Daily Papers

Agents based on Large Language Models (LLMs) have shown promise for performing sophisticated software engineering tasks autonomously. In addition, there has been progress towards developing agents that can perform parts of the research pipeline in machine learning and the natural sciences. We argue that research extension and its implementation is a critical capability for such systems, and introduce RExBench to support the evaluation of this capability. RExBench is a benchmark consisting of 12 realistic research experiment implementation tasks that aim to investigate research hypotheses that have not previously been implemented. Each task is set up as an extension to an existing research paper and codebase, accompanied by domain expert-written instructions. RExBench is robust to data contamination, and supports an automatic evaluation infrastructure that executes agent outputs to determine whether the success criteria are met. We use this benchmark to evaluate nine LLM agents implemented using three different frameworks: aider, Claude Code, and OpenHands. We find that all agents evaluated fail to autonomously implement the majority of the extensions. Although the success rate improves with additional human-written hints, the best performance under this setting remains below 40%. This indicates that current agents are still short of being able to handle realistic research extension tasks without substantial human guidance.

PubMed-OCR is an OCR-centric corpus of scientific articles derived from PubMed Central Open Access PDFs. Each page image is annotated with Google Cloud Vision and released in a compact JSON schema with word-, line-, and paragraph-level bounding boxes. The corpus spans 209.5K articles (1.5M pages; ~1.3B words) and supports layout-aware modeling, coordinate-grounded QA, and evaluation of OCR-dependent pipelines. We analyze corpus characteristics (e.g., journal coverage and detected layout features) and discuss limitations, including reliance on a single OCR engine and heuristic line reconstruction. We release the data and schema to facilitate downstream research and invite extensions.

Tool-integrated reasoning has emerged as a key focus for enabling agentic applications. Among these, DeepResearch Agents have gained significant attention for their strong performance on complex, open-ended information-seeking tasks. We introduce Fathom-DeepResearch, an agentic system composed of two specialized models. The first is Fathom-Search-4B, a DeepSearch model trained from Qwen3-4B and optimized for evidence-based investigation through live web search and targeted webpage querying. Its training combines three advances: (i) DUETQA, a 5K-sample dataset generated via multi-agent self-play that enforces strict web-search dependence and heterogeneous source grounding; (ii) RAPO, a zero-overhead extension of GRPO that stabilizes multi-turn Reinforcement Learning with Verifiable Rewards through curriculum pruning, reward-aware advantage scaling, and per-prompt replay buffers; and (iii) a steerable step-level reward that classifies each tool call by cognitive behavior and marginal utility, enabling explicit control over search trajectory breadth, depth, and horizon. These improvements enable reliable extension of tool-calling beyond 20 calls when warranted. The second is Fathom-Synthesizer-4B, trained from Qwen3-4B, which converts multi-turn DeepSearch traces into structured, citation-dense DeepResearch Reports for comprehensive synthesis. Evaluated on DeepSearch benchmarks (SimpleQA, FRAMES, WebWalker, Seal0, MuSiQue) and DeepResearch-Bench, the system achieves state-of-the-art performance in the open-weights category while demonstrating strong generalization to diverse reasoning tasks including HLE, AIME-25, GPQA-Diamond, and MedQA.

Process Reward Models (PRMs) provide step-level supervision that improves the reliability of reasoning in large language models. While PRMs have been extensively studied in text-based domains, their extension to Vision Language Models (VLMs) remains limited. Existing Vision-Language PRMs (VL-PRMs) rely on Monte Carlo Tree Search (MCTS) for data construction, which can often produce noisy supervision signals and limit generalization across tasks. In this work, we aim to elucidate the design space of VL-PRMs by exploring diverse strategies for dataset construction, training, and test-time scaling. First, we introduce a hybrid data synthesis framework that combines MCTS with judgments from a strong VLM, producing more accurate step-level labels. Second, we propose perception-focused supervision, enabling our PRM to explicitly detect errors at the visual grounding stage of reasoning. Third, we systematically evaluate multiple test-time scaling strategies, showing that our PRMs can reliably guide VLMs toward more accurate solutions. Our experiments covering five diverse multimodal benchmarks (MMMU, PuzzleVQA, AlgoPuzzleVQA, MathVista, and MathVision) reveal several key insights: (i) VL-PRMs when used as Outcome Reward Models (ORMs) during test-time scaling (TTS) can outperform VL-PRM guided process step selection, (ii) smaller VL-PRMs can match or even surpass larger ones in detecting process errors, (iii) VL-PRMs uncover latent reasoning abilities in stronger VLM backbones, (iv) perception-level supervision leads to significant gains in test-time scaling, and (v) TTS performance of different policies improve on advanced math reasoning datasets despite not training VL-PRMs on such datasets. We hope our work will motivate further research and support the advancement of VLMs.

The emerging area of computational pathology (CPath) is ripe ground for the application of deep learning (DL) methods to healthcare due to the sheer volume of raw pixel data in whole-slide images (WSIs) of cancerous tissue slides. However, it is imperative for the DL algorithms relying on nuclei-level details to be able to cope with data from `the clinical wild', which tends to be quite challenging. We study, and extend recently released PanNuke dataset consisting of ~200,000 nuclei categorized into 5 clinically important classes for the challenging tasks of segmenting and classifying nuclei in WSIs. Previous pan-cancer datasets consisted of only up to 9 different tissues and up to 21,000 unlabeled nuclei and just over 24,000 labeled nuclei with segmentation masks. PanNuke consists of 19 different tissue types that have been semi-automatically annotated and quality controlled by clinical pathologists, leading to a dataset with statistics similar to the clinical wild and with minimal selection bias. We study the performance of segmentation and classification models when applied to the proposed dataset and demonstrate the application of models trained on PanNuke to whole-slide images. We provide comprehensive statistics about the dataset and outline recommendations and research directions to address the limitations of existing DL tools when applied to real-world CPath applications.

While Large Language Models (LLMs) like ChatGPT and GPT-4 have demonstrated exceptional proficiency in natural language processing, their efficacy in addressing complex, multifaceted tasks remains limited. A growing area of research focuses on LLM-based agents equipped with external tools capable of performing diverse tasks. However, existing LLM-based agents only support a limited set of tools which is unable to cover a diverse range of user queries, especially for those involving expertise domains. It remains a challenge for LLM-based agents to extend their tools autonomously when confronted with various user queries. As GitHub has hosted a multitude of repositories which can be seen as a good resource for tools, a promising solution is that LLM-based agents can autonomously integrate the repositories in GitHub according to the user queries to extend their tool set. In this paper, we introduce GitAgent, an agent capable of achieving the autonomous tool extension from GitHub. GitAgent follows a four-phase procedure to incorporate repositories and it can learn human experience by resorting to GitHub Issues/PRs to solve problems encountered during the procedure. Experimental evaluation involving 30 user queries demonstrates GitAgent's effectiveness, achieving a 69.4% success rate on average.

Vision-language pre-training has significantly elevated performance across a wide range of image-language applications. Yet, the pre-training process for video-related tasks demands exceptionally large computational and data resources, which hinders the progress of video-language models. This paper investigates a straightforward, highly efficient, and resource-light approach to adapting an existing image-language pre-trained model for dense video understanding. Our preliminary experiments reveal that directly fine-tuning pre-trained image-language models with multiple frames as inputs on video datasets leads to performance saturation or even a drop. Our further investigation reveals that it is largely attributed to the bias of learned high-norm visual features. Motivated by this finding, we propose a simple but effective pooling strategy to smooth the feature distribution along the temporal dimension and thus reduce the dominant impacts from the extreme features. The new model is termed Pooling LLaVA, or in short. achieves new state-of-the-art performance on modern benchmark datasets for both video question-answer and captioning tasks. Notably, on the recent popular Video ChatGPT benchmark, PLLaVA achieves a score of 3.48 out of 5 on average of five evaluated dimensions, exceeding the previous SOTA results from GPT4V (IG-VLM) by 9\%. On the latest multi-choice benchmark MVBench, PLLaVA achieves 58.1\% accuracy on average across 20 sub-tasks, 14.5\% higher than GPT4V (IG-VLM). Code is available at https://github.com/magic-research/PLLaVA.

Multi-agent systems perform well on general reasoning tasks. However, the lack of training in specialized areas hinders their accuracy. Current training methods train a unified large language model (LLM) for all agents in the system. This may limit the performances due to different distributions underlying for different agents. Therefore, training multi-agent systems with distinct LLMs should be the next step to solve. However, this approach introduces optimization challenges. For example, agents operate at different frequencies, rollouts involve varying sub-agent invocations, and agents are often deployed across separate servers, disrupting end-to-end gradient flow. To address these issues, we propose M-GRPO, a hierarchical extension of Group Relative Policy Optimization designed for vertical Multi-agent systems with a main agent (planner) and multiple sub-agents (multi-turn tool executors). M-GRPO computes group-relative advantages for both main and sub-agents, maintaining hierarchical credit assignment. It also introduces a trajectory-alignment scheme that generates fixed-size batches despite variable sub-agent invocations. We deploy a decoupled training pipeline in which agents run on separate servers and exchange minimal statistics via a shared store. This enables scalable training without cross-server backpropagation. In experiments on real-world benchmarks (e.g., GAIA, XBench-DeepSearch, and WebWalkerQA), M-GRPO consistently outperforms both single-agent GRPO and multi-agent GRPO with frozen sub-agents, demonstrating improved stability and sample efficiency. These results show that aligning heterogeneous trajectories and decoupling optimization across specialized agents enhances tool-augmented reasoning tasks.

With the proliferation of open-sourced Large Language Models (LLMs) and efficient finetuning techniques, we are on the cusp of the emergence of numerous domain-specific LLMs that have been finetuned for expertise across specialized fields and applications for which the current general-purpose LLMs are unsuitable. In academia, this technology has the potential to revolutionize the way we conduct systematic literature reviews (SLRs), access knowledge and generate new insights. This paper proposes an AI-enabled methodological framework that combines the power of LLMs with the rigorous reporting guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). By finetuning LLMs on domain-specific academic papers that have been selected as a result of a rigorous SLR process, the proposed PRISMA-DFLLM (for Domain-specific Finetuned LLMs) reporting guidelines offer the potential to achieve greater efficiency, reusability and scalability, while also opening the potential for conducting incremental living systematic reviews with the aid of LLMs. Additionally, the proposed approach for leveraging LLMs for SLRs enables the dissemination of finetuned models, empowering researchers to accelerate advancements and democratize cutting-edge research. This paper presents the case for the feasibility of finetuned LLMs to support rigorous SLRs and the technical requirements for realizing this. This work then proposes the extended PRISMA-DFLLM checklist of reporting guidelines as well as the advantages, challenges, and potential implications of implementing PRISMA-DFLLM. Finally, a future research roadmap to develop this line of AI-enabled SLRs is presented, paving the way for a new era of evidence synthesis and knowledge discovery.

Replaying data is a principal mechanism underlying the stability and data efficiency of off-policy reinforcement learning (RL). We present an effective yet simple framework to extend the use of replays across multiple experiments, minimally adapting the RL workflow for sizeable improvements in controller performance and research iteration times. At its core, Replay Across Experiments (RaE) involves reusing experience from previous experiments to improve exploration and bootstrap learning while reducing required changes to a minimum in comparison to prior work. We empirically show benefits across a number of RL algorithms and challenging control domains spanning both locomotion and manipulation, including hard exploration tasks from egocentric vision. Through comprehensive ablations, we demonstrate robustness to the quality and amount of data available and various hyperparameter choices. Finally, we discuss how our approach can be applied more broadly across research life cycles and can increase resilience by reloading data across random seeds or hyperparameter variations.

In tandem with the recent advancements in foundation model research, there has been a surge of generative music AI applications within the past few years. As the idea of AI-generated or AI-augmented music becomes more mainstream, many researchers in the music AI community may be wondering what avenues of research are left. With regards to music generative models, we outline the current areas of research with significant room for exploration. Firstly, we pose the question of foundational representation of these generative models and investigate approaches towards explainability. Next, we discuss the current state of music datasets and their limitations. We then overview different generative models, forms of evaluating these models, and their computational constraints/limitations. Subsequently, we highlight applications of these generative models towards extensions to multiple modalities and integration with artists' workflow as well as music education systems. Finally, we survey the potential copyright implications of generative music and discuss strategies for protecting the rights of musicians. While it is not meant to be exhaustive, our survey calls to attention a variety of research directions enabled by music foundation models.

Broad textual understanding and in-context learning require language models that utilize full document contexts. Due to the implementation challenges associated with directly training long-context models, many methods have been proposed for extending models to handle long contexts. However, owing to differences in data and model classes, it has been challenging to compare these approaches, leading to uncertainty as to how to evaluate long-context performance and whether it differs from standard evaluation. We implement a controlled protocol for extension methods with a standardized evaluation, utilizing consistent base models and extension data. Our study yields several insights into long-context behavior. First, we reaffirm the critical role of perplexity as a general-purpose performance indicator even in longer-context tasks. Second, we find that current approximate attention methods systematically underperform across long-context tasks. Finally, we confirm that exact fine-tuning based methods are generally effective within the range of their extension, whereas extrapolation remains challenging. All codebases, models, and checkpoints will be made available open-source, promoting transparency and facilitating further research in this critical area of AI development.

This paper describes ESPnet2-TTS, an end-to-end text-to-speech (E2E-TTS) toolkit. ESPnet2-TTS extends our earlier version, ESPnet-TTS, by adding many new features, including: on-the-fly flexible pre-processing, joint training with neural vocoders, and state-of-the-art TTS models with extensions like full-band E2E text-to-waveform modeling, which simplify the training pipeline and further enhance TTS performance. The unified design of our recipes enables users to quickly reproduce state-of-the-art E2E-TTS results. We also provide many pre-trained models in a unified Python interface for inference, offering a quick means for users to generate baseline samples and build demos. Experimental evaluations with English and Japanese corpora demonstrate that our provided models synthesize utterances comparable to ground-truth ones, achieving state-of-the-art TTS performance. The toolkit is available online at https://github.com/espnet/espnet.

The advent of Large Language Models (LLMs) represents a notable breakthrough in Natural Language Processing (NLP), contributing to substantial progress in both text comprehension and generation. However, amidst these advancements, it is noteworthy that LLMs often face a limitation in terms of context length extrapolation. Understanding and extending the context length for LLMs is crucial in enhancing their performance across various NLP applications. In this survey paper, we delve into the multifaceted aspects of exploring why it is essential, and the potential transformations that superior techniques could bring to NLP applications. We study the inherent challenges associated with extending context length and present an organized overview of the existing strategies employed by researchers. Additionally, we discuss the intricacies of evaluating context extension techniques and highlight the open challenges that researchers face in this domain. Furthermore, we explore whether there is a consensus within the research community regarding evaluation standards and identify areas where further agreement is needed. This comprehensive survey aims to serve as a valuable resource for researchers, guiding them through the nuances of context length extension techniques and fostering discussions on future advancements in this evolving field.

This paper presents a novel approach to audio restoration, focusing on the enhancement of low-quality music recordings, and in particular historical ones. Building upon a previous algorithm called BABE, or Blind Audio Bandwidth Extension, we introduce BABE-2, which presents a series of improvements. This research broadens the concept of bandwidth extension to generative equalization, a novel task that, to the best of our knowledge, has not been explicitly addressed in previous studies. BABE-2 is built around an optimization algorithm utilizing priors from diffusion models, which are trained or fine-tuned using a curated set of high-quality music tracks. The algorithm simultaneously performs two critical tasks: estimation of the filter degradation magnitude response and hallucination of the restored audio. The proposed method is objectively evaluated on historical piano recordings, showing an enhancement over the prior version. The method yields similarly impressive results in rejuvenating the works of renowned vocalists Enrico Caruso and Nellie Melba. This research represents an advancement in the practical restoration of historical music.

Electronic sports (esports) and research on this emerging field are interdisciplinary in nature. By extension, it is essential to understand how to standardize and structure training with the help of existing tools developed by years of research in sports sciences and informatics. Our goal in this article was to verify if the current body of research contains substantial evidence of the training systems applied to training esports players. To verify the existing sources, we have applied a framework of scoping review to address the search from multiple scientific databases with further local processing. We conclude that the current research on esports dealt mainly with describing and modeling performance metrics spanned over multiple fragmented research areas (psychology, nutrition, informatics), and yet these building blocks were not assembled into an existing well-functioning theory of performance in esports by providing exercise regimes, and ways of periodization for esports.

The Large Vision-Language Model (LVLM) field has seen significant advancements, yet its progression has been hindered by challenges in comprehending fine-grained visual content due to limited resolution. Recent efforts have aimed to enhance the high-resolution understanding capabilities of LVLMs, yet they remain capped at approximately 1500 x 1500 pixels and constrained to a relatively narrow resolution range. This paper represents InternLM-XComposer2-4KHD, a groundbreaking exploration into elevating LVLM resolution capabilities up to 4K HD (3840 x 1600) and beyond. Concurrently, considering the ultra-high resolution may not be necessary in all scenarios, it supports a wide range of diverse resolutions from 336 pixels to 4K standard, significantly broadening its scope of applicability. Specifically, this research advances the patch division paradigm by introducing a novel extension: dynamic resolution with automatic patch configuration. It maintains the training image aspect ratios while automatically varying patch counts and configuring layouts based on a pre-trained Vision Transformer (ViT) (336 x 336), leading to dynamic training resolution from 336 pixels to 4K standard. Our research demonstrates that scaling training resolution up to 4K HD leads to consistent performance enhancements without hitting the ceiling of potential improvements. InternLM-XComposer2-4KHD shows superb capability that matches or even surpasses GPT-4V and Gemini Pro in 10 of the 16 benchmarks. The InternLM-XComposer2-4KHD model series with 7B parameters are publicly available at https://github.com/InternLM/InternLM-XComposer.

Existing LLM test-time scaling laws emphasize the emergence of self-reflective behaviors through extended reasoning length. Nevertheless, this vertical scaling strategy often encounters plateaus in exploration as the model becomes locked into specific thinking pattern. By shifting from depth to parallelism, parallel thinking mitigates the narrowing of exploration. However, the extension of this paradigm to visual domain remains an open research question. In this paper, we first examine the role of visual partitioning in parallelized reasoning and subsequently propose two distinct strategies. Based on the above, we introduce Visual Para-Thinker, representing the inaugural parallel reasoning framework for MLLMs. To maintain path independence and promote diversity in reasoning, our approach integrates Pa-Attention alongside LPRoPE. Leveraging the vLLM framework, we have developed a native multimodal implementation that facilitates high-efficiency parallel processing. Empirical results on benchmark datasets such as V*, CountBench, RefCOCO, and HallusionBench confirm that Visual Para-Thinker successfully extends the benefits of parallel reasoning to the visual domain.

A central challenge in reinforcement learning (RL) is its dependence on extensive real-world interaction data to learn task-specific policies. While recent work demonstrates that large language models (LLMs) can mitigate this limitation by generating synthetic experience (noted as imaginary rollouts) for mastering novel tasks, progress in this emerging field is hindered due to the lack of a standard benchmark. To bridge this gap, we introduce ImagineBench, the first comprehensive benchmark for evaluating offline RL algorithms that leverage both real rollouts and LLM-imaginary rollouts. The key features of ImagineBench include: (1) datasets comprising environment-collected and LLM-imaginary rollouts; (2) diverse domains of environments covering locomotion, robotic manipulation, and navigation tasks; and (3) natural language task instructions with varying complexity levels to facilitate language-conditioned policy learning. Through systematic evaluation of state-of-the-art offline RL algorithms, we observe that simply applying existing offline RL algorithms leads to suboptimal performance on unseen tasks, achieving 35.44% success rate in hard tasks in contrast to 64.37% of method training on real rollouts for hard tasks. This result highlights the need for algorithm advancements to better leverage LLM-imaginary rollouts. Additionally, we identify key opportunities for future research: including better utilization of imaginary rollouts, fast online adaptation and continual learning, and extension to multi-modal tasks. Our code is publicly available at https://github.com/LAMDA-RL/ImagineBench.

Recent research trends in computational biology have increasingly focused on integrating text and bio-entity modeling, especially in the context of molecules and proteins. However, previous efforts like BioT5 faced challenges in generalizing across diverse tasks and lacked a nuanced understanding of molecular structures, particularly in their textual representations (e.g., IUPAC). This paper introduces BioT5+, an extension of the BioT5 framework, tailored to enhance biological research and drug discovery. BioT5+ incorporates several novel features: integration of IUPAC names for molecular understanding, inclusion of extensive bio-text and molecule data from sources like bioRxiv and PubChem, the multi-task instruction tuning for generality across tasks, and a novel numerical tokenization technique for improved processing of numerical data. These enhancements allow BioT5+ to bridge the gap between molecular representations and their textual descriptions, providing a more holistic understanding of biological entities, and largely improving the grounded reasoning of bio-text and bio-sequences. The model is pre-trained and fine-tuned with a large number of experiments, including 3 types of problems (classification, regression, generation), 15 kinds of tasks, and 21 total benchmark datasets, demonstrating the remarkable performance and state-of-the-art results in most cases. BioT5+ stands out for its ability to capture intricate relationships in biological data, thereby contributing significantly to bioinformatics and computational biology. Our code is available at https://github.com/QizhiPei/BioT5.

The rapid evolution of Large Language Model (LLM) agents has necessitated robust memory systems to support cohesive long-term interaction and complex reasoning. Benefiting from the strong capabilities of LLMs, recent research focus has shifted from simple context extension to the development of dedicated agentic memory systems. However, existing approaches typically rely on rigid retrieval granularity, accumulation-heavy maintenance strategies, and coarse-grained update mechanisms. These design choices create a persistent mismatch between stored information and task-specific reasoning demands, while leading to the unchecked accumulation of logical inconsistencies over time. To address these challenges, we propose Adaptive Memory via Multi-Agent Collaboration (AMA), a novel framework that leverages coordinated agents to manage memory across multiple granularities. AMA employs a hierarchical memory design that dynamically aligns retrieval granularity with task complexity. Specifically, the Constructor and Retriever jointly enable multi-granularity memory construction and adaptive query routing. The Judge verifies the relevance and consistency of retrieved content, triggering iterative retrieval when evidence is insufficient or invoking the Refresher upon detecting logical conflicts. The Refresher then enforces memory consistency by performing targeted updates or removing outdated entries. Extensive experiments on challenging long-context benchmarks show that AMA significantly outperforms state-of-the-art baselines while reducing token consumption by approximately 80% compared to full-context methods, demonstrating its effectiveness in maintaining retrieval precision and long-term memory consistency.

Text embeddings have attracted growing interest due to their effectiveness across a wide range of natural language processing (NLP) tasks, such as retrieval, classification, clustering, bitext mining, and summarization. With the emergence of pretrained language models (PLMs), general-purpose text embeddings (GPTE) have gained significant traction for their ability to produce rich, transferable representations. The general architecture of GPTE typically leverages PLMs to derive dense text representations, which are then optimized through contrastive learning on large-scale pairwise datasets. In this survey, we provide a comprehensive overview of GPTE in the era of PLMs, focusing on the roles PLMs play in driving its development. We first examine the fundamental architecture and describe the basic roles of PLMs in GPTE, i.e., embedding extraction, expressivity enhancement, training strategies, learning objectives, and data construction. Then, we describe advanced roles enabled by PLMs, such as multilingual support, multimodal integration, code understanding, and scenario-specific adaptation. Finally, we highlight potential future research directions that move beyond traditional improvement goals, including ranking integration, safety considerations, bias mitigation, structural information incorporation, and the cognitive extension of embeddings. This survey aims to serve as a valuable reference for both newcomers and established researchers seeking to understand the current state and future potential of GPTE.

Synthetic Data Generation (SDG) based on Artificial Intelligence (AI) can transform the way clinical medicine is delivered by overcoming privacy barriers that currently render clinical data sharing difficult. This is the key to accelerating the development of digital tools contributing to enhanced patient safety. Such tools include robust data-driven clinical decision support systems, and example-based digital training tools that will enable healthcare professionals to improve their diagnostic performance for enhanced patient safety. This study focuses on the clinical evaluation of medical SDG, with a proof-of-concept investigation on diagnosing Inflammatory Bowel Disease (IBD) using Wireless Capsule Endoscopy (WCE) images. Its scientific contributions include a) a novel protocol for the systematic Clinical Evaluation of Medical Image Synthesis (CEMIS); b) a novel variational autoencoder-based model for the generation of high-resolution synthetic WCE images; and c) a comprehensive evaluation of the synthetic images using the CEMIS protocol by 10 international WCE specialists, in terms of image quality, diversity, and realism, as well as their utility for clinical decision-making. The results show that TIDE-II generates clinically plausible, very realistic WCE images, of improved quality compared to relevant state-of-the-art generative models. Concludingly, CEMIS can serve as a reference for future research on medical image-generation techniques, while the adaptation/extension of the architecture of TIDE-II to other imaging domains can be promising.

We present RoboManipBaselines, an open-source software framework for imitation learning research in robotic manipulation. The framework supports the entire imitation learning pipeline, including data collection, policy training, and rollout, across both simulation and real-world environments. Its design emphasizes integration through a consistent workflow, generality across diverse environments and robot platforms, extensibility for easily adding new robots, tasks, and policies, and reproducibility through evaluations using publicly available datasets. RoboManipBaselines systematically implements the core components of imitation learning: environment, dataset, and policy. Through a unified interface, the framework supports multiple simulators and real robot environments, as well as multimodal sensors and a wide variety of policy models. We further present benchmark evaluations in both simulation and real-world environments and introduce several research applications, including data augmentation, integration with tactile models, interactive robotic systems, 3D sensing evaluation, and hardware extensions. These results demonstrate that RoboManipBaselines provides a useful foundation for advancing research and experimental validation in robotic manipulation using imitation learning. https://isri-aist.github.io/RoboManipBaselines-ProjectPage

Developers often dedicate significant time to maintaining and refactoring existing code. However, most prior work on generative models for code focuses solely on creating new code, overlooking the distinctive needs of editing existing code. In this work, we explore a multi-round code auto-editing setting, aiming to predict edits to a code region based on recent changes within the same codebase. Our model, Coeditor, is a fine-tuned language model specifically designed for code editing tasks. We represent code changes using a line diff format and employ static analysis to form large customized model contexts, ensuring the availability of appropriate information for prediction. We collect a code editing dataset from the commit histories of 1650 open-source Python projects for training and evaluation. In a simplified single-round, single-edit task, Coeditor significantly outperforms GPT-3.5 and SOTA open-source code completion models (bringing exact-match accuracy from 34.7 up to 60.4), demonstrating the benefits of incorporating editing history for code completion. In a multi-round, multi-edit setting, we observe substantial gains by iteratively conditioning on additional user edits. We have open-sourced our code, data, and model weights to encourage future research and have released a VSCode extension powered by our model for interactive IDE usage.

Researchers spend a great deal of time reading research papers. Keshav (2012) provides a three-pass method to researchers to improve their reading skills. This article extends Keshav's method for reading a research compendium. Research compendia are an increasingly used form of publication, which packages not only the research paper's text and figures, but also all data and software for better reproducibility. We introduce the existing conventions for research compendia and suggest how to utilise their shared properties in a structured reading process. Unlike the original, this article is not build upon a long history but intends to provide guidance at the outset of an emerging practice.

In scientific research, limitations refer to the shortcomings, constraints, or weaknesses within a study. Transparent reporting of such limitations can enhance the quality and reproducibility of research and improve public trust in science. However, authors often a) underreport them in the paper text and b) use hedging strategies to satisfy editorial requirements at the cost of readers' clarity and confidence. This underreporting behavior, along with an explosion in the number of publications, has created a pressing need to automatically extract or generate such limitations from scholarly papers. In this direction, we present a complete architecture for the computational analysis of research limitations. Specifically, we create a dataset of limitations in ACL, NeurIPS, and PeerJ papers by extracting them from papers' text and integrating them with external reviews; we propose methods to automatically generate them using a novel Retrieval Augmented Generation (RAG) technique; we create a fine-grained evaluation framework for generated limitations; and we provide a meta-evaluation for the proposed evaluation techniques.

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

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

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.

While Large Language Models (LLMs) have demonstrated proficiency in Deep Research or Wide Search, their capacity to solve highly complex questions-those requiring long-horizon planning, massive evidence gathering, and synthesis across heterogeneous sources-remains largely unexplored. We introduce Super Research, a task for complex autonomous research tasks that integrates (i) structured decomposition into a research plan, (ii) super wide retrieval for diverse perspectives, and (iii) super deep investigation to resolve uncertainties through iterative queries. To evaluate this capability, we curated a benchmark of 300 expert-written questions across diverse domains, each requiring up to 100+ retrieval steps and 1,000+ web pages to reconcile conflicting evidence. Super Research produces verifiable reports with fine-grained citations and intermediate artifacts (e.g., outlines and tables) to ensure traceable reasoning. Furthermore, we present a graph-anchored auditing protocol that evaluates Super Research along five dimensions: Coverage, Logical Consistency, Report Utility, Objectivity and Citation Health. While super-complex questions may be infrequent in standard applications, Super Research serves as a critical ceiling evaluation and stress test for LLM capabilities. A model's proficiency within Super Research acts as a powerful proxy for its general research competence; success here suggests the robustness necessary to navigate nearly any subordinate research task. Leaderboard is available at: https://cnsdqd-dyb.github.io/Super-Research-Benchmark/

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/

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

Large Language Models 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.

The exponential growth of academic publications poses challenges for the research process, such as literature review and procedural planning. Large Language Models (LLMs) have emerged as powerful AI tools, especially when combined with additional tools and resources. Recent LLM-powered frameworks offer promising solutions for handling complex domain-specific tasks, yet their domain-specific implementation limits broader applicability. This highlights the need for LLM-integrated systems that can assist in cross-disciplinary tasks, such as streamlining the research process across science and engineering disciplines. To address this need, we introduce Artificial Research Innovator Assistant (ARIA), a four-agent, multi-LLM framework. By emulating a team of expert assistants, ARIA systematically replicates the human research workflow to autonomously search, retrieve, and filter hundreds of papers, subsequently synthesizing relevant literature into actionable research procedures. In a case study on dropwise condensation enhancement, ARIA demonstrates its capability to streamline research tasks within an hour, maintaining user oversight during execution and ultimately liberating researchers from time-intensive tasks.

The rapid move to remote work due to COVID-19 social distancing policies has slowed or stopped most in-person qualitative user research activities. The limitation on in-person activities has pushed many user researchers to consider how they can continue their research remotely and presents an opportunity for user research teams to (re)design their research processes for remote work. In this position statement, I outline prior work in remote qualitative user research methods and discuss how this work can help us to (re)design new tools, methods, and frameworks that can enable remote work. I then propose a set of research questions that can further our knowledge and abilities to conduct effective remote user research. With creative development, we can create remote research methods that afford new ways of understanding user experience today and build more environmentally conscious and accessible research practices for a future where remote user research is much more common.

We present SetExpander, a corpus-based system for expanding a seed set of terms into amore complete set of terms that belong to the same semantic class. SetExpander implements an iterative end-to-end workflow. It enables users to easily select a seed set of terms, expand it, view the expanded set, validate it, re-expand the validated set and store it, thus simplifying the extraction of domain-specific fine-grained semantic classes.SetExpander has been used successfully in real-life use cases including integration into an automated recruitment system and an issues and defects resolution system. A video demo of SetExpander is available at https://drive.google.com/open?id=1e545bB87Autsch36DjnJHmq3HWfSd1Rv (some images were blurred for privacy reasons)

A research division plays an important role of driving innovation in an organization. Drawing insights, following trends, keeping abreast of new research, and formulating strategies are increasingly becoming more challenging for both researchers and executives as the amount of information grows in both velocity and volume. In this paper we present a use case of how a corporate research community, IBM Research, utilizes Semantic Web technologies to induce a unified Knowledge Graph from both structured and textual data obtained by integrating various applications used by the community related to research projects, academic papers, datasets, achievements and recognition. In order to make the Knowledge Graph more accessible to application developers, we identified a set of common patterns for exploiting the induced knowledge and exposed them as APIs. Those patterns were born out of user research which identified the most valuable use cases or user pain points to be alleviated. We outline two distinct scenarios: recommendation and analytics for business use. We will discuss these scenarios in detail and provide an empirical evaluation on entity recommendation specifically. The methodology used and the lessons learned from this work can be applied to other organizations facing similar challenges.

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

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

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

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

Paper search is an important activity for researchers, typically involving using a query with description of a topic to find relevant papers. As research deepens, paper search requirements may become more flexible, sometimes involving specific details such as module configuration rather than being limited to coarse-grained topics. However, previous paper search systems are unable to meet these flexible-grained requirements, as these systems mainly collect paper abstracts to construct index of corpus, which lack detailed information to support retrieval by finer-grained queries. In this work, we propose PaperRegister, consisted of offline hierarchical indexing and online adaptive retrieval, transforming traditional abstract-based index into hierarchical index tree for paper search, thereby supporting queries at flexible granularity. Experiments on paper search tasks across a range of granularity demonstrate that PaperRegister achieves the state-of-the-art performance, and particularly excels in fine-grained scenarios, highlighting the good potential as an effective solution for flexible-grained paper search in real-world applications. Code for this work is in https://github.com/Li-Z-Q/PaperRegister.

Effective research ideation is a critical step for scientific research. However, the exponential increase in scientific literature makes it challenging for researchers to stay current with recent advances and identify meaningful research directions. Recent developments in large language models~(LLMs) suggest a promising avenue for automating the generation of novel research ideas. However, existing methods for idea generation either trivially prompt LLMs or directly expose LLMs to extensive literature without indicating useful information. Inspired by the research process of human researchers, we propose a Chain-of-Ideas~(CoI) agent, an LLM-based agent that organizes relevant literature in a chain structure to effectively mirror the progressive development in a research domain. This organization facilitates LLMs to capture the current advancements in research, thereby enhancing their ideation capabilities. Furthermore, we propose Idea Arena, an evaluation protocol that can comprehensively evaluate idea generation methods from different perspectives, aligning closely with the preferences of human researchers. Experimental results indicate that the CoI agent consistently outperforms other methods and shows comparable quality as humans in research idea generation. Moreover, our CoI agent is budget-friendly, with a minimum cost of \$0.50 to generate a candidate idea and its corresponding experimental design.

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

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

Autonomous scientific discovery with large language model (LLM)-based agents has recently made substantial progress, demonstrating the ability to automate end-to-end research workflows. However, existing systems largely rely on runtime-centric execution paradigms, repeatedly reading, summarizing, and reasoning over large volumes of scientific literature online. This on-the-spot computation strategy incurs high computational cost, suffers from context window limitations, and often leads to brittle reasoning and hallucination. We propose Idea2Story, a pre-computation-driven framework for autonomous scientific discovery that shifts literature understanding from online reasoning to offline knowledge construction. Idea2Story continuously collects peer-reviewed papers together with their review feedback, extracts core methodological units, composes reusable research patterns, and organizes them into a structured methodological knowledge graph. At runtime, underspecified user research intents are aligned to established research paradigms, enabling efficient retrieval and reuse of high-quality research patterns instead of open-ended generation and trial-and-error. By grounding research planning and execution in a pre-built knowledge graph, Idea2Story alleviates the context window bottleneck of LLMs and substantially reduces repeated runtime reasoning over literature. We conduct qualitative analyses and preliminary empirical studies demonstrating that Idea2Story can generate coherent, methodologically grounded, and novel research patterns, and can produce several high-quality research demonstrations in an end-to-end setting. These results suggest that offline knowledge construction provides a practical and scalable foundation for reliable autonomous scientific discovery.

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

We present SetExpander, a corpus-based system for expanding a seed set of terms into a more complete set of terms that belong to the same semantic class. SetExpander implements an iterative end-to end workflow for term set expansion. It enables users to easily select a seed set of terms, expand it, view the expanded set, validate it, re-expand the validated set and store it, thus simplifying the extraction of domain-specific fine-grained semantic classes. SetExpander has been used for solving real-life use cases including integration in an automated recruitment system and an issues and defects resolution system. A video demo of SetExpander is available at https://drive.google.com/open?id=1e545bB87Autsch36DjnJHmq3HWfSd1Rv (some images were blurred for privacy reasons).

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.

This paper describes the design, implementation, and evaluation of a browser extension that provides contextual help to users who hover over technological acronyms and abbreviations on web pages. The extension combines a curated technical dictionary with OpenAI's large language model (LLM) to deliver on-demand definitions through lightweight tooltip overlays. A dual-layer artificial intelligence (AI) pipeline, comprising Google Cloud's Natural Language Processing (NLP) taxonomy API and OpenAI's ChatGPT, classifies each visited page as technology-related before activating the tooltip logic, thereby reducing false-positive detections. A mixed-methods study with 25 participants evaluated the tool's effect on reading comprehension and information-retrieval time among users with low to intermediate digital literacy. Results show that 92% of participants reported improved understanding of technical terms, 96% confirmed time savings over manual web searches, and all participants found the tooltips non-disruptive. Dictionary-based definitions were appended in an average of 2135 ms, compared to 16429 ms for AI-generated definitions and a mean manual search time of 17200 ms per acronym. The work demonstrates a practical, real-time approach to bridging the digital literacy gap and points toward extending contextual help to other domains such as medicine, law, and finance.

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.

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

Recent advancements in artificial intelligence (AI), particularly in large language models (LLMs) such as OpenAI-o1 and DeepSeek-R1, have demonstrated remarkable capabilities in complex domains such as logical reasoning and experimental coding. Motivated by these advancements, numerous studies have explored the application of AI in the innovation process, particularly in the context of scientific research. These AI technologies primarily aim to develop systems that can autonomously conduct research processes across a wide range of scientific disciplines. Despite these significant strides, a comprehensive survey on AI for Research (AI4Research) remains absent, which hampers our understanding and impedes further development in this field. To address this gap, we present a comprehensive survey and offer a unified perspective on AI4Research. Specifically, the main contributions of our work are as follows: (1) Systematic taxonomy: We first introduce a systematic taxonomy to classify five mainstream tasks in AI4Research. (2) New frontiers: Then, we identify key research gaps and highlight promising future directions, focusing on the rigor and scalability of automated experiments, as well as the societal impact. (3) Abundant applications and resources: Finally, we compile a wealth of resources, including relevant multidisciplinary applications, data corpora, and tools. We hope our work will provide the research community with quick access to these resources and stimulate innovative breakthroughs in AI4Research.

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.

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

Query expansion, pivotal in search engines, enhances the representation of user information needs with additional terms. While existing methods expand queries using retrieved or generated contextual documents, each approach has notable limitations. Retrieval-based methods often fail to accurately capture search intent, particularly with brief or ambiguous queries. Generation-based methods, utilizing large language models (LLMs), generally lack corpus-specific knowledge and entail high fine-tuning costs. To address these gaps, we propose a novel zero-shot query expansion framework utilizing LLMs for mutual verification. Specifically, we first design a query-query-document generation method, leveraging LLMs' zero-shot reasoning ability to produce diverse sub-queries and corresponding documents. Then, a mutual verification process synergizes generated and retrieved documents for optimal expansion. Our proposed method is fully zero-shot, and extensive experiments on three public benchmark datasets are conducted to demonstrate its effectiveness over existing methods. Our code is available online at https://github.com/Applied-Machine-Learning-Lab/MILL to ease reproduction.

We propose a design pattern for tackling text ranking problems, dubbed "Expando-Mono-Duo", that has been empirically validated for a number of ad hoc retrieval tasks in different domains. At the core, our design relies on pretrained sequence-to-sequence models within a standard multi-stage ranking architecture. "Expando" refers to the use of document expansion techniques to enrich keyword representations of texts prior to inverted indexing. "Mono" and "Duo" refer to components in a reranking pipeline based on a pointwise model and a pairwise model that rerank initial candidates retrieved using keyword search. We present experimental results from the MS MARCO passage and document ranking tasks, the TREC 2020 Deep Learning Track, and the TREC-COVID challenge that validate our design. In all these tasks, we achieve effectiveness that is at or near the state of the art, in some cases using a zero-shot approach that does not exploit any training data from the target task. To support replicability, implementations of our design pattern are open-sourced in the Pyserini IR toolkit and PyGaggle neural reranking library.

This paper tackles open-ended deep research (OEDR), a complex challenge where AI agents must synthesize vast web-scale information into insightful reports. Current approaches are plagued by dual-fold limitations: static research pipelines that decouple planning from evidence acquisition and one-shot generation paradigms that easily suffer from long-context failure issues like "loss in the middle" and hallucinations. To address these challenges, we introduce WebWeaver, a novel dual-agent framework that emulates the human research process. The planner operates in a dynamic cycle, iteratively interleaving evidence acquisition with outline optimization to produce a comprehensive, source-grounded outline linking to a memory bank of evidence. The writer then executes a hierarchical retrieval and writing process, composing the report section by section. By performing targeted retrieval of only the necessary evidence from the memory bank for each part, it effectively mitigates long-context issues. Our framework establishes a new state-of-the-art across major OEDR benchmarks, including DeepResearch Bench, DeepConsult, and DeepResearchGym. These results validate our human-centric, iterative methodology, demonstrating that adaptive planning and focused synthesis are crucial for producing high-quality, reliable, and well-structured reports.

Query expansion aims to mitigate the mismatch between the language used in a query and in a document. However, query expansion methods can suffer from introducing non-relevant information when expanding the query. To bridge this gap, inspired by recent advances in applying contextualized models like BERT to the document retrieval task, this paper proposes a novel query expansion model that leverages the strength of the BERT model to select relevant document chunks for expansion. In evaluation on the standard TREC Robust04 and GOV2 test collections, the proposed BERT-QE model significantly outperforms BERT-Large models.

Knowing that the generative capabilities of large language models (LLM) are sometimes hampered by tendencies to hallucinate or create non-factual responses, researchers have increasingly focused on methods to ground generated outputs in factual data. Retrieval Augmented Generation (RAG) has emerged as a key approach for integrating knowledge from data sources outside of the LLM's training set, including proprietary and up-to-date information. While many research papers explore various RAG strategies, their true efficacy is tested in real-world applications with actual data. The journey from conceiving an idea to actualizing it in the real world is a lengthy process. We present insights from the development and field-testing of a pilot project that integrates LLMs with RAG for information retrieval. Additionally, we examine the impacts on the information value chain, encompassing people, processes, and technology. Our aim is to identify the opportunities and challenges of implementing this emerging technology, particularly within the context of behavioral research in the information systems (IS) field. The contributions of this work include the development of best practices and recommendations for adopting this promising technology while ensuring compliance with industry regulations through a proposed AI governance model.

Research is a fundamental process driving the advancement of human civilization, yet it demands substantial time and effort from researchers. In recent years, the rapid development of artificial intelligence (AI) technologies has inspired researchers to explore how AI can accelerate and enhance research. To monitor relevant advancements, this paper presents a systematic review of the progress in this domain. Specifically, we organize the relevant studies into three main categories: hypothesis formulation, hypothesis validation, and manuscript publication. Hypothesis formulation involves knowledge synthesis and hypothesis generation. Hypothesis validation includes the verification of scientific claims, theorem proving, and experiment validation. Manuscript publication encompasses manuscript writing and the peer review process. Furthermore, we identify and discuss the current challenges faced in these areas, as well as potential future directions for research. Finally, we also offer a comprehensive overview of existing benchmarks and tools across various domains that support the integration of AI into the research process. We hope this paper serves as an introduction for beginners and fosters future research. Resources have been made publicly available at https://github.com/zkzhou126/AI-for-Research.

The Archives Unleashed project aims to improve scholarly access to web archives through a multi-pronged strategy involving tool creation, process modeling, and community building - all proceeding concurrently in mutually-reinforcing efforts. As we near the end of our initially-conceived three-year project, we report on our progress and share lessons learned along the way. The main contribution articulated in this paper is a process model that decomposes scholarly inquiries into four main activities: filter, extract, aggregate, and visualize. Based on the insight that these activities can be disaggregated across time, space, and tools, it is possible to generate "derivative products", using our Archives Unleashed Toolkit, that serve as useful starting points for scholarly inquiry. Scholars can download these products from the Archives Unleashed Cloud and manipulate them just like any other dataset, thus providing access to web archives without requiring any specialized knowledge. Over the past few years, our platform has processed over a thousand different collections from about two hundred users, totaling over 280 terabytes of web archives.

Recent advancements in large language models (LLMs) have shown promise in generating novel research ideas. However, these ideas often face challenges related to feasibility and expected effectiveness. This paper explores how augmenting LLMs with relevant data during the idea generation process can enhance the quality of generated ideas. We introduce two ways of incorporating data: (1) providing metadata during the idea generation stage to guide LLMs toward feasible directions, and (2) adding automatic validation during the idea selection stage to assess the empirical plausibility of hypotheses within ideas. We conduct experiments in the social science domain, specifically with climate negotiation topics, and find that metadata improves the feasibility of generated ideas by 20%, while automatic validation improves the overall quality of selected ideas by 7%. A human study shows that LLM-generated ideas, along with their related data and validation processes, inspire researchers to propose research ideas with higher quality. Our work highlights the potential of data-driven research idea generation, and underscores the practical utility of LLM-assisted ideation in real-world academic settings.

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

Recent studies demonstrate that query expansions generated by large language models (LLMs) can considerably enhance information retrieval systems by generating hypothetical documents that answer the queries as expansions. However, challenges arise from misalignments between the expansions and the retrieval corpus, resulting in issues like hallucinations and outdated information due to the limited intrinsic knowledge of LLMs. Inspired by Pseudo Relevance Feedback (PRF), we introduce Corpus-Steered Query Expansion (CSQE) to promote the incorporation of knowledge embedded within the corpus. CSQE utilizes the relevance assessing capability of LLMs to systematically identify pivotal sentences in the initially-retrieved documents. These corpus-originated texts are subsequently used to expand the query together with LLM-knowledge empowered expansions, improving the relevance prediction between the query and the target documents. Extensive experiments reveal that CSQE exhibits strong performance without necessitating any training, especially with queries for which LLMs lack knowledge.

The paper presents a methodology for uncovering knowledge gaps on the internet using the Retrieval Augmented Generation (RAG) model. By simulating user search behaviour, the RAG system identifies and addresses gaps in information retrieval systems. The study demonstrates the effectiveness of the RAG system in generating relevant suggestions with a consistent accuracy of 93%. The methodology can be applied in various fields such as scientific discovery, educational enhancement, research development, market analysis, search engine optimisation, and content development. The results highlight the value of identifying and understanding knowledge gaps to guide future endeavours.

We apply category theory to extract multimodal document structure which leads us to develop information theoretic measures, content summarization and extension, and self-supervised improvement of large pretrained models. We first develop a mathematical representation of a document as a category of question-answer pairs. Second, we develop an orthogonalization procedure to divide the information contained in one or more documents into non-overlapping pieces. The structures extracted in the first and second steps lead us to develop methods to measure and enumerate the information contained in a document. We also build on those steps to develop new summarization techniques, as well as to develop a solution to a new problem viz. exegesis resulting in an extension of the original document. Our question-answer pair methodology enables a novel rate distortion analysis of summarization techniques. We implement our techniques using large pretrained models, and we propose a multimodal extension of our overall mathematical framework. Finally, we develop a novel self-supervised method using RLVR to improve large pretrained models using consistency constraints such as composability and closure under certain operations that stem naturally from our category theoretic framework.

Scientific innovation is pivotal for humanity, and harnessing large language models (LLMs) to generate research ideas could transform discovery. However, existing LLMs often produce simplistic and repetitive suggestions due to their limited ability in acquiring external knowledge for innovation. To address this problem, we introduce an enhanced planning and search methodology designed to boost the creative potential of LLM-based systems. Our approach involves an iterative process to purposely plan the retrieval of external knowledge, progressively enriching the idea generation with broader and deeper insights. Validation through automated and human assessments indicates that our framework substantially elevates the quality of generated ideas, particularly in novelty and diversity. The number of unique novel ideas produced by our framework is 3.4 times higher than without it. Moreover, our method outperforms the current state-of-the-art, generating at least 2.5 times more top-rated ideas based on 170 seed papers in a Swiss Tournament evaluation.

Clinical trials disruption has always represented a non negligible part of the ending of interventional studies. While the SARS-CoV-2 (COVID-19) pandemic has led to an impressive and unprecedented initiation of clinical research, it has also led to considerable disruption of clinical trials in other disease areas, with around 80% of non-COVID-19 trials stopped or interrupted during the pandemic. In many cases the disrupted trials will not have the planned statistical power necessary to yield interpretable results. This paper describes methods to compensate for the information loss arising from trial disruptions by incorporating additional information available from auxiliary data sources. The methods described include the use of auxiliary data on baseline and early outcome data available from the trial itself and frequentist and Bayesian approaches for the incorporation of information from external data sources. The methods are illustrated by application to the analysis of artificial data based on the Primary care pediatrics Learning Activity Nutrition (PLAN) study, a clinical trial assessing a diet and exercise intervention for overweight children, that was affected by the COVID-19 pandemic. We show how all of the methods proposed lead to an increase in precision relative to use of complete case data only.

The question-answering system for Life science research, which is characterized by the rapid pace of discovery, evolving insights, and complex interactions among knowledge entities, presents unique challenges in maintaining a comprehensive knowledge warehouse and accurate information retrieval. To address these issues, we introduce BioRAG, a novel Retrieval-Augmented Generation (RAG) with the Large Language Models (LLMs) framework. Our approach starts with parsing, indexing, and segmenting an extensive collection of 22 million scientific papers as the basic knowledge, followed by training a specialized embedding model tailored to this domain. Additionally, we enhance the vector retrieval process by incorporating a domain-specific knowledge hierarchy, which aids in modeling the intricate interrelationships among each query and context. For queries requiring the most current information, BioRAG deconstructs the question and employs an iterative retrieval process incorporated with the search engine for step-by-step reasoning. Rigorous experiments have demonstrated that our model outperforms fine-tuned LLM, LLM with search engines, and other scientific RAG frameworks across multiple life science question-answering tasks.

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

We propose EAR, a query Expansion And Reranking approach for improving passage retrieval, with the application to open-domain question answering. EAR first applies a query expansion model to generate a diverse set of queries, and then uses a query reranker to select the ones that could lead to better retrieval results. Motivated by the observation that the best query expansion often is not picked by greedy decoding, EAR trains its reranker to predict the rank orders of the gold passages when issuing the expanded queries to a given retriever. By connecting better the query expansion model and retriever, EAR significantly enhances a traditional sparse retrieval method, BM25. Empirically, EAR improves top-5/20 accuracy by 3-8 and 5-10 points in in-domain and out-of-domain settings, respectively, when compared to a vanilla query expansion model, GAR, and a dense retrieval model, DPR.

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

Query expansion has been employed for a long time to improve the accuracy of query retrievers. Earlier works relied on pseudo-relevance feedback (PRF) techniques, which augment a query with terms extracted from documents retrieved in a first stage. However, the documents may be noisy hindering the effectiveness of the ranking. To avoid this, recent studies have instead used Large Language Models (LLMs) to generate additional content to expand a query. These techniques are prone to hallucination and also focus on the LLM usage cost. However, the cost may be dominated by the retrieval in several important practical scenarios, where the corpus is only available via APIs which charge a fee per retrieved document. We propose combining classic PRF techniques with LLMs and create a progressive query expansion algorithm ProQE that iteratively expands the query as it retrieves more documents. ProQE is compatible with both sparse and dense retrieval systems. Our experimental results on four retrieval datasets show that ProQE outperforms state-of-the-art baselines by 37% and is the most cost-effective.

Large Language Models (LLMs) have shown promise in accelerating the scientific research pipeline. A key capability for this process is the ability to generate novel research ideas, and prior studies have found settings in which LLM-generated research ideas were judged as more novel than human-expert ideas. However, a good idea should not simply appear to be novel, it should also result in better research after being executed. To test whether AI-generated ideas lead to better research outcomes, we conduct an execution study by recruiting 43 expert researchers to execute randomly-assigned ideas, either written by experts or generated by an LLM. Each expert spent over 100 hours implementing the idea and wrote a 4-page short paper to document the experiments. All the executed projects are then reviewed blindly by expert NLP researchers. Comparing the review scores of the same ideas before and after execution, the scores of the LLM-generated ideas decrease significantly more than expert-written ideas on all evaluation metrics (novelty, excitement, effectiveness, and overall; p < 0.05), closing the gap between LLM and human ideas observed at the ideation stage. When comparing the aggregated review scores from the execution study, we even observe that for many metrics there is a flip in rankings where human ideas score higher than LLM ideas. This ideation-execution gap highlights the limitations of current LLMs in generating truly effective research ideas and the challenge of evaluating research ideas in the absence of execution outcomes.

Recent research in the field of reflexive metrics have studied the emergence and consequences of evaluation gaps in science. The concept of evaluation gaps captures potential discrepancies between what researchers value about their research, in particular research quality, and what metrics measure. As a result, scientists may experience anomie and adopt innovative ways to cope. These often value quantity over quality and may even compromise research integrity. A consequence of such gaps may therefore be research misconduct and a decrease in research quality. In the language of rational choice theory, an evaluation gap persists if motivational factors arising out of the internal component of an actors situation are incongruent with those arising out of the external components. The aim of this research is therefore to study and compare autonomous and controlled motivations to become an astronomer, to do research in astronomy and to publish scientific papers. Moreover, we study how these different motivational factors affect publication pressure, the experience of organisational justice and the observation of research misconduct. In summary, we find evidence for an evaluation gap and that controlled motivational factors arising from evaluation procedures based on publication record drives up publication pressure, which, in turn, was found to increase the likelihood of perceived frequency of misbehaviour.

Query expansion (QE) enhances retrieval by incorporating relevant terms, with large language models (LLMs) offering an effective alternative to traditional rule-based and statistical methods. However, LLM-based QE suffers from a fundamental limitation: it often fails to generate relevant knowledge, degrading search performance. Prior studies have focused on hallucination, yet its underlying cause--LLM knowledge deficiencies--remains underexplored. This paper systematically examines two failure cases in LLM-based QE: (1) when the LLM lacks query knowledge, leading to incorrect expansions, and (2) when the query is ambiguous, causing biased refinements that narrow search coverage. We conduct controlled experiments across multiple datasets, evaluating the effects of knowledge and query ambiguity on retrieval performance using sparse and dense retrieval models. Our results reveal that LLM-based QE can significantly degrade the retrieval effectiveness when knowledge in the LLM is insufficient or query ambiguity is high. We introduce a framework for evaluating QE under these conditions, providing insights into the limitations of LLM-based retrieval augmentation.

Given that Large Language Models (LLMs) have made significant progress in writing code, can they now be used to autonomously reproduce results from research repositories? Such a capability would be a boon to the research community, helping researchers validate, understand, and extend prior work. To advance towards this goal, we introduce SUPER, the first benchmark designed to evaluate the capability of LLMs in setting up and executing tasks from research repositories. SUPERaims to capture the realistic challenges faced by researchers working with Machine Learning (ML) and Natural Language Processing (NLP) research repositories. Our benchmark comprises three distinct problem sets: 45 end-to-end problems with annotated expert solutions, 152 sub problems derived from the expert set that focus on specific challenges (e.g., configuring a trainer), and 602 automatically generated problems for larger-scale development. We introduce various evaluation measures to assess both task success and progress, utilizing gold solutions when available or approximations otherwise. We show that state-of-the-art approaches struggle to solve these problems with the best model (GPT-4o) solving only 16.3% of the end-to-end set, and 46.1% of the scenarios. This illustrates the challenge of this task, and suggests that SUPER can serve as a valuable resource for the community to make and measure progress.

The rapid expansion of scholarly literature presents significant challenges in synthesizing comprehensive, high-quality academic surveys. Recent advancements in agentic systems offer considerable promise for automating tasks that traditionally require human expertise, including literature review, synthesis, and iterative refinement. However, existing automated survey-generation solutions often suffer from inadequate quality control, poor formatting, and limited adaptability to iterative feedback, which are core elements intrinsic to scholarly writing. To address these limitations, we introduce ARISE, an Agentic Rubric-guided Iterative Survey Engine designed for automated generation and continuous refinement of academic survey papers. ARISE employs a modular architecture composed of specialized large language model agents, each mirroring distinct scholarly roles such as topic expansion, citation curation, literature summarization, manuscript drafting, and peer-review-based evaluation. Central to ARISE is a rubric-guided iterative refinement loop in which multiple reviewer agents independently assess manuscript drafts using a structured, behaviorally anchored rubric, systematically enhancing the content through synthesized feedback. Evaluating ARISE against state-of-the-art automated systems and recent human-written surveys, our experimental results demonstrate superior performance, achieving an average rubric-aligned quality score of 92.48. ARISE consistently surpasses baseline methods across metrics of comprehensiveness, accuracy, formatting, and overall scholarly rigor. All code, evaluation rubrics, and generated outputs are provided openly at https://github.com/ziwang11112/ARISE

With the advent of large multimodal language models, science is now at a threshold of an AI-based technological transformation. Recently, a plethora of new AI models and tools has been proposed, promising to empower researchers and academics worldwide to conduct their research more effectively and efficiently. This includes all aspects of the research cycle, especially (1) searching for relevant literature; (2) generating research ideas and conducting experimentation; generating (3) text-based and (4) multimodal content (e.g., scientific figures and diagrams); and (5) AI-based automatic peer review. In this survey, we provide an in-depth overview over these exciting recent developments, which promise to fundamentally alter the scientific research process for good. Our survey covers the five aspects outlined above, indicating relevant datasets, methods and results (including evaluation) as well as limitations and scope for future research. Ethical concerns regarding shortcomings of these tools and potential for misuse (fake science, plagiarism, harms to research integrity) take a particularly prominent place in our discussion. We hope that our survey will not only become a reference guide for newcomers to the field but also a catalyst for new AI-based initiatives in the area of "AI4Science".

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

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

We extend the context length of Llama-3-8B-Instruct from 8K to 80K via QLoRA fine-tuning. The entire training cycle is super efficient, which takes 8 hours on one 8xA800 (80G) GPU machine. The resulted model exhibits superior performances across a broad range of evaluation tasks, such as NIHS, topic retrieval, and long-context language understanding; meanwhile, it also well preserves the original capability over short contexts. The dramatic context extension is mainly attributed to merely 3.5K synthetic training samples generated by GPT-4 , which indicates the LLMs' inherent (yet largely underestimated) potential to extend its original context length. In fact, the context length could be extended far beyond 80K with more computation resources. Therefore, the team will publicly release the entire resources (including data, model, data generation pipeline, training code) so as to facilitate the future research from the community: https://github.com/FlagOpen/FlagEmbedding.

Query expansion is a widely used technique to improve the recall of search systems. In this paper, we propose an approach to query expansion that leverages the generative abilities of Large Language Models (LLMs). Unlike traditional query expansion approaches such as Pseudo-Relevance Feedback (PRF) that relies on retrieving a good set of pseudo-relevant documents to expand queries, we rely on the generative and creative abilities of an LLM and leverage the knowledge inherent in the model. We study a variety of different prompts, including zero-shot, few-shot and Chain-of-Thought (CoT). We find that CoT prompts are especially useful for query expansion as these prompts instruct the model to break queries down step-by-step and can provide a large number of terms related to the original query. Experimental results on MS-MARCO and BEIR demonstrate that query expansions generated by LLMs can be more powerful than traditional query expansion methods.

Large Language Models (LLMs) have demonstrated remarkable success in various tasks such as natural language understanding, text summarization, and machine translation. However, their general-purpose nature often limits their effectiveness in domain-specific applications that require specialized knowledge, such as healthcare, chemistry, or legal analysis. To address this, researchers have explored diverse methods to enhance LLMs by integrating domain-specific knowledge. In this survey, we provide a comprehensive overview of these methods, which we categorize into four key approaches: dynamic knowledge injection, static knowledge embedding, modular adapters, and prompt optimization. Each approach offers unique mechanisms to equip LLMs with domain expertise, balancing trade-offs between flexibility, scalability, and efficiency. We discuss how these methods enable LLMs to tackle specialized tasks, compare their advantages and disadvantages, evaluate domain-specific LLMs against general LLMs, and highlight the challenges and opportunities in this emerging field. For those interested in delving deeper into this area, we also summarize the commonly used datasets and benchmarks. To keep researchers updated on the latest studies, we maintain an open-source at: https://github.com/abilliyb/Knowledge_Injection_Survey_Papers, dedicated to documenting research in the field of specialized LLM.

Case-oriented physics education research - which seeks to refine and develop theory by linking that theory to cases - incorporates distinct practices for selecting data for analysis, generalizing results, and making causal claims. Unanswered questions about these practices may constrain researchers more familiar with the recurrence-oriented research paradigm - which seeks to inform instructional predictions by discerning reproducible, representative patterns and relationships - from participating in or critically engaging with case-oriented research. We use results from interviews with physics education researchers, a synthesis of the literature on research methodologies, and published examples of case-oriented and recurrence-oriented research to answer "hard-hitting questions" that researchers may pose. In doing so, we aim to substantiate our position that both case-oriented and recurrence- oriented PER are rigorous but that the rigor is of a different nature in each paradigm.

With the exponential growth of research facilitated by modern technology and improved accessibility, scientific discoveries have become increasingly fragmented within and across fields. This makes it challenging to assess the significance, novelty, incremental findings, and equivalent ideas between related works, particularly those from different research communities. Large language models (LLMs) have recently demonstrated strong quantitative and qualitative reasoning abilities, and multi-agent LLM debates have shown promise in handling complex reasoning tasks by exploring diverse perspectives and reasoning paths. Inspired by this, we introduce Tree-of-Debate (ToD), a framework which converts scientific papers into LLM personas that debate their respective novelties. To emphasize structured, critical reasoning rather than focusing solely on outcomes, ToD dynamically constructs a debate tree, enabling fine-grained analysis of independent novelty arguments within scholarly articles. Through experiments on scientific literature across various domains, evaluated by expert researchers, we demonstrate that ToD generates informative arguments, effectively contrasts papers, and supports researchers in their literature review.

The advent of Large Language Models has revolutionized information retrieval, ushering in a new era of expansive knowledge accessibility. While these models excel in providing open-world knowledge, effectively extracting answers in diverse linguistic environments with varying levels of literacy remains a formidable challenge. Retrieval Augmented Generation (RAG) emerges as a promising solution, bridging the gap between information availability and multilingual comprehension. However, deploying RAG models in real-world scenarios demands careful consideration of various factors. This paper addresses the critical challenges associated with implementing RAG models in multicultural environments. We delve into essential considerations, including data feeding strategies, timely updates, mitigation of hallucinations, prevention of erroneous responses, and optimization of delivery speed. Our work involves the integration of a diverse array of tools, meticulously combined to facilitate the seamless adoption of RAG models across languages and literacy levels within a multicultural organizational context. Through strategic tweaks in our approaches, we achieve not only effectiveness but also efficiency, ensuring the accelerated and accurate delivery of information in a manner that is tailored to the unique requirements of multilingual and multicultural settings.

As an efficient approach to understand, generate, and process natural language texts, research in natural language processing (NLP) has exhibited a rapid spread and wide adoption in recent years. Given the increasing research work in this area, several NLP-related approaches have been surveyed in the research community. However, a comprehensive study that categorizes established topics, identifies trends, and outlines areas for future research remains absent. Contributing to closing this gap, we have systematically classified and analyzed research papers in the ACL Anthology. As a result, we present a structured overview of the research landscape, provide a taxonomy of fields of study in NLP, analyze recent developments in NLP, summarize our findings, and highlight directions for future work.

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

The increasing threat of emerging infectious diseases and antimicrobial resistance requires more efficient, high-quality research. Perpetual Observational Studies (POS) nested within a clinical research network can improve planning, quality and efficiency of interventional and observational studies, although real-life benefits and challenges need to be assessed. Ecraid (European Clinical Research Alliance on Infectious Diseases) has initiated POS and will monitor the impact for five specific infectious syndromes.

As researchers increasingly adopt LLMs as writing assistants, generating high-quality research paper introductions remains both challenging and essential. We introduce Scientific Introduction Generation (SciIG), a task that evaluates LLMs' ability to produce coherent introductions from titles, abstracts, and related works. Curating new datasets from NAACL 2025 and ICLR 2025 papers, we assess five state-of-the-art models, including both open-source (DeepSeek-v3, Gemma-3-12B, LLaMA 4-Maverick, MistralAI Small 3.1) and closed-source GPT-4o systems, across multiple dimensions: lexical overlap, semantic similarity, content coverage, faithfulness, consistency, citation correctness, and narrative quality. Our comprehensive framework combines automated metrics with LLM-as-a-judge evaluations. Results demonstrate LLaMA-4 Maverick's superior performance on most metrics, particularly in semantic similarity and faithfulness. Moreover, three-shot prompting consistently outperforms fewer-shot approaches. These findings provide practical insights into developing effective research writing assistants and set realistic expectations for LLM-assisted academic writing. To foster reproducibility and future research, we will publicly release all code and datasets.

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

Extending context windows (i.e., Long Context, LC) and using retrievers to selectively access relevant information (i.e., Retrieval-Augmented Generation, RAG) are the two main strategies to enable LLMs to incorporate extremely long external contexts. This paper revisits recent studies on this topic, highlighting their key insights and discrepancies. We then provide a more comprehensive evaluation by filtering out questions answerable without external context, identifying the most effective retrieval methods, and expanding the datasets. We show that LC generally outperforms RAG in question-answering benchmarks, especially for Wikipedia-based questions. Summarization-based retrieval performs comparably to LC, while chunk-based retrieval lags behind. However, RAG has advantages in dialogue-based and general question queries. These insights underscore the trade-offs between RAG and LC strategies, offering guidance for future optimization of LLMs with external knowledge sources. We also provide an in-depth discussion on this topic, highlighting the overlooked importance of context relevance in existing studies.

Deep Research (DR) is an emerging agent application that leverages large language models (LLMs) to address open-ended queries. It requires the integration of several capabilities, including multi-step reasoning, cross-document synthesis, and the generation of evidence-backed, long-form answers. Evaluating DR remains challenging because responses are lengthy and diverse, admit many valid solutions, and often depend on dynamic information sources. We introduce ResearchRubrics, a standardized benchmark for DR built with over 2,800+ hours of human labor that pairs realistic, domain-diverse prompts with 2,500+ expert-written, fine-grained rubrics to assess factual grounding, reasoning soundness, and clarity. We also propose a new complexity framework for categorizing DR tasks along three axes: conceptual breadth, logical nesting, and exploration. In addition, we develop human and model-based evaluation protocols that measure rubric adherence for DR agents. We evaluate several state-of-the-art DR systems and find that even leading agents like Gemini's DR and OpenAI's DR achieve under 68% average compliance with our rubrics, primarily due to missed implicit context and inadequate reasoning about retrieved information. Our results highlight the need for robust, scalable assessment of deep research capabilities, to which end we release ResearchRubrics(including all prompts, rubrics, and evaluation code) to facilitate progress toward well-justified research assistants.

Existing dense retrieval models struggle with reasoning-intensive retrieval task as they fail to capture implicit relevance that requires reasoning beyond surface-level semantic information. To address these challenges, we propose Scenario-Profiled Indexing with Knowledge Expansion (SPIKE), a dense retrieval framework that explicitly indexes implicit relevance by decomposing documents into scenario-based retrieval units. SPIKE organizes documents into scenario, which encapsulates the reasoning process necessary to uncover implicit relationships between hypothetical information needs and document content. SPIKE constructs a scenario-augmented dataset using a powerful teacher large language model (LLM), then distills these reasoning capabilities into a smaller, efficient scenario generator. During inference, SPIKE incorporates scenario-level relevance alongside document-level relevance, enabling reasoning-aware retrieval. Extensive experiments demonstrate that SPIKE consistently enhances retrieval performance across various query types and dense retrievers. It also enhances the retrieval experience for users through scenario and offers valuable contextual information for LLMs in retrieval-augmented generation (RAG).

With the rapid growth of research in AI and robotics now producing over 10,000 papers annually it has become increasingly difficult for researchers to stay up to date. Fast evolving trends, the rise of interdisciplinary work, and the need to explore domains beyond one's expertise all contribute to this challenge. To address these issues, we propose a generalizable pipeline capable of systematically analyzing any research area: identifying emerging trends, uncovering cross domain opportunities, and offering concrete starting points for new inquiry. In this work, we present Real Deep Research (RDR) a comprehensive framework applied to the domains of AI and robotics, with a particular focus on foundation models and robotics advancements. We also briefly extend our analysis to other areas of science. The main paper details the construction of the RDR pipeline, while the appendix provides extensive results across each analyzed topic. We hope this work sheds light for researchers working in the field of AI and beyond.

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

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.

This study investigates retrieval-augmented summarization by specifically examining the impact of exemplar summary lengths under length constraints, not covered by previous work. We propose a Diverse Length-aware Maximal Marginal Relevance (DL-MMR) algorithm to better control summary lengths. This algorithm combines the query relevance with diverse target lengths in retrieval-augmented summarization. Unlike previous methods that necessitate exhaustive exemplar exemplar relevance comparisons using MMR, DL-MMR considers the exemplar target length as well and avoids comparing exemplars to each other, thereby reducing computational cost and conserving memory during the construction of an exemplar pool. Experimental results showed the effectiveness of DL-MMR, which considers length diversity, compared to the original MMR algorithm. DL-MMR additionally showed the effectiveness in memory saving of 781,513 times and computational cost reduction of 500,092 times, while maintaining the same level of informativeness.

A comprehensive bibliographic review with R statistical methods of the COVID pandemic in PubMed literature and Web of Science Core Collection, supported with Google Scholar search. In addition, a case study review of emerging new approaches in different regions, using medical literature, academic literature, news articles and other reliable data sources. Public responses of mistrust about privacy data misuse differ across countries, depending on the chosen public communication strategy.

Large-scale language models (LLMs) have achieved remarkable success across various language tasks but suffer from hallucinations and temporal misalignment. To mitigate these shortcomings, Retrieval-augmented generation (RAG) has been utilized to provide external knowledge to facilitate the answer generation. However, applying such models to the medical domain faces several challenges due to the lack of domain-specific knowledge and the intricacy of real-world scenarios. In this study, we explore LLMs with RAG framework for knowledge-intensive tasks in the medical field. To evaluate the capabilities of LLMs, we introduce MedicineQA, a multi-round dialogue benchmark that simulates the real-world medication consultation scenario and requires LLMs to answer with retrieved evidence from the medicine database. MedicineQA contains 300 multi-round question-answering pairs, each embedded within a detailed dialogue history, highlighting the challenge posed by this knowledge-intensive task to current LLMs. We further propose a new Distill-Retrieve-Read framework instead of the previous Retrieve-then-Read. Specifically, the distillation and retrieval process utilizes a tool calling mechanism to formulate search queries that emulate the keyword-based inquiries used by search engines. With experimental results, we show that our framework brings notable performance improvements and surpasses the previous counterparts in the evidence retrieval process in terms of evidence retrieval accuracy. This advancement sheds light on applying RAG to the medical domain.

The BigScience Workshop was a value-driven initiative that spanned one and half years of interdisciplinary research and culminated in the creation of ROOTS, a 1.6TB multilingual dataset that was used to train BLOOM, one of the largest multilingual language models to date. In addition to the technical outcomes and artifacts, the workshop fostered multidisciplinary collaborations around large models, datasets, and their analysis. This in turn led to a wide range of research publications spanning topics from ethics to law, data governance, modeling choices and distributed training. This paper focuses on the collaborative research aspects of BigScience and takes a step back to look at the challenges of large-scale participatory research, with respect to participant diversity and the tasks required to successfully carry out such a project. Our main goal is to share the lessons we learned from this experience, what we could have done better and what we did well. We show how the impact of such a social approach to scientific research goes well beyond the technical artifacts that were the basis of its inception.

Paywalls, licenses and copyright rules often restrict the broad dissemination and reuse of scientific knowledge. We take the position that it is both legally and technically feasible to extract the scientific knowledge in scholarly texts. Current methods, like text embeddings, fail to reliably preserve factual content, and simple paraphrasing may not be legally sound. We urge the community to adopt a new idea: convert scholarly documents into Knowledge Units using LLMs. These units use structured data capturing entities, attributes and relationships without stylistic content. We provide evidence that Knowledge Units: (1) form a legally defensible framework for sharing knowledge from copyrighted research texts, based on legal analyses of German copyright law and U.S. Fair Use doctrine, and (2) preserve most (~95%) factual knowledge from original text, measured by MCQ performance on facts from the original copyrighted text across four research domains. Freeing scientific knowledge from copyright promises transformative benefits for scientific research and education by allowing language models to reuse important facts from copyrighted text. To support this, we share open-source tools for converting research documents into Knowledge Units. Overall, our work posits the feasibility of democratizing access to scientific knowledge while respecting copyright.

While hallucinations of large language models could been alleviated through retrieval-augmented generation and citation generation, how the model utilizes internal knowledge is still opaque, and the trustworthiness of its generated answers remains questionable. In this work, we introduce Context-Prior Augmented Citation Generation task, requiring models to generate citations considering both external and internal knowledge while providing trustworthy references, with 5 evaluation metrics focusing on 3 aspects: answer helpfulness, citation faithfulness, and trustworthiness. We introduce RAEL, the paradigm for our task, and also design INTRALIGN, an integrated method containing customary data generation and an alignment algorithm. Our experimental results show that our method achieves a better cross-scenario performance with regard to other baselines. Our extended experiments further reveal that retrieval quality, question types, and model knowledge have considerable influence on the trustworthiness in citation generation.

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

Addressing the challenge of effectively processing long contexts has become a critical issue for Large Language Models (LLMs). Two common strategies have emerged: 1) reducing the input length, such as retrieving relevant chunks by Retrieval-Augmented Generation (RAG), and 2) expanding the context window limit of LLMs. However, both strategies have drawbacks: input reduction has no guarantee of covering the part with needed information, while window extension struggles with focusing on the pertinent information for solving the task. To mitigate these limitations, we propose Chain-of-Agents (CoA), a novel framework that harnesses multi-agent collaboration through natural language to enable information aggregation and context reasoning across various LLMs over long-context tasks. CoA consists of multiple worker agents who sequentially communicate to handle different segmented portions of the text, followed by a manager agent who synthesizes these contributions into a coherent final output. CoA processes the entire input by interleaving reading and reasoning, and it mitigates long context focus issues by assigning each agent a short context. We perform comprehensive evaluation of CoA on a wide range of long-context tasks in question answering, summarization, and code completion, demonstrating significant improvements by up to 10% over strong baselines of RAG, Full-Context, and multi-agent LLMs.

Deep research models perform multi-step research to produce long-form, well-attributed answers. However, most open deep research models are trained on easily verifiable short-form QA tasks via reinforcement learning with verifiable rewards (RLVR), which does not extend to realistic long-form tasks. We address this with Reinforcement Learning with Evolving Rubrics (RLER), in which we construct and maintain rubrics that co-evolve with the policy model during training; this allows the rubrics to incorporate information that the model has newly explored and to provide discriminative, on-policy feedback. Using RLER, we develop Deep Research Tulu (DR Tulu-8B), the first open model that is directly trained for open-ended, long-form deep research. Across four long-form deep research benchmarks in science, healthcare and general domains, DR Tulu substantially outperforms existing open deep research models, and matches or exceeds proprietary deep research systems, while being significantly smaller and cheaper per query. To facilitate future research, we release all data, models, and code, including our new MCP-based agent infrastructure for deep research systems.

Retrieval-augmented generation (RAG) provides LLMs with relevant documents. Although previous studies noted that retrieving many documents can degrade performance, they did not isolate how the quantity of documents affects performance while controlling for context length. We evaluate various language models on custom datasets derived from a multi-hop QA task. We keep the context length and position of relevant information constant while varying the number of documents, and find that increasing the document count in RAG settings poses significant challenges for LLMs. Additionally, our results indicate that processing multiple documents is a separate challenge from handling long contexts. We also make the datasets and code available: https://github.com/shaharl6000/MoreDocsSameLen .

Recent advancements in Large Language Models (LLMs) have significantly enhanced their ability to process long contexts, yet a notable gap remains in generating long, aligned outputs. This limitation stems from a training gap where pre-training lacks effective instructions for long-text generation, and post-training data primarily consists of short query-response pairs. Current approaches, such as instruction backtranslation and behavior imitation, face challenges including data quality, copyright issues, and constraints on proprietary model usage. In this paper, we introduce an innovative iterative training framework called Self-Lengthen that leverages only the intrinsic knowledge and skills of LLMs without the need for auxiliary data or proprietary models. The framework consists of two roles: the Generator and the Extender. The Generator produces the initial response, which is then split and expanded by the Extender. This process results in a new, longer response, which is used to train both the Generator and the Extender iteratively. Through this process, the models are progressively trained to handle increasingly longer responses. Experiments on benchmarks and human evaluations show that Self-Lengthen outperforms existing methods in long-text generation, when applied to top open-source LLMs such as Qwen2 and LLaMA3. Our code is publicly available at https://github.com/QwenLM/Self-Lengthen.

Literature research, vital for scientific work, faces the challenge of the surging torrent of information in the vast ocean of literature exceeding researchers' processing capabilities. To address this issue, we present an automated review generation method based on Large Language Models (LLMs), aimed at overcoming efficiency bottlenecks in literature processing and reducing cognitive load. Our statistically validated evaluation framework demonstrates that the generated reviews match or exceed manual quality, offering broad applicability across research fields due to minimal domain knowledge requirements. In a case study on propane dehydrogenation (PDH) catalysts, our method swiftly analyzed 343 articles, averaging seconds per article per LLM account, producing comprehensive reviews spanning 35 topics. Extended analysis of 1041 articles provided deep insights into catalysts' composition, structure, and performance. Recognizing LLMs' hallucinations, we implemented a multi-layered quality control strategy, effectively mitigating risks and ensuring reliability, as quantitatively demonstrated through manual verification. Expert verification confirms the accuracy and citation integrity of generated reviews, demonstrating LLM hallucination risks reduced to below 0.5\% with over 95\% confidence. Released Windows application enables one-click review generation, aiding researchers in tracking advancements and recommending literature. This approach showcases LLMs' role in enhancing scientific research productivity and sets the stage for further exploration.

This survey examines the rapidly evolving field of Deep Research systems -- AI-powered applications that automate complex research workflows through the integration of large language models, advanced information retrieval, and autonomous reasoning capabilities. We analyze more than 80 commercial and non-commercial implementations that have emerged since 2023, including OpenAI/Deep Research, Gemini/Deep Research, Perplexity/Deep Research, and numerous open-source alternatives. Through comprehensive examination, we propose a novel hierarchical taxonomy that categorizes systems according to four fundamental technical dimensions: foundation models and reasoning engines, tool utilization and environmental interaction, task planning and execution control, and knowledge synthesis and output generation. We explore the architectural patterns, implementation approaches, and domain-specific adaptations that characterize these systems across academic, scientific, business, and educational applications. Our analysis reveals both the significant capabilities of current implementations and the technical and ethical challenges they present regarding information accuracy, privacy, intellectual property, and accessibility. The survey concludes by identifying promising research directions in advanced reasoning architectures, multimodal integration, domain specialization, human-AI collaboration, and ecosystem standardization that will likely shape the future evolution of this transformative technology. By providing a comprehensive framework for understanding Deep Research systems, this survey contributes to both the theoretical understanding of AI-augmented knowledge work and the practical development of more capable, responsible, and accessible research technologies. The paper resources can be viewed at https://github.com/scienceaix/deepresearch.

The rapid expansion of chemistry literature poses significant challenges for researchers seeking to efficiently access domain-specific knowledge. To support advancements in chemistry-focused natural language processing (NLP), we present ChemRxivQuest, a curated dataset of 970 high-quality question-answer (QA) pairs derived from 155 ChemRxiv preprints across 17 subfields of chemistry. Each QA pair is explicitly linked to its source text segment to ensure traceability and contextual accuracy. ChemRxivQuest was constructed using an automated pipeline that combines optical character recognition (OCR), GPT-4o-based QA generation, and a fuzzy matching technique for answer verification. The dataset emphasizes conceptual, mechanistic, applied, and experimental questions, enabling applications in retrieval-based QA systems, search engine development, and fine-tuning of domain-adapted large language models. We analyze the dataset's structure, coverage, and limitations, and outline future directions for expansion and expert validation. ChemRxivQuest provides a foundational resource for chemistry NLP research, education, and tool development.

Judging the novelty of research ideas is crucial for advancing science, enabling the identification of unexplored directions, and ensuring contributions meaningfully extend existing knowledge rather than reiterate minor variations. However, given the exponential growth of scientific literature, manually judging the novelty of research ideas through literature reviews is labor-intensive, subjective, and infeasible at scale. Therefore, recent efforts have proposed automated approaches for research idea novelty judgment. Yet, evaluation of these approaches remains largely inconsistent and is typically based on non-standardized human evaluations, hindering large-scale, comparable evaluations. To address this, we introduce RINoBench, the first comprehensive benchmark for large-scale evaluation of research idea novelty judgments. It comprises 1,381 research ideas derived from and judged by human experts as well as nine automated evaluation metrics designed to assess both rubric-based novelty scores and textual justifications of novelty judgments. Using this benchmark, we evaluate several state-of-the-art large language models (LLMs) on their ability to judge the novelty of research ideas. Our findings reveal that while LLM-generated reasoning closely mirrors human rationales, this alignment does not reliably translate into accurate novelty judgments, which diverge significantly from human gold standard judgments - even among leading reasoning-capable models. Data and code available at: https://github.com/TimSchopf/RINoBench.

Designing a generalist scientific agent capable of performing tasks in laboratory settings to assist researchers has become a key goal in recent Artificial Intelligence (AI) research. Unlike everyday tasks, scientific tasks are inherently more delicate and complex, requiring agents to possess a higher level of reasoning ability, structured and temporal understanding of their environment, and a strong emphasis on safety. Existing approaches often fail to address these multifaceted requirements. To tackle these challenges, we present DAVIS. Unlike traditional retrieval-augmented generation (RAG) approaches, DAVIS incorporates structured and temporal memory, which enables model-based planning. Additionally, DAVIS implements an agentic, multi-turn retrieval system, similar to a human's inner monologue, allowing for a greater degree of reasoning over past experiences. DAVIS demonstrates substantially improved performance on the ScienceWorld benchmark comparing to previous approaches on 8 out of 9 elementary science subjects. In addition, DAVIS's World Model demonstrates competitive performance on the famous HotpotQA and MusiqueQA dataset for multi-hop question answering. To the best of our knowledge, DAVIS is the first RAG agent to employ an interactive retrieval method in a RAG pipeline.

Bibliometric and usage-based analyses and tools highlight the value of information about scholarship contained within the network of authors, articles and usage data. Less progress has been made on populating and using the author side of this network than the article side, in part because of the difficulty of unambiguously identifying authors. I briefly review a sample of author identifier schemes, and consider use in scholarly repositories. I then describe preliminary work at arXiv to implement public author identifiers, services based on them, and plans to make this information useful beyond the boundaries of arXiv.

In this work, we focus on the problem of retrieving relevant arguments for a query claim covering diverse aspects. State-of-the-art methods rely on explicit mappings between claims and premises, and thus are unable to utilize large available collections of premises without laborious and costly manual annotation. Their diversity approach relies on removing duplicates via clustering which does not directly ensure that the selected premises cover all aspects. This work introduces a new multi-step approach for the argument retrieval problem. Rather than relying on ground-truth assignments, our approach employs a machine learning model to capture semantic relationships between arguments. Beyond that, it aims to cover diverse facets of the query, instead of trying to identify duplicates explicitly. Our empirical evaluation demonstrates that our approach leads to a significant improvement in the argument retrieval task even though it requires less data.

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.

Large language models (LLMs) have sparked growing interest in automatic machine learning research agents. Among them, agents capable of autonomously proposing ideas and conducting machine learning experiments are particularly promising, as they maximize research automation and accelerate scientific progress by iteratively refining ideas based on experimental results. However, comprehensively evaluating such agents remains challenging. Existing benchmarks tend to overemphasize engineering aspects while neglecting academic rigor, creating barriers that obscure a clear assessment of an agent's scientific capabilities in machine learning research. They also suffer from limited task diversity, an overemphasis on application-oriented tasks over fundamental research problems, and limited scalability to realistic research settings. To address these limitations, we introduce FML-bench, a benchmark designed to evaluate automatic machine learning research agents on 8 diverse and fundamental machine learning research problems. It reduces coding burden, emphasizes fundamental problems rather than specific use cases, offers high task diversity, and is extensible to real-world machine learning GitHub repositories. Furthermore, we present a unified evaluation framework with five complementary metrics, designed to comprehensively assess agent performance on our benchmark. We evaluate state-of-the-art automatic research agents on FML-bench, and find that agents employing broad research exploration strategies outperform those focusing on narrow but deep exploration. These findings suggest that emphasizing the breadth of exploration may lead to more effective research outcomes than focusing solely on incremental refinement. Our benchmark is available at https://github.com/qrzou/FML-bench.