the field of scientific publications is driven by arguments and automatic argument identification is helpful in various use-cases. One of our findings is that arguments used in the peer-review process differ from arguments in other domains making the transfer of pre-trained models difficult. Therefore, we provide the community with a new peer-review dataset from different computer science conferences with annotated arguments. In our extensive empirical evaluation, we show that Argument Mining can be used to efficiently extract the most relevant parts from reviews, which are paramount for the publication decision. The process remains interpretable since the extracted arguments can be highlighted in a review without detaching them from their context.

Publishing open-source academic video recordings is an emergent and prevalent approach to sharing knowledge online. Such videos carry rich multimodal information including speech, the facial and body movements of the speakers, as well as the texts and pictures in the slides and possibly even the papers. Although multiple academic video datasets have been constructed and released, few of them support both multimodal content recognition and understanding tasks, which is partially due to the lack of high-quality human annotations. In this paper, we propose a novel multimodal, multigenre, and multipurpose audio-visual academic lecture dataset (M^3AV), which has almost 367 hours of videos from five sources covering computer science, mathematics, and medical and biology topics. With high-quality human annotations of the spoken and written words, in particular high-valued name entities, the dataset can be used for multiple audio-visual recognition and understanding tasks. Evaluations performed on contextual speech recognition, speech synthesis, and slide and script generation tasks demonstrate that the diversity of M^3AV makes it a challenging dataset.

Large language models (LLMs) have demonstrated potential in assisting scientific research, yet their ability to discover high-quality research hypotheses remains unexamined due to the lack of a dedicated benchmark. To address this gap, we introduce the first large-scale benchmark for evaluating LLMs with a near-sufficient set of sub-tasks of scientific discovery: inspiration retrieval, hypothesis composition, and hypothesis ranking. We develop an automated framework that extracts critical components - research questions, background surveys, inspirations, and hypotheses - from scientific papers across 12 disciplines, with expert validation confirming its accuracy. To prevent data contamination, we focus exclusively on papers published in 2024, ensuring minimal overlap with LLM pretraining data. Our evaluation reveals that LLMs perform well in retrieving inspirations, an out-of-distribution task, suggesting their ability to surface novel knowledge associations. This positions LLMs as "research hypothesis mines", capable of facilitating automated scientific discovery by generating innovative hypotheses at scale with minimal human intervention.

The vast majority of existing datasets for Named Entity Recognition (NER) are built primarily on news, research papers and Wikipedia with a few exceptions, created from historical and literary texts. What is more, English is the main source for data for further labelling. This paper aims to fill in multiple gaps by creating a novel dataset "Razmecheno", gathered from the diary texts of the project "Prozhito" in Russian. Our dataset is of interest for multiple research lines: literary studies of diary texts, transfer learning from other domains, low-resource or cross-lingual named entity recognition. Razmecheno comprises 1331 sentences and 14119 tokens, sampled from diaries, written during the Perestroika. The annotation schema consists of five commonly used entity tags: person, characteristics, location, organisation, and facility. The labelling is carried out on the crowdsourcing platfrom Yandex.Toloka in two stages. First, workers selected sentences, which contain an entity of particular type. Second, they marked up entity spans. As a result 1113 entities were obtained. Empirical evaluation of Razmecheno is carried out with off-the-shelf NER tools and by fine-tuning pre-trained contextualized encoders. We release the annotated dataset for open access.

Many recent approaches to natural language tasks are built on the remarkable abilities of large language models. Large language models can perform in-context learning, where they learn a new task from a few task demonstrations, without any parameter updates. This work examines the implications of in-context learning for the creation of datasets for new natural language tasks. Departing from recent in-context learning methods, we formulate an annotation-efficient, two-step framework: selective annotation that chooses a pool of examples to annotate from unlabeled data in advance, followed by prompt retrieval that retrieves task examples from the annotated pool at test time. Based on this framework, we propose an unsupervised, graph-based selective annotation method, voke-k, to select diverse, representative examples to annotate. Extensive experiments on 10 datasets (covering classification, commonsense reasoning, dialogue, and text/code generation) demonstrate that our selective annotation method improves the task performance by a large margin. On average, vote-k achieves a 12.9%/11.4% relative gain under an annotation budget of 18/100, as compared to randomly selecting examples to annotate. Compared to state-of-the-art supervised finetuning approaches, it yields similar performance with 10-100x less annotation cost across 10 tasks. We further analyze the effectiveness of our framework in various scenarios: language models with varying sizes, alternative selective annotation methods, and cases where there is a test data domain shift. We hope that our studies will serve as a basis for data annotations as large language models are increasingly applied to new tasks. Our code is available at https://github.com/HKUNLP/icl-selective-annotation.

Political scientists are rapidly adopting large language models (LLMs) for text annotation, yet the sensitivity of annotation results to implementation choices remains poorly understood. Most evaluations test a single model or configuration; how model choice, model size, learning approach, and prompt style interact, and whether popular "best practices" survive controlled comparison, are largely unexplored. We present a controlled evaluation of these pipeline choices, testing six open-weight models across four political science annotation tasks under identical quantisation, hardware, and prompt-template conditions. Our central finding is methodological: interaction effects dominate main effects, so seemingly reasonable pipeline choices can become consequential researcher degrees of freedom. No single model, prompt style, or learning approach is uniformly superior, and the best-performing model varies across tasks. Two corollaries follow. First, model size is an unreliable guide both to cost and to performance: cross-family efficiency differences are so large that some larger models are less resource-intensive than much smaller alternatives, while within model families mid-range variants often match or exceed larger counterparts. Second, widely recommended prompt engineering techniques yield inconsistent and sometimes negative effects on annotation performance. We use these benchmark results to develop a validation-first framework - with a principled ordering of pipeline decisions, guidance on prompt freezing and held-out evaluation, reporting standards, and open-source tools - to help researchers navigate this decision space transparently.

In this paper we address the scarcity of annotated data for NArabizi, a Romanized form of North African Arabic used mostly on social media, which poses challenges for Natural Language Processing (NLP). We introduce an enriched version of NArabizi Treebank (Seddah et al., 2020) with three main contributions: the addition of two novel annotation layers (named entity recognition and offensive language detection) and a re-annotation of the tokenization, morpho-syntactic and syntactic layers that ensure annotation consistency. Our experimental results, using different tokenization schemes, showcase the value of our contributions and highlight the impact of working with non-gold tokenization for NER and dependency parsing. To facilitate future research, we make these annotations publicly available. Our enhanced NArabizi Treebank paves the way for creating sophisticated language models and NLP tools for this under-represented language.

Current state-of-the-art methods for object detection rely on annotated bounding boxes of large data sets for training. However, obtaining such annotations is expensive and can require up to hundreds of hours of manual labor. This poses a challenge, especially since such annotations can only be provided by experts, as they require knowledge about the scientific domain. To tackle this challenge, we propose a domain-specific weakly supervised object detection algorithm that only relies on image-level annotations, which are significantly easier to acquire. Our method distills the knowledge of a pre-trained model, on the task of predicting the presence or absence of a virus in an image, to obtain a set of pseudo-labels that can be used to later train a state-of-the-art object detection model. To do so, we use an optimization approach with a shrinking receptive field to extract virus particles directly without specific network architectures. Through a set of extensive studies, we show how the proposed pseudo-labels are easier to obtain, and, more importantly, are able to outperform other existing weak labeling methods, and even ground truth labels, in cases where the time to obtain the annotation is limited.

The success of deep learning has sparked interest in improving relational table tasks, like data preparation and search, with table representation models trained on large table corpora. Existing table corpora primarily contain tables extracted from HTML pages, limiting the capability to represent offline database tables. To train and evaluate high-capacity models for applications beyond the Web, we need resources with tables that resemble relational database tables. Here we introduce GitTables, a corpus of 1M relational tables extracted from GitHub. Our continuing curation aims at growing the corpus to at least 10M tables. Analyses of GitTables show that its structure, content, and topical coverage differ significantly from existing table corpora. We annotate table columns in GitTables with semantic types, hierarchical relations and descriptions from Schema.org and DBpedia. The evaluation of our annotation pipeline on the T2Dv2 benchmark illustrates that our approach provides results on par with human annotations. We present three applications of GitTables, demonstrating its value for learned semantic type detection models, schema completion methods, and benchmarks for table-to-KG matching, data search, and preparation. We make the corpus and code available at https://gittables.github.io.

As large language models reshape scientific research, literature retrieval faces a twofold challenge: ensuring source authenticity while maintaining a deep comprehension of academic search intents. While reliable, traditional keyword-centric search fails to capture complex research intents. Frontier LLMs can handle complex research intents, but their high cost and tendency to hallucinate remain key limitations. Here we introduce PaSaMaster, a self-evolving agentic literature retrieval system that produces relevance-scored paper rankings with evidence-grounded recommendations through iterative intent analysis, retrieval, and ranking. It is built on three key designs. First, it transforms literature retrieval from a one shot query--document matching problem into a search process that evolves over time, using ranked evidence to reveal gaps, refine intents, and guide follow-up searches. Second, it prevents hallucinated sources by treating retrieval as intent--paper relevance ranking rather than generation. Finally, PaSaMaster improves cost efficiency by separating planning from retrieval: a frontier LLM is used only for intent understanding, while large scale retrieval and relevance scoring are delegated to customized corpora and lightweight models. Evaluated on the PaSaMaster Benchmark across 38 scientific disciplines, our system exposes the severe inaccuracy and incompleteness of traditional keyword retrieval (improving F1-score by 15.6X) and the unreliability of generative LLMs (which exhibit hallucination rates up to 37.79%). Remarkably, PaSaMaster outperforms GPT-5.2 by 30.0% at a mere 1% of the computational cost while ensuring zero source hallucination: https://github.com/sjtu-sai-agents/PaSaMaster

We present POTATO, the Portable text annotation tool, a free, fully open-sourced annotation system that 1) supports labeling many types of text and multimodal data; 2) offers easy-to-configure features to maximize the productivity of both deployers and annotators (convenient templates for common ML/NLP tasks, active learning, keypress shortcuts, keyword highlights, tooltips); and 3) supports a high degree of customization (editable UI, inserting pre-screening questions, attention and qualification tests). Experiments over two annotation tasks suggest that POTATO improves labeling speed through its specially-designed productivity features, especially for long documents and complex tasks. POTATO is available at https://github.com/davidjurgens/potato and will continue to be updated.

Data annotation is an essential step for constructing new datasets. However, the conventional approach of data annotation through crowdsourcing is both time-consuming and expensive. In addition, the complexity of this process increases when dealing with low-resource languages owing to the difference in the language pool of crowdworkers. To address these issues, this study proposes an autonomous annotation method by utilizing large language models, which have been recently demonstrated to exhibit remarkable performance. Through our experiments, we demonstrate that the proposed method is not just cost-efficient but also applicable for low-resource language annotation. Additionally, we constructed an image captioning dataset using our approach and are committed to open this dataset for future study. We have opened our source code for further study and reproducibility.

Large Language Models (LLMs)' search capabilities have garnered significant attention. Existing benchmarks, such as OpenAI's BrowseComp, primarily focus on general search scenarios and fail to adequately address the specific demands of academic search. These demands include deeper literature tracing and organization, professional support for academic databases, the ability to navigate long-tail academic knowledge, and ensuring academic rigor. Here, we proposed ScholarSearch, the first dataset specifically designed to evaluate the complex information retrieval capabilities of Large Language Models (LLMs) in academic research. ScholarSearch possesses the following key characteristics: Academic Practicality, where question content closely mirrors real academic learning and research environments, avoiding deliberately misleading models; High Difficulty, with answers that are challenging for single models (e.g., Grok DeepSearch or Gemini Deep Research) to provide directly, often requiring at least three deep searches to derive; Concise Evaluation, where limiting conditions ensure answers are as unique as possible, accompanied by clear sources and brief solution explanations, greatly facilitating subsequent audit and verification, surpassing the current lack of analyzed search datasets both domestically and internationally; and Broad Coverage, as the dataset spans at least 15 different academic disciplines. Through ScholarSearch, we expect to more precisely measure and promote the performance improvement of LLMs in complex academic information retrieval tasks. The data is available at: https://huggingface.co/datasets/PKU-DS-LAB/ScholarSearch

We present ShapeNet: a richly-annotated, large-scale repository of shapes represented by 3D CAD models of objects. ShapeNet contains 3D models from a multitude of semantic categories and organizes them under the WordNet taxonomy. It is a collection of datasets providing many semantic annotations for each 3D model such as consistent rigid alignments, parts and bilateral symmetry planes, physical sizes, keywords, as well as other planned annotations. Annotations are made available through a public web-based interface to enable data visualization of object attributes, promote data-driven geometric analysis, and provide a large-scale quantitative benchmark for research in computer graphics and vision. At the time of this technical report, ShapeNet has indexed more than 3,000,000 models, 220,000 models out of which are classified into 3,135 categories (WordNet synsets). In this report we describe the ShapeNet effort as a whole, provide details for all currently available datasets, and summarize future plans.

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

We present DreamPoster, a Text-to-Image generation framework that intelligently synthesizes high-quality posters from user-provided images and text prompts while maintaining content fidelity and supporting flexible resolution and layout outputs. Specifically, DreamPoster is built upon our T2I model, Seedream3.0 to uniformly process different poster generating types. For dataset construction, we propose a systematic data annotation pipeline that precisely annotates textual content and typographic hierarchy information within poster images, while employing comprehensive methodologies to construct paired datasets comprising source materials (e.g., raw graphics/text) and their corresponding final poster outputs. Additionally, we implement a progressive training strategy that enables the model to hierarchically acquire multi-task generation capabilities while maintaining high-quality generation. Evaluations on our testing benchmarks demonstrate DreamPoster's superiority over existing methods, achieving a high usability rate of 88.55\%, compared to GPT-4o (47.56\%) and SeedEdit3.0 (25.96\%). DreamPoster will be online in Jimeng and other Bytedance Apps.

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

Many NLP applications require manual data annotations for a variety of tasks, notably to train classifiers or evaluate the performance of unsupervised models. Depending on the size and degree of complexity, the tasks may be conducted by crowd-workers on platforms such as MTurk as well as trained annotators, such as research assistants. Using a sample of 2,382 tweets, we demonstrate that ChatGPT outperforms crowd-workers for several annotation tasks, including relevance, stance, topics, and frames detection. Specifically, the zero-shot accuracy of ChatGPT exceeds that of crowd-workers for four out of five tasks, while ChatGPT's intercoder agreement exceeds that of both crowd-workers and trained annotators for all tasks. Moreover, the per-annotation cost of ChatGPT is less than $0.003 -- about twenty times cheaper than MTurk. These results show the potential of large language models to drastically increase the efficiency of text classification.

This paper proposes a novel named entity recognition (NER) technique specifically tailored for the open-source software systems. Our approach aims to address the scarcity of annotated software data by employing a comprehensive two-step distantly supervised annotation process. This process strategically leverages language heuristics, unique lookup tables, external knowledge sources, and an active learning approach. By harnessing these powerful techniques, we not only enhance model performance but also effectively mitigate the limitations associated with cost and the scarcity of expert annotators. It is noteworthy that our framework significantly outperforms the state-of-the-art LLMs by a substantial margin. We also show the effectiveness of NER in the downstream task of relation extraction.

Scientific discoveries must be communicated clearly to realize their full potential. Without effective communication, even the most groundbreaking findings risk being overlooked or misunderstood. The primary way scientists communicate their work and receive feedback from the community is through peer review. However, the current system often provides inconsistent feedback between reviewers, ultimately hindering the improvement of a manuscript and limiting its potential impact. In this paper, we introduce a novel method APRES powered by Large Language Models (LLMs) to update a scientific papers text based on an evaluation rubric. Our automated method discovers a rubric that is highly predictive of future citation counts, and integrate it with APRES in an automated system that revises papers to enhance their quality and impact. Crucially, this objective should be met without altering the core scientific content. We demonstrate the success of APRES, which improves future citation prediction by 19.6% in mean averaged error over the next best baseline, and show that our paper revision process yields papers that are preferred over the originals by human expert evaluators 79% of the time. Our findings provide strong empirical support for using LLMs as a tool to help authors stress-test their manuscripts before submission. Ultimately, our work seeks to augment, not replace, the essential role of human expert reviewers, for it should be humans who discern which discoveries truly matter, guiding science toward advancing knowledge and enriching lives.

In recent decades, chemistry publications and patents have increased rapidly. A significant portion of key information is embedded in molecular structure figures, complicating large-scale literature searches and limiting the application of large language models in fields such as biology, chemistry, and pharmaceuticals. The automatic extraction of precise chemical structures is of critical importance. However, the presence of numerous Markush structures in real-world documents, along with variations in molecular image quality, drawing styles, and noise, significantly limits the performance of existing optical chemical structure recognition (OCSR) methods. We present MolParser, a novel end-to-end OCSR method that efficiently and accurately recognizes chemical structures from real-world documents, including difficult Markush structure. We use a extended SMILES encoding rule to annotate our training dataset. Under this rule, we build MolParser-7M, the largest annotated molecular image dataset to our knowledge. While utilizing a large amount of synthetic data, we employed active learning methods to incorporate substantial in-the-wild data, specifically samples cropped from real patents and scientific literature, into the training process. We trained an end-to-end molecular image captioning model, MolParser, using a curriculum learning approach. MolParser significantly outperforms classical and learning-based methods across most scenarios, with potential for broader downstream applications. The dataset is publicly available.

The automation of scientific discovery represents a critical milestone in Artificial Intelligence (AI) research. However, existing agentic systems for science suffer from two fundamental limitations: rigid, pre-programmed workflows that cannot adapt to intermediate findings, and inadequate context management that hinders long-horizon research. We present freephdlabor, an open-source multiagent framework featuring fully dynamic workflows determined by real-time agent reasoning and a \textit{modular architecture} enabling seamless customization -- users can modify, add, or remove agents to address domain-specific requirements. The framework provides comprehensive infrastructure including automatic context compaction, workspace-based communication to prevent information degradation, memory persistence across sessions, and non-blocking human intervention mechanisms. These features collectively transform automated research from isolated, single-run attempts into continual research programs that build systematically on prior explorations and incorporate human feedback. By providing both the architectural principles and practical implementation for building customizable co-scientist systems, this work aims to facilitate broader adoption of automated research across scientific domains, enabling practitioners to deploy interactive multiagent systems that autonomously conduct end-to-end research -- from ideation through experimentation to publication-ready manuscripts.

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.

The peer review process is crucial for ensuring the quality and reliability of scholarly work, yet assigning suitable reviewers remains a significant challenge. Traditional manual methods are labor-intensive and often ineffective, leading to nonconstructive or biased reviews. This paper introduces the exHarmony (eHarmony but for connecting experts to manuscripts) benchmark, designed to address these challenges by re-imagining the Reviewer Assignment Problem (RAP) as a retrieval task. Utilizing the extensive data from OpenAlex, we propose a novel approach that considers a host of signals from the authors, most similar experts, and the citation relations as potential indicators for a suitable reviewer for a manuscript. This approach allows us to develop a standard benchmark dataset for evaluating the reviewer assignment problem without needing explicit labels. We benchmark various methods, including traditional lexical matching, static neural embeddings, and contextualized neural embeddings, and introduce evaluation metrics that assess both relevance and diversity in the context of RAP. Our results indicate that while traditional methods perform reasonably well, contextualized embeddings trained on scholarly literature show the best performance. The findings underscore the importance of further research to enhance the diversity and effectiveness of reviewer assignments.

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.

Long-form article generation (LFAG) presents challenges such as maintaining logical consistency, comprehensive topic coverage, and narrative coherence across extended articles. Existing datasets often lack both the hierarchical structure and fine-grained annotation needed to effectively decompose tasks, resulting in shallow, disorganized article generation. To address these limitations, we introduce DeFine, a Decomposed and Fine-grained annotated dataset for long-form article generation. DeFine is characterized by its hierarchical decomposition strategy and the integration of domain-specific knowledge with multi-level annotations, ensuring granular control and enhanced depth in article generation. To construct the dataset, a multi-agent collaborative pipeline is proposed, which systematically segments the generation process into four parts: Data Miner, Cite Retreiver, Q&A Annotator and Data Cleaner. To validate the effectiveness of DeFine, we designed and tested three LFAG baselines: the web retrieval, the local retrieval, and the grounded reference. We fine-tuned the Qwen2-7b-Instruct model using the DeFine training dataset. The experimental results showed significant improvements in text quality, specifically in topic coverage, depth of information, and content fidelity. Our dataset publicly available to facilitate future research.

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

Multimodal Review Helpfulness Prediction (MRHP) is an essential task in recommender systems, particularly in E-commerce platforms. Determining the helpfulness of user-generated reviews enhances user experience and improves consumer decision-making. However, existing datasets focus predominantly on English and Indonesian, resulting in a lack of linguistic diversity, especially for low-resource languages such as Vietnamese. In this paper, we introduce ViMRHP (Vietnamese Multimodal Review Helpfulness Prediction), a large-scale benchmark dataset for MRHP task in Vietnamese. This dataset covers four domains, including 2K products with 46K reviews. Meanwhile, a large-scale dataset requires considerable time and cost. To optimize the annotation process, we leverage AI to assist annotators in constructing the ViMRHP dataset. With AI assistance, annotation time is reduced (90 to 120 seconds per task down to 20 to 40 seconds per task) while maintaining data quality and lowering overall costs by approximately 65%. However, AI-generated annotations still have limitations in complex annotation tasks, which we further examine through a detailed performance analysis. In our experiment on ViMRHP, we evaluate baseline models on human-verified and AI-generated annotations to assess their quality differences. The ViMRHP dataset is publicly available at https://github.com/trng28/ViMRHP

Researchers often summarize their work in the form of posters. Posters provide a coherent and efficient way to convey core ideas from scientific papers. Generating a good scientific poster, however, is a complex and time consuming cognitive task, since such posters need to be readable, informative, and visually aesthetic. In this paper, for the first time, we study the challenging problem of learning to generate posters from scientific papers. To this end, a data-driven framework, that utilizes graphical models, is proposed. Specifically, given content to display, the key elements of a good poster, including panel layout and attributes of each panel, are learned and inferred from data. Then, given inferred layout and attributes, composition of graphical elements within each panel is synthesized. To learn and validate our model, we collect and make public a Poster-Paper dataset, which consists of scientific papers and corresponding posters with exhaustively labelled panels and attributes. Qualitative and quantitative results indicate the effectiveness of our approach.

With the advancement of AI capabilities, AI reviewers are beginning to be deployed in scientific peer review, yet their capability and credibility remain in question: many scientists simply view them as probabilistic systems without the expertise to evaluate research, while other researchers are more optimistic about their readiness without concrete evidence. Understanding what AI reviewers do well, where they fall short, and what challenges remain is essential. However, existing evaluations of AI reviewers have focused on whether their verdicts match human verdicts (e.g., score alignment, acceptance prediction), which is insufficient to characterize their capabilities and limits. In this paper, we close this gap through a large-scale expert annotation study, in which 45 domain scientists in Physical, Biological, and Health Sciences spent 469 hours rating 2,960 individual criticisms (each targeting one specific aspect of a paper) from human-written and AI-generated reviews of 82 Nature-family papers on correctness, significance, and sufficiency of evidence. On a composite of all three dimensions, a reviewing agent powered by GPT-5.2 scores above each paper's top-rated human reviewer (60.0% vs. 48.2%, p = 0.009), while all three AI reviewers (including Gemini 3.0 Pro and Claude Opus 4.5) exceed the lowest-rated human across every dimension. AI reviewers' accurate criticisms are also more often rated significant and well-evidenced, and surface a distinct 26% of issues no human raises. However, AI reviewers overlap far more than humans do (21% vs. 3% for cross-reviewer pairs), and exhibit 16 recurring weaknesses humans do not share, such as limited subfield knowledge, lack of long context management over multiple files, and overly critical stance on minor issues. Overall, our results position current AI reviewers as complements to, not substitutes for, human reviewers.

Academic writing requires both coherent text generation and precise citation of relevant literature. Although recent Retrieval-Augmented Generation (RAG) systems have significantly improved factual accuracy in general-purpose text generation, their capacity to adequately support professional academic writing remains limited. In this work, we introduce ScholarCopilot, a unified framework designed to enhance existing large language models for generating professional academic articles with accurate and contextually relevant citations. ScholarCopilot dynamically determines when to retrieve scholarly references by generating a retrieval token [RET], and then utilizes its representation to look up relevant citations from a database. The retrieved references are fed into the model to augment the generation process. We jointly optimize both the generation and citation tasks within a single framework to increase efficiency. Trained on 500K papers from arXiv, our model achieves a top-1 retrieval accuracy of 40.1% on our evaluation dataset, outperforming baselines such as E5-Mistral-7B-Instruct (15.0%) and BM25 (9.8%). On a dataset of 1,000 academic writing samples, ScholarCopilot scores 16.2/25 in generation quality (measured across relevance, coherence, academic rigor, completeness, and innovation), surpassing models with 10x more parameters such as Qwen-2.5-72B-Instruct (15.8/25). Human studies also confirm ScholarCopilot's superior performance in citation recall, writing efficiency, and overall user experience, confirming the effectiveness of our approach.

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.

As text generated by large language models proliferates, it becomes vital to understand how humans engage with such text, and whether or not they are able to detect when the text they are reading did not originate with a human writer. Prior work on human detection of generated text focuses on the case where an entire passage is either human-written or machine-generated. In this paper, we study a more realistic setting where text begins as human-written and transitions to being generated by state-of-the-art neural language models. We show that, while annotators often struggle at this task, there is substantial variance in annotator skill and that given proper incentives, annotators can improve at this task over time. Furthermore, we conduct a detailed comparison study and analyze how a variety of variables (model size, decoding strategy, fine-tuning, prompt genre, etc.) affect human detection performance. Finally, we collect error annotations from our participants and use them to show that certain textual genres influence models to make different types of errors and that certain sentence-level features correlate highly with annotator selection. We release the RoFT dataset: a collection of over 21,000 human annotations paired with error classifications to encourage future work in human detection and evaluation of generated text.

The rise of large language models (LLMs) has brought a critical need for high-quality human-labeled data, particularly for processes like human feedback and evaluation. A common practice is to label data via consensus annotation over crowdworker judgments. However, annotators' judgments for subjective tasks can differ in many ways: they may have different qualitative judgments about an example, and they may map those to a labeling scheme in different ways. We show that these nuances can be captured by natural language explanations, and propose a method to rescale ordinal annotations and explanations using LLMs. Specifically, we feed annotators' Likert ratings and corresponding explanations into an LLM and prompt it to produce a numeric score anchored in a scoring rubric. These scores should reflect the annotators' underlying assessments of the example. The rubric can be designed or modified after annotation, and include distinctions that may not have been known when the original error taxonomy was devised. We explore our technique in the context of rating system outputs for a document-grounded question answering task, where LLMs achieve near-human performance. Our method rescales the raw judgments without impacting agreement and brings the scores closer to human judgments grounded in the same scoring rubric.

Text-based foundation models have become an important part of scientific discovery, with molecular foundation models accelerating advancements in material science and molecular design.However, existing models are constrained by closed-vocabulary tokenizers that capture only a fraction of molecular space. In this work, we systematically evaluate 34 tokenizers, including 19 chemistry-specific ones, and reveal significant gaps in their coverage of the SMILES molecular representation. To assess the impact of tokenizer choice, we introduce n-gram language models as a low-cost proxy and validate their effectiveness by pretraining and finetuning 18 RoBERTa-style encoders for molecular property prediction. To overcome the limitations of existing tokenizers, we propose two new tokenizers -- Smirk and Smirk-GPE -- with full coverage of the OpenSMILES specification. The proposed tokenizers systematically integrate nuclear, electronic, and geometric degrees of freedom; facilitating applications in pharmacology, agriculture, biology, and energy storage. Our results highlight the need for open-vocabulary modeling and chemically diverse benchmarks in cheminformatics.

AI co-scientists are emerging as a tool to assist human researchers in achieving their research goals. A crucial feature of these AI co-scientists is the ability to generate a research plan given a set of aims and constraints. The plan may be used by researchers for brainstorming, or may even be implemented after further refinement. However, language models currently struggle to generate research plans that follow all constraints and implicit requirements. In this work, we study how to leverage the vast corpus of existing research papers to train language models that generate better research plans. We build a scalable, diverse training corpus by automatically extracting research goals and goal-specific grading rubrics from papers across several domains. We then train models for research plan generation via reinforcement learning with self-grading. A frozen copy of the initial policy acts as the grader during training, with the rubrics creating a generator-verifier gap that enables improvements without external human supervision. To validate this approach, we conduct a study with human experts for machine learning research goals, spanning 225 hours. The experts prefer plans generated by our finetuned Qwen3-30B-A3B model over the initial model for 70% of research goals, and approve 84% of the automatically extracted goal-specific grading rubrics. To assess generality, we also extend our approach to research goals from medical papers, and new arXiv preprints, evaluating with a jury of frontier models. Our finetuning yields 12-22% relative improvements and significant cross-domain generalization, proving effective even in problem settings like medical research where execution feedback is infeasible. Together, these findings demonstrate the potential of a scalable, automated training recipe as a step towards improving general AI co-scientists.

Engaging the public with science is critical for a well-informed population. A popular method of scientific communication is documentaries. Once released, it can be difficult to assess the impact of such works on a large scale, due to the overhead required for in-depth audience feedback studies. In what follows, we overview our complementary approach to qualitative studies through quantitative impact and sentiment analysis of Amazon reviews for several scientific documentaries. In addition to developing a novel impact category taxonomy for this analysis, we release a dataset containing 1296 human-annotated sentences from 1043 Amazon reviews for six movies created in whole or part by a team of visualization designers who focus on cinematic presentations of scientific data. Using this data, we train and evaluate several machine learning and large language models, discussing their effectiveness and possible generalizability for documentaries beyond those focused on for this work. Themes are also extracted from our annotated dataset which, along with our large language model analysis, demonstrate a measure of the ability of scientific documentaries to engage with the public.

Skill extraction and recommendation systems have been studied from recruiter, applicant, and education perspectives. While AI applications in job advertisements have received broad attention, deficiencies in the instructed skills side remain a challenge. In this work, we address the scarcity of publicly available datasets by releasing both manually annotated and synthetic datasets of skills from the European Skills, Competences, Qualifications and Occupations (ESCO) taxonomy and university course pairs and publishing corresponding annotation guidelines. Specifically, we match graduate-level university courses with skills from the Systems Analysts and Management and Organization Analyst ESCO occupation groups at two granularities: course title with a skill, and course sentence with a skill. We train language models on this dataset to serve as a baseline for retrieval and recommendation systems for course-to-skill and skill-to-course matching. We evaluate the models on a portion of the annotated data. Our BERT model achieves 87% F1-score, showing that course and skill matching is a feasible task.