Daily Papers

Animal ecology data collection using drones represents a substantial investment of time, expertise, and financial resources. Yet most existing datasets serve only a single research community, limiting interdisciplinary reuse. We propose a unified drone dataset standard, FAIR^2 Drones, that bridges ecology, robotics, and computer vision by building on existing FAIR and AI-ready data frameworks while adding essential platform metadata and annotation specifications. Our standard enables datasets to simultaneously support ecological analysis, robotics algorithm development, and computer vision benchmarking. We provide open-source validation tools, reference implementations, and multimodal extensions linking drone imagery with complementary sensors such as camera traps, GPS, and acoustics. By standardizing metadata across disciplines, this framework maximizes the scientific return on investment for costly field deployments and accelerates cross-domain collaboration in environmental monitoring.

As Engineering Education Research (EER) develops as a discipline it is necessary for EER scholars to contribute to the development of learning theory rather than simply being informed by it. It has been suggested that to do this effectively will require partnerships between Engineering scholars and psychologists, education researchers, including other social scientists. The formation of such partnerships is particularly important when considering the introduction of business-related skills into engineering curriculum designed to prepare 21st Century Engineering Students for workplace challenges. In order to encourage scholars beyond Engineering to engage with EER, it is necessary to provide an introduction to the complexities of EER. With this aim in mind, this paper provides an outline review of what is considered rigorous research from an EER perspective as well as highlighting some of the core methodological traditions of EER. The paper aims to facilitate further discussion between EER scholars and researchers from other disciplines, ultimately leading to future collaboration on innovative and rigorous EER.

This paper introduces ClimateGPT, a model family of domain-specific large language models that synthesize interdisciplinary research on climate change. We trained two 7B models from scratch on a science-oriented dataset of 300B tokens. For the first model, the 4.2B domain-specific tokens were included during pre-training and the second was adapted to the climate domain after pre-training. Additionally, ClimateGPT-7B, 13B and 70B are continuously pre-trained from Llama~2 on a domain-specific dataset of 4.2B tokens. Each model is instruction fine-tuned on a high-quality and human-generated domain-specific dataset that has been created in close cooperation with climate scientists. To reduce the number of hallucinations, we optimize the model for retrieval augmentation and propose a hierarchical retrieval strategy. To increase the accessibility of our model to non-English speakers, we propose to make use of cascaded machine translation and show that this approach can perform comparably to natively multilingual models while being easier to scale to a large number of languages. Further, to address the intrinsic interdisciplinary aspect of climate change we consider different research perspectives. Therefore, the model can produce in-depth answers focusing on different perspectives in addition to an overall answer. We propose a suite of automatic climate-specific benchmarks to evaluate LLMs. On these benchmarks, ClimateGPT-7B performs on par with the ten times larger Llama-2-70B Chat model while not degrading results on general domain benchmarks. Our human evaluation confirms the trends we saw in our benchmarks. All models were trained and evaluated using renewable energy and are released publicly.

Innovation is a key driving force of human civilization. As the body of knowledge has grown considerably, bridging knowledge across different disciplines, where significant innovation often emerges, has become increasingly challenging. The recent advancements in machine learning models, particularly Large Language Models (LLMs), have provided effective access to extensive knowledge sources and shown impressive abilities in reasoning, rendering significant opportunities for interdisciplinary discovery. Our research aims to understand the capabilities of state-of-the-art LLMs in integrating knowledge from different fields for interdisciplinary research (IDR). To address this fundamental problem, we introduce IDRBench, a pioneering framework that includes both datasets and evaluation tasks: (1) IDR Paper Identification, (2) IDR Idea Integration, and (3) IDR Idea Recommendation. Our study on ten mainstream LLMs provides a comprehensive analysis of their behavior and establishes benchmarks and baselines for future research. To the best of our knowledge, IDRBench is the first to provide a comprehensive investigation of LLMs' IDR capability.

Identifying and predicting the factors that contribute to the success of interdisciplinary research is crucial for advancing scientific discovery. However, there is a lack of methods to quantify the integration of new ideas and technological advancements in astronomical research and how these new technologies drive further scientific breakthroughs. Large language models, with their ability to extract key concepts from vast literature beyond keyword searches, provide a new tool to quantify such processes. In this study, we extracted concepts in astronomical research from 297,807 publications between 1993 and 2024 using large language models, resulting in a set of 24,939 concepts. These concepts were then used to form a knowledge graph, where the link strength between any two concepts was determined by their relevance through the citation-reference relationships. By calculating this relevance across different time periods, we quantified the impact of numerical simulations and machine learning on astronomical research. The knowledge graph demonstrates two phases of development: a phase where the technology was integrated and another where the technology was explored in scientific discovery. The knowledge graph reveals that despite machine learning has made much inroad in astronomy, there is currently a lack of new concept development at the intersection of AI and Astronomy, which may be the current bottleneck preventing machine learning from further transforming the field of astronomy.

Despite interdisciplinary research leading to larger and longer-term impact, most work remains confined to single-domain academic silos. Recent AI-based approaches to scientific discovery show promise for interdisciplinary research, but many prioritize rapidly designing experiments and solutions, bypassing the exploratory, collaborative reasoning processes that drive creative interdisciplinary breakthroughs. As a result, prior efforts largely prioritize automating scientific discovery rather than augmenting the reasoning processes that underlie scientific disruption. We present Idea-Catalyst, a novel framework that systematically identifies interdisciplinary insights to support creative reasoning in both humans and large language models. Starting from an abstract research goal, Idea-Catalyst is designed to assist the brainstorming stage, explicitly avoiding premature anchoring on specific solutions. The framework embodies key metacognitive features of interdisciplinary reasoning: (a) defining and assessing research goals, (b) awareness of a domain's opportunities and unresolved challenges, and (c) strategic exploration of interdisciplinary ideas based on impact potential. Concretely, Idea-Catalyst decomposes an abstract goal (e.g., improving human-AI collaboration) into core target-domain research questions that guide the analysis of progress and open challenges within that domain. These challenges are reformulated as domain-agnostic conceptual problems, enabling retrieval from external disciplines (e.g., Psychology, Sociology) that address analogous issues. By synthesizing and recontextualizing insights from these domains back into the target domain, Idea-Catalyst ranks source domains by their interdisciplinary potential. Empirically, this targeted integration improves average novelty by 21% and insightfulness by 16%, while remaining grounded in the original research problem.

Large Language Models (LLMs) have demonstrated remarkable potential in scientific domains, yet a fundamental question remains unanswered: Can we simulate human research communities with LLMs? Addressing this question can deepen our understanding of the processes behind idea brainstorming and inspire the automatic discovery of novel scientific insights. In this work, we propose ResearchTown, a multi-agent framework for research community simulation. Within this framework, the human research community is simplified and modeled as an agent-data graph, where researchers and papers are represented as agent-type and data-type nodes, respectively, and connected based on their collaboration relationships. We also introduce TextGNN, a text-based inference framework that models various research activities (e.g., paper reading, paper writing, and review writing) as special forms of a unified message-passing process on the agent-data graph. To evaluate the quality of the research simulation, we present ResearchBench, a benchmark that uses a node-masking prediction task for scalable and objective assessment based on similarity. Our experiments reveal three key findings: (1) ResearchTown can provide a realistic simulation of collaborative research activities, including paper writing and review writing; (2) ResearchTown can maintain robust simulation with multiple researchers and diverse papers; (3) ResearchTown can generate interdisciplinary research ideas that potentially inspire novel research directions.

This paper presents a scientometric analysis of research output from the University of Lagos, focusing on the two decades spanning 2004 to 2023. Using bibliometric data retrieved from the Web of Science, we examine trends in publication volume, collaboration patterns, citation impact, and the most prolific authors, departments, and research domains at the university. The study reveals a consistent increase in research productivity, with the highest publication output recorded in 2023. Health Sciences, Engineering, and Social Sciences are identified as dominant fields, reflecting the university's interdisciplinary research strengths. Collaborative efforts, both locally and internationally, show a positive correlation with higher citation impact, with the United States and the United Kingdom being the leading international collaborators. Notably, open-access publications account for a significant portion of the university's research output, enhancing visibility and citation rates. The findings offer valuable insights into the university's research performance over the past two decades, providing a foundation for strategic planning and policy formulation to foster research excellence and global impact.

In recent years, groundbreaking advancements in natural language processing have culminated in the emergence of powerful large language models (LLMs), which have showcased remarkable capabilities across a vast array of domains, including the understanding, generation, and translation of natural language, and even tasks that extend beyond language processing. In this report, we delve into the performance of LLMs within the context of scientific discovery, focusing on GPT-4, the state-of-the-art language model. Our investigation spans a diverse range of scientific areas encompassing drug discovery, biology, computational chemistry (density functional theory (DFT) and molecular dynamics (MD)), materials design, and partial differential equations (PDE). Evaluating GPT-4 on scientific tasks is crucial for uncovering its potential across various research domains, validating its domain-specific expertise, accelerating scientific progress, optimizing resource allocation, guiding future model development, and fostering interdisciplinary research. Our exploration methodology primarily consists of expert-driven case assessments, which offer qualitative insights into the model's comprehension of intricate scientific concepts and relationships, and occasionally benchmark testing, which quantitatively evaluates the model's capacity to solve well-defined domain-specific problems. Our preliminary exploration indicates that GPT-4 exhibits promising potential for a variety of scientific applications, demonstrating its aptitude for handling complex problem-solving and knowledge integration tasks. Broadly speaking, we evaluate GPT-4's knowledge base, scientific understanding, scientific numerical calculation abilities, and various scientific prediction capabilities.

People rely on social skills like conflict resolution to communicate effectively and to thrive in both work and personal life. However, practice environments for social skills are typically out of reach for most people. How can we make social skill training more available, accessible, and inviting? Drawing upon interdisciplinary research from communication and psychology, this perspective paper identifies social skill barriers to enter specialized fields. Then we present a solution that leverages large language models for social skill training via a generic framework. Our AI Partner, AI Mentor framework merges experiential learning with realistic practice and tailored feedback. This work ultimately calls for cross-disciplinary innovation to address the broader implications for workforce development and social equality.

Work in Computational Affective Science and Computational Social Science explores a wide variety of research questions about people, emotions, behavior, and health. Such work often relies on language data that is first labeled with relevant information, such as the use of emotion words or the age of the speaker. Although many resources and algorithms exist to enable this type of labeling, discovering, accessing, and using them remains a substantial impediment, particularly for practitioners outside of computer science. Here, we present the ABCDE dataset (Affect, Body, Cognition, Demographics, and Emotion), a large-scale collection of over 400 million text utterances drawn from social media, blogs, books, and AI-generated sources. The dataset is annotated with a wide range of features relevant to computational affective and social science. ABCDE facilitates interdisciplinary research across numerous fields, including affective science, cognitive science, the digital humanities, sociology, political science, and computational linguistics.

Recent advances of data-driven machine learning have revolutionized fields like computer vision, reinforcement learning, and many scientific and engineering domains. In many real-world and scientific problems, systems that generate data are governed by physical laws. Recent work shows that it provides potential benefits for machine learning models by incorporating the physical prior and collected data, which makes the intersection of machine learning and physics become a prevailing paradigm. By integrating the data and mathematical physics models seamlessly, it can guide the machine learning model towards solutions that are physically plausible, improving accuracy and efficiency even in uncertain and high-dimensional contexts. In this survey, we present this learning paradigm called Physics-Informed Machine Learning (PIML) which is to build a model that leverages empirical data and available physical prior knowledge to improve performance on a set of tasks that involve a physical mechanism. We systematically review the recent development of physics-informed machine learning from three perspectives of machine learning tasks, representation of physical prior, and methods for incorporating physical prior. We also propose several important open research problems based on the current trends in the field. We argue that encoding different forms of physical prior into model architectures, optimizers, inference algorithms, and significant domain-specific applications like inverse engineering design and robotic control is far from being fully explored in the field of physics-informed machine learning. We believe that the interdisciplinary research of physics-informed machine learning will significantly propel research progress, foster the creation of more effective machine learning models, and also offer invaluable assistance in addressing long-standing problems in related disciplines.

Recent advances in generative AI for music have achieved remarkable fidelity and stylistic diversity, yet these systems often fail to align with nuanced human preferences due to the specific loss functions they use. This paper advocates for the systematic application of preference alignment techniques to music generation, addressing the fundamental gap between computational optimization and human musical appreciation. Drawing on recent breakthroughs including MusicRL's large-scale preference learning, multi-preference alignment frameworks like diffusion-based preference optimization in DiffRhythm+, and inference-time optimization techniques like Text2midi-InferAlign, we discuss how these techniques can address music's unique challenges: temporal coherence, harmonic consistency, and subjective quality assessment. We identify key research challenges including scalability to long-form compositions, reliability amongst others in preference modelling. Looking forward, we envision preference-aligned music generation enabling transformative applications in interactive composition tools and personalized music services. This work calls for sustained interdisciplinary research combining advances in machine learning, music-theory to create music AI systems that truly serve human creative and experiential needs.

Through iterative, cross-disciplinary discussions, we define and propose next-steps for Human-centered Generative AI (HGAI) from a technical perspective. We contribute a roadmap that lays out future directions of Generative AI spanning three levels: Aligning with human values; Accommodating humans' expression of intents; and Augmenting humans' abilities in a collaborative workflow. This roadmap intends to draw interdisciplinary research teams to a comprehensive list of emergent ideas in HGAI, identifying their interested topics while maintaining a coherent big picture of the future work landscape.

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.

Machine learning is a general-purpose technology holding promises for many interdisciplinary research problems. However, significant barriers exist in crossing disciplinary boundaries when most machine learning tools are developed in different areas separately. We present Pykale - a Python library for knowledge-aware machine learning on graphs, images, texts, and videos to enable and accelerate interdisciplinary research. We formulate new green machine learning guidelines based on standard software engineering practices and propose a novel pipeline-based application programming interface (API). PyKale focuses on leveraging knowledge from multiple sources for accurate and interpretable prediction, thus supporting multimodal learning and transfer learning (particularly domain adaptation) with latest deep learning and dimensionality reduction models. We build PyKale on PyTorch and leverage the rich PyTorch ecosystem. Our pipeline-based API design enforces standardization and minimalism, embracing green machine learning concepts via reducing repetitions and redundancy, reusing existing resources, and recycling learning models across areas. We demonstrate its interdisciplinary nature via examples in bioinformatics, knowledge graph, image/video recognition, and medical imaging.

Recent advances in deep learning inspired neural network-based approaches to computational materials discovery (CMD). A plethora of problems in this field involve finding materials that optimize a target property. Nevertheless, the increasingly popular generative modeling methods are ineffective at boldly exploring attractive regions of the materials space due to their maximum likelihood training. In this work, we offer an alternative CMD technique based on offline model-based optimization (MBO) that fuses direct optimization of a target material property into generation. To that end, we introduce a domain-specific model, dubbed CliqueFlowmer, that incorporates recent advances of clique-based MBO into transformer and flow generation. We validate CliqueFlowmer's optimization abilities and show that materials it produces strongly outperform those provided by generative baselines. To enable employment of CliqueFlowmer in specialized materials optimization problems and support interdisciplinary research, we open-source our code at https://github.com/znowu/CliqueFlowmer.

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.

The growing prevalence of conversational voice interfaces, powered by developments in both speech and language technologies, raises important questions about their influence on human communication. While written communication can signal identity through lexical and stylistic choices, voice-based interactions inherently amplify socioindexical elements - such as accent, intonation, and speech style - which more prominently convey social identity and group affiliation. There is evidence that even passive media such as television is likely to influence the audience's linguistic patterns. Unlike passive media, conversational AI is interactive, creating a more immersive and reciprocal dynamic that holds a greater potential to impact how individuals speak in everyday interactions. Such heightened influence can be expected to arise from phenomena such as acoustic-prosodic entrainment and linguistic accommodation, which occur naturally during interaction and enable users to adapt their speech patterns in response to the system. While this phenomenon is still emerging, its potential societal impact could provide organisations, movements, and brands with a subtle yet powerful avenue for shaping and controlling public perception and social identity. We argue that the socioindexical influence of AI-generated speech warrants attention and should become a focus of interdisciplinary research, leveraging new and existing methodologies and technologies to better understand its implications.

Large Language Models (LLMs) have extended their impact beyond Natural Language Processing, substantially fostering the development of interdisciplinary research. Recently, various LLM-based agents have been developed to assist scientific discovery progress across multiple aspects and domains. Among these, computer-using agents, capable of interacting with operating systems as humans do, are paving the way to automated scientific problem-solving and addressing routines in researchers' workflows. Recognizing the transformative potential of these agents, we introduce ScienceBoard, which encompasses two complementary contributions: (i) a realistic, multi-domain environment featuring dynamic and visually rich scientific workflows with integrated professional software, where agents can autonomously interact via different interfaces to accelerate complex research tasks and experiments; and (ii) a challenging benchmark of 169 high-quality, rigorously validated real-world tasks curated by humans, spanning scientific-discovery workflows in domains such as biochemistry, astronomy, and geoinformatics. Extensive evaluations of agents with state-of-the-art backbones (e.g., GPT-4o, Claude 3.7, UI-TARS) show that, despite some promising results, they still fall short of reliably assisting scientists in complex workflows, achieving only a 15% overall success rate. In-depth analysis further provides valuable insights for addressing current agent limitations and more effective design principles, paving the way to build more capable agents for scientific discovery. Our code, environment, and benchmark are at https://qiushisun.github.io/ScienceBoard-Home/.

Large language models (LLMs) have shown remarkable capabilities, but still struggle with processing extensive contexts, limiting their ability to maintain coherence and accuracy over long sequences. In contrast, the human brain excels at organising and retrieving episodic experiences across vast temporal scales, spanning a lifetime. In this work, we introduce EM-LLM, a novel approach that integrates key aspects of human episodic memory and event cognition into LLMs, enabling them to effectively handle practically infinite context lengths while maintaining computational efficiency. EM-LLM organises sequences of tokens into coherent episodic events using a combination of Bayesian surprise and graph-theoretic boundary refinement in an on-line fashion. When needed, these events are retrieved through a two-stage memory process, combining similarity-based and temporally contiguous retrieval for efficient and human-like access to relevant information. Experiments on the LongBench dataset demonstrate EM-LLM's superior performance, outperforming the state-of-the-art InfLLM model with an overall relative improvement of 4.3% across various tasks, including a 33% improvement on the PassageRetrieval task. Furthermore, our analysis reveals strong correlations between EM-LLM's event segmentation and human-perceived events, suggesting a bridge between this artificial system and its biological counterpart. This work not only advances LLM capabilities in processing extended contexts but also provides a computational framework for exploring human memory mechanisms, opening new avenues for interdisciplinary research in AI and cognitive science.

Making moral judgments is an essential step toward developing ethical AI systems. Prevalent approaches are mostly implemented in a bottom-up manner, which uses a large set of annotated data to train models based on crowd-sourced opinions about morality. These approaches have been criticized for potentially overgeneralizing a limited group of annotators' moral stances and lacking explainability. In contrast, top-down approaches make moral judgments grounded in a set of principles. However, it remains conceptual due to the incapability of previous language models and the unsolved debate among moral principles. In this study, we propose a flexible framework to steer Large Language Models (LLMs) to perform moral reasoning with well-established moral theories from interdisciplinary research. The theory-guided top-down framework can incorporate various moral theories. Our experiments demonstrate the effectiveness of the proposed framework on datasets derived from moral theories. Furthermore, we show the alignment between different moral theories and existing morality datasets. Our analysis exhibits the potentials and flaws in existing resources (models and datasets) in developing explainable moral judgment-making systems.

As large language models (LLMs) are more frequently used in retrieval-augmented generation pipelines, it is increasingly relevant to study their behavior under knowledge conflicts. Thus far, the role of the source of the retrieved information has gone unexamined. We address this gap with a novel framework to investigate how source preferences affect LLM resolution of inter-context knowledge conflicts in English, motivated by interdisciplinary research on credibility. With a comprehensive, tightly-controlled evaluation of 13 open-weight LLMs, we find that LLMs prefer institutionally-corroborated information (e.g., government or newspaper sources) over information from people and social media. However, these source preferences can be reversed by simply repeating information from less credible sources. To mitigate repetition effects and maintain consistent preferences, we propose a novel method that reduces repetition bias by up to 99.8%, while also maintaining at least 88.8% of original preferences. We release all data and code to encourage future work on credibility and source preferences in knowledge-intensive NLP.

Scientific literature is growing exponentially, creating a critical bottleneck for researchers to efficiently synthesize knowledge. While general-purpose Large Language Models (LLMs) show potential in text processing, they often fail to capture scientific domain-specific nuances (e.g., technical jargon, methodological rigor) and struggle with complex scientific tasks, limiting their utility for interdisciplinary research. To address these gaps, this paper presents SciGPT, a domain-adapted foundation model for scientific literature understanding and ScienceBench, an open source benchmark tailored to evaluate scientific LLMs. Built on the Qwen3 architecture, SciGPT incorporates three key innovations: (1) low-cost domain distillation via a two-stage pipeline to balance performance and efficiency; (2) a Sparse Mixture-of-Experts (SMoE) attention mechanism that cuts memory consumption by 55\% for 32,000-token long-document reasoning; and (3) knowledge-aware adaptation integrating domain ontologies to bridge interdisciplinary knowledge gaps. Experimental results on ScienceBench show that SciGPT outperforms GPT-4o in core scientific tasks including sequence labeling, generation, and inference. It also exhibits strong robustness in unseen scientific tasks, validating its potential to facilitate AI-augmented scientific discovery.

Large Language Models (LLMs) are reshaping many aspects of materials science and chemistry research, enabling advances in molecular property prediction, materials design, scientific automation, knowledge extraction, and more. Recent developments demonstrate that the latest class of models are able to integrate structured and unstructured data, assist in hypothesis generation, and streamline research workflows. To explore the frontier of LLM capabilities across the research lifecycle, we review applications of LLMs through 34 total projects developed during the second annual Large Language Model Hackathon for Applications in Materials Science and Chemistry, a global hybrid event. These projects spanned seven key research areas: (1) molecular and material property prediction, (2) molecular and material design, (3) automation and novel interfaces, (4) scientific communication and education, (5) research data management and automation, (6) hypothesis generation and evaluation, and (7) knowledge extraction and reasoning from the scientific literature. Collectively, these applications illustrate how LLMs serve as versatile predictive models, platforms for rapid prototyping of domain-specific tools, and much more. In particular, improvements in both open source and proprietary LLM performance through the addition of reasoning, additional training data, and new techniques have expanded effectiveness, particularly in low-data environments and interdisciplinary research. As LLMs continue to improve, their integration into scientific workflows presents both new opportunities and new challenges, requiring ongoing exploration, continued refinement, and further research to address reliability, interpretability, and reproducibility.

Vector data is one of the two core data structures in geographic information science (GIS), essential for accurately storing and representing geospatial information. Shapefile, the most widely used vector data format, has become the industry standard supported by all major geographic information systems. However, processing this data typically requires specialized GIS knowledge and skills, creating a barrier for researchers from other fields and impeding interdisciplinary research in spatial data analysis. Moreover, while large language models (LLMs) have made significant advancements in natural language processing and task automation, they still face challenges in handling the complex spatial and topological relationships inherent in GIS vector data. To address these challenges, we propose ShapefileGPT, an innovative framework powered by LLMs, specifically designed to automate Shapefile tasks. ShapefileGPT utilizes a multi-agent architecture, in which the planner agent is responsible for task decomposition and supervision, while the worker agent executes the tasks. We developed a specialized function library for handling Shapefiles and provided comprehensive API documentation, enabling the worker agent to operate Shapefiles efficiently through function calling. For evaluation, we developed a benchmark dataset based on authoritative textbooks, encompassing tasks in categories such as geometric operations and spatial queries. ShapefileGPT achieved a task success rate of 95.24%, outperforming the GPT series models. In comparison to traditional LLMs, ShapefileGPT effectively handles complex vector data analysis tasks, overcoming the limitations of traditional LLMs in spatial analysis. This breakthrough opens new pathways for advancing automation and intelligence in the GIS field, with significant potential in interdisciplinary data analysis and application contexts.

Generalizable manipulation skills, which can be composed to tackle long-horizon and complex daily chores, are one of the cornerstones of Embodied AI. However, existing benchmarks, mostly composed of a suite of simulatable environments, are insufficient to push cutting-edge research works because they lack object-level topological and geometric variations, are not based on fully dynamic simulation, or are short of native support for multiple types of manipulation tasks. To this end, we present ManiSkill2, the next generation of the SAPIEN ManiSkill benchmark, to address critical pain points often encountered by researchers when using benchmarks for generalizable manipulation skills. ManiSkill2 includes 20 manipulation task families with 2000+ object models and 4M+ demonstration frames, which cover stationary/mobile-base, single/dual-arm, and rigid/soft-body manipulation tasks with 2D/3D-input data simulated by fully dynamic engines. It defines a unified interface and evaluation protocol to support a wide range of algorithms (e.g., classic sense-plan-act, RL, IL), visual observations (point cloud, RGBD), and controllers (e.g., action type and parameterization). Moreover, it empowers fast visual input learning algorithms so that a CNN-based policy can collect samples at about 2000 FPS with 1 GPU and 16 processes on a regular workstation. It implements a render server infrastructure to allow sharing rendering resources across all environments, thereby significantly reducing memory usage. We open-source all codes of our benchmark (simulator, environments, and baselines) and host an online challenge open to interdisciplinary researchers.

Recent technological advances, especially in the field of machine learning, provide astonishing progress on the road towards artificial general intelligence. However, tasks in current real-world business applications cannot yet be solved by machines alone. We, therefore, identify the need for developing socio-technological ensembles of humans and machines. Such systems possess the ability to accomplish complex goals by combining human and artificial intelligence to collectively achieve superior results and continuously improve by learning from each other. Thus, the need for structured design knowledge for those systems arises. Following a taxonomy development method, this article provides three main contributions: First, we present a structured overview of interdisciplinary research on the role of humans in the machine learning pipeline. Second, we envision hybrid intelligence systems and conceptualize the relevant dimensions for system design for the first time. Finally, we offer useful guidance for system developers during the implementation of such applications.

In Open Source Software, the source code and any other resources available in a project can be viewed or reused by anyone subject to often permissive licensing restrictions. In contrast to some studies of dependency-based reuse supported via package managers, no studies of OSS-wide copy-based reuse exist. This dataset seeks to encourage the studies of OSS-wide copy-based reuse by providing copying activity data that captures whole-file reuse in nearly all OSS. To accomplish that, we develop approaches to detect copy-based reuse by developing an efficient algorithm that exploits World of Code infrastructure: a curated and cross referenced collection of nearly all open source repositories. We expect this data to enable future research and tool development that support such reuse and minimize associated risks.

Despite efforts to mitigate the inherent risks and biases of artificial intelligence (AI) algorithms, these algorithms can disproportionately impact culturally marginalized groups. A range of approaches has been proposed to address or reduce these risks, including the development of ethical guidelines and principles for responsible AI, as well as technical solutions that promote algorithmic fairness. Drawing on design justice, expansive learning theory, and recent empirical work on participatory AI, we argue that mitigating these harms requires a fundamental re-architecture of the AI production pipeline. This re-design should center co-production, diversity, equity, inclusion (DEI), and multidisciplinary collaboration. We introduce an augmented AI lifecycle consisting of five interconnected phases: co-framing, co-design, co-implementation, co-deployment, and co-maintenance. The lifecycle is informed by four multidisciplinary workshops and grounded in themes of distributed authority and iterative knowledge exchange. Finally, we relate the proposed lifecycle to several leading ethical frameworks and outline key research questions that remain for scaling participatory governance.

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

The availability of vast amounts of publicly accessible data of source code and the advances in modern language models, coupled with increasing computational resources, have led to a remarkable surge in the development of large language models for code (LLM4Code, for short). The interaction between code datasets and models gives rise to a complex ecosystem characterized by intricate dependencies that are worth studying. This paper introduces a pioneering analysis of the code model ecosystem. Utilizing Hugging Face -- the premier hub for transformer-based models -- as our primary source, we curate a list of datasets and models that are manually confirmed to be relevant to software engineering. By analyzing the ecosystem, we first identify the popular and influential datasets, models, and contributors. The popularity is quantified by various metrics, including the number of downloads, the number of likes, the number of reuses, etc. The ecosystem follows a power-law distribution, indicating that users prefer widely recognized models and datasets. Then, we manually categorize how models in the ecosystem are reused into nine categories, analyzing prevalent model reuse practices. The top 3 most popular reuse types are fine-tuning, architecture sharing, and quantization. We also explore the practices surrounding the publication of LLM4Code, specifically focusing on documentation practice and license selection. We find that the documentation in the ecosystem contains less information than that in general artificial intelligence (AI)-related repositories hosted on GitHub. Additionally, the license usage is also different from other software repositories. Models in the ecosystem adopt some AI-specific licenses, e.g., RAIL (Responsible AI Licenses) and AI model license agreement.

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

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

The rise of unifying frameworks that enable seamless interoperability of Large Language Models (LLMs) has made LLM-LLM collaboration for open-ended tasks a possibility. Despite this, there have not been efforts to explore such collaborative writing. We take the next step beyond human-LLM collaboration to explore this multi-LLM scenario by generating the first exclusively LLM-generated collaborative stories dataset called CollabStory. We focus on single-author (N=1) to multi-author (up to N=5) scenarios, where multiple LLMs co-author stories. We generate over 32k stories using open-source instruction-tuned LLMs. Further, we take inspiration from the PAN tasks that have set the standard for human-human multi-author writing tasks and analysis. We extend their authorship-related tasks for multi-LLM settings and present baselines for LLM-LLM collaboration. We find that current baselines are not able to handle this emerging scenario. Thus, CollabStory is a resource that could help propel an understanding as well as the development of techniques to discern the use of multiple LLMs. This is crucial to study in the context of writing tasks since LLM-LLM collaboration could potentially overwhelm ongoing challenges related to plagiarism detection, credit assignment, maintaining academic integrity in educational settings, and addressing copyright infringement concerns. We make our dataset and code available at \url{https://github.com/saranya-venkatraman/multi_llm_story_writing}.

Traditional sociological research often relies on human participation, which, though effective, is expensive, challenging to scale, and with ethical concerns. Recent advancements in large language models (LLMs) highlight their potential to simulate human behavior, enabling the replication of individual responses and facilitating studies on many interdisciplinary studies. In this paper, we conduct a comprehensive survey of this field, illustrating the recent progress in simulation driven by LLM-empowered agents. We categorize the simulations into three types: (1) Individual Simulation, which mimics specific individuals or demographic groups; (2) Scenario Simulation, where multiple agents collaborate to achieve goals within specific contexts; and (3) Society Simulation, which models interactions within agent societies to reflect the complexity and variety of real-world dynamics. These simulations follow a progression, ranging from detailed individual modeling to large-scale societal phenomena. We provide a detailed discussion of each simulation type, including the architecture or key components of the simulation, the classification of objectives or scenarios and the evaluation method. Afterward, we summarize commonly used datasets and benchmarks. Finally, we discuss the trends across these three types of simulation. A repository for the related sources is at {https://github.com/FudanDISC/SocialAgent}.

AI scientists are emerging computational systems that serve as collaborative partners in discovery. These systems remain difficult to build because they are bespoke, tied to rigid workflows, and lack shared environments that unify tools, data, and analyses into a common ecosystem. In omics, unified ecosystems have transformed research by enabling interoperability, reuse, and community-driven development; AI scientists require comparable infrastructure. We present ToolUniverse, an ecosystem for building AI scientists from any language or reasoning model, whether open or closed. TOOLUNIVERSE standardizes how AI scientists identify and call tools, integrating more than 600 machine learning models, datasets, APIs, and scientific packages for data analysis, knowledge retrieval, and experimental design. It automatically refines tool interfaces for correct use by AI scientists, creates new tools from natural language descriptions, iteratively optimizes tool specifications, and composes tools into agentic workflows. In a case study of hypercholesterolemia, ToolUniverse was used to create an AI scientist to identify a potent analog of a drug with favorable predicted properties. The open-source ToolUniverse is available at https://aiscientist.tools.

In modern data-driven science, reproducibility and reusability are key challenges. Scientists are well skilled in the process from data to publication. Although some publication channels require source code and data to be made accessible, rerunning and verifying experiments is usually hard due to a lack of standards. Therefore, reusing existing scientific data processing code from state-of-the-art research is hard as well. This is why we introduce CLAIMED, which has a proven track record in scientific research for addressing the repeatability and reusability issues in modern data-driven science. CLAIMED is a framework to build reusable operators and scalable scientific workflows by supporting the scientist to draw from previous work by re-composing workflows from existing libraries of coarse-grained scientific operators. Although various implementations exist, CLAIMED is programming language, scientific library, and execution environment agnostic.

The decentralized deployment of LLM agents with diverse capabilities across diverse tasks motivates infrastructure for knowledge sharing across heterogeneous agent populations. Just as search engines index human-generated artifacts to support human problem solving, retrieval systems can organize agent-generated artifacts for reuse across agent populations. We extend retrieval-augmented generation - which demonstrates the value of human-authored artifacts to individual agents - to retrieval of agent-generated artifacts supporting a population of agents. In particular, agent trajectories encode reusable procedural knowledge, yet these artifacts are typically discarded after a single use or retained only by the producing agent, forcing newly instantiated agents to repeatedly rediscover existing solutions. We propose Multi-Agent Transactive Memory (MATM), a framework for population-level storage and retrieval of agent-generated trajectories, where producer agents contribute trajectories to a shared repository and consumer agents retrieve them to improve task execution. We focus on interactive environments (ALFWorld and WebArena), where trajectories are long and encode especially rich procedural structure. Our experiments demonstrate that retrieving trajectories from MATM improves downstream task performance and reduces interaction steps without coordination or joint training. These results position MATM as a design pattern for population-level experience sharing in open agent ecosystems.

The widespread availability of open-source repositories has led to a vast collection of reusable software components, yet their utilization remains manual, error-prone, and disconnected. Developers must navigate documentation, understand APIs, and write integration code, creating significant barriers to efficient software reuse. To address this, we present EnvX, a framework that leverages Agentic AI to agentize GitHub repositories, transforming them into intelligent, autonomous agents capable of natural language interaction and inter-agent collaboration. Unlike existing approaches that treat repositories as static code resources, EnvX reimagines them as active agents through a three-phase process: (1) TODO-guided environment initialization, which sets up the necessary dependencies, data, and validation datasets; (2) human-aligned agentic automation, allowing repository-specific agents to autonomously perform real-world tasks; and (3) Agent-to-Agent (A2A) protocol, enabling multiple agents to collaborate. By combining large language model capabilities with structured tool integration, EnvX automates not just code generation, but the entire process of understanding, initializing, and operationalizing repository functionality. We evaluate EnvX on the GitTaskBench benchmark, using 18 repositories across domains such as image processing, speech recognition, document analysis, and video manipulation. Our results show that EnvX achieves a 74.07% execution completion rate and 51.85% task pass rate, outperforming existing frameworks. Case studies further demonstrate EnvX's ability to enable multi-repository collaboration via the A2A protocol. This work marks a shift from treating repositories as passive code resources to intelligent, interactive agents, fostering greater accessibility and collaboration within the open-source ecosystem.

As a high-level discipline, the development of remote sensing depends on the contribution of many other basic and applied disciplines and technologies. For example, due to the close relationship between remote sensing and photogrammetry, remote sensing would inevitably integrate disciplines such as optics and color science. Also, remote sensing integrates the knowledge of electronics in the conversion from optical signals to electrical signals via CCD (Charge-Coupled Device) or other image sensors. Moreover, when conducting object identification and classification with remote sensing data, mathematical morphology and other digital image processing technologies are used. These examples are only the tip of the iceberg of interdisciplinary integration of remote sensing. This work briefly reviews the interdisciplinary integration of remote sensing with four examples - ecology, mathematical morphology, machine learning, and electronics.

Many engineering organizations are reimplementing and extending deep neural networks from the research community. We describe this process as deep learning model reengineering. Deep learning model reengineering - reusing, reproducing, adapting, and enhancing state-of-the-art deep learning approaches - is challenging for reasons including under-documented reference models, changing requirements, and the cost of implementation and testing. In addition, individual engineers may lack expertise in software engineering, yet teams must apply knowledge of software engineering and deep learning to succeed. Prior work has examined on DL systems from a "product" view, examining defects from projects regardless of the engineers' purpose. Our study is focused on reengineering activities from a "process" view, and focuses on engineers specifically engaged in the reengineering process. Our goal is to understand the characteristics and challenges of deep learning model reengineering. We conducted a case study of this phenomenon, focusing on the context of computer vision. Our results draw from two data sources: defects reported in open-source reeengineering projects, and interviews conducted with open-source project contributors and the leaders of a reengineering team. Our results describe how deep learning-based computer vision techniques are reengineered, analyze the distribution of defects in this process, and discuss challenges and practices. Integrating our quantitative and qualitative data, we proposed a novel reengineering workflow. Our findings inform several future directions, including: measuring additional unknown aspects of model reengineering; standardizing engineering practices to facilitate reengineering; and developing tools to support model reengineering and model reuse.

Real-world information needs require access to structurally diverse knowledge sources, from unstructured text and relational tables to knowledge graphs and property graphs. Existing retrievers, however, operate over one source at a time under a fixed query language, leaving the broader landscape of available knowledge fragmented behind incompatible interfaces. A natural attempt at unification would collapse these sources into a shared space, but this erases the structural affordances (such as schemas, ontologies, compositional operators) that give each source its expressive power. Effective retrieval over diverse knowledge, therefore, requires not homogenization but an overarching layer that meets each source on its own terms. To achieve this, we present OmniRetrieval, a framework that takes any natural-language query, identifies appropriate knowledge sources, and dispatches source-native queries to their native execution engines. Across an extensive benchmark spanning 13 datasets and 309 distinct knowledge bases over text, relational, and graph-structured sources, OmniRetrieval exceeds single-source baselines, demonstrating that it can serve as a general-purpose interface to the heterogeneous sources while preserving the structural distinctions that make each source valuable.

The study of biological materials and bio-inspired materials science is well established; however, surprisingly little knowledge has been systematically translated to engineering solutions. To accelerate discovery and guide insights, an open-source autoregressive transformer large language model (LLM), BioinspiredLLM, is reported. The model was finetuned with a corpus of over a thousand peer-reviewed articles in the field of structural biological and bio-inspired materials and can be prompted to recall information, assist with research tasks, and function as an engine for creativity. The model has proven that it is able to accurately recall information about biological materials and is further enhanced with enhanced reasoning ability, as well as with retrieval-augmented generation to incorporate new data during generation that can also help to traceback sources, update the knowledge base, and connect knowledge domains. BioinspiredLLM also has been shown to develop sound hypotheses regarding biological materials design and remarkably so for materials that have never been explicitly studied before. Lastly, the model showed impressive promise in collaborating with other generative artificial intelligence models in a workflow that can reshape the traditional materials design process. This collaborative generative artificial intelligence method can stimulate and enhance bio-inspired materials design workflows. Biological materials are at a critical intersection of multiple scientific fields and models like BioinspiredLLM help to connect knowledge domains.

Deep Neural Networks (DNNs) are being adopted as components in software systems. Creating and specializing DNNs from scratch has grown increasingly difficult as state-of-the-art architectures grow more complex. Following the path of traditional software engineering, machine learning engineers have begun to reuse large-scale pre-trained models (PTMs) and fine-tune these models for downstream tasks. Prior works have studied reuse practices for traditional software packages to guide software engineers towards better package maintenance and dependency management. We lack a similar foundation of knowledge to guide behaviors in pre-trained model ecosystems. In this work, we present the first empirical investigation of PTM reuse. We interviewed 12 practitioners from the most popular PTM ecosystem, Hugging Face, to learn the practices and challenges of PTM reuse. From this data, we model the decision-making process for PTM reuse. Based on the identified practices, we describe useful attributes for model reuse, including provenance, reproducibility, and portability. Three challenges for PTM reuse are missing attributes, discrepancies between claimed and actual performance, and model risks. We substantiate these identified challenges with systematic measurements in the Hugging Face ecosystem. Our work informs future directions on optimizing deep learning ecosystems by automated measuring useful attributes and potential attacks, and envision future research on infrastructure and standardization for model registries.

LLM-powered multi-agent systems can now automate the full research pipeline from ideation to paper writing, but a fundamental question remains: automation for whom? Researchers operate under different resource configurations, hold different methodological preferences, and target different output formats. A system that produces uniform outputs regardless of these differences will systematically under-serve every individual user, making personalization a precondition for research automation to be genuinely usable. However, achieving it requires three capabilities that current systems lack: accumulating reusable procedural knowledge across projects, retaining user-specific experience across sessions, and internalizing implicit preferences that resist explicit formalization. We propose NanoResearch, a multi-agent framework that addresses these gaps through tri-level co-evolution. A skill bank distills recurring operations into compact procedural rules reusable across projects. A memory module maintains user- and project-specific experience that grounds planning decisions in each user's research history. A label-free policy learning converts free-form feedback into persistent parameter updates of the planner, reshaping subsequent coordination. These three layers co-evolve: reliable skills produce richer memory, richer memory informs better planning, and preference internalization continuously realigns the loop to each user. Extensive experiments demonstrate that NanoResearch delivers substantial gains over state-of-the-art AI research systems, and progressively refines itself to produce better research at lower cost over successive cycles.

Large language models trained on source code can support a variety of software development tasks, such as code recommendation and program repair. Large amounts of data for training such models benefit the models' performance. However, the size of the data and models results in long training times and high energy consumption. While publishing source code allows for replicability, users need to repeat the expensive training process if models are not shared. The main goal of the study is to investigate if publications that trained language models for software engineering (SE) tasks share source code and trained artifacts. The second goal is to analyze the transparency on training energy usage. We perform a snowballing-based literature search to find publications on language models for source code, and analyze their reusability from a sustainability standpoint. From 494 unique publications, we identified 293 relevant publications that use language models to address code-related tasks. Among them, 27% (79 out of 293) make artifacts available for reuse. This can be in the form of tools or IDE plugins designed for specific tasks or task-agnostic models that can be fine-tuned for a variety of downstream tasks. Moreover, we collect insights on the hardware used for model training, as well as training time, which together determine the energy consumption of the development process. We find that there are deficiencies in the sharing of information and artifacts for current studies on source code models for software engineering tasks, with 40% of the surveyed papers not sharing source code or trained artifacts. We recommend the sharing of source code as well as trained artifacts, to enable sustainable reproducibility. Moreover, comprehensive information on training times and hardware configurations should be shared for transparency on a model's carbon footprint.

A key challenge in artificial intelligence is the creation of systems capable of autonomously advancing scientific understanding by exploring novel domains, identifying complex patterns, and uncovering previously unseen connections in vast scientific data. In this work, we present SciAgents, an approach that leverages three core concepts: (1) the use of large-scale ontological knowledge graphs to organize and interconnect diverse scientific concepts, (2) a suite of large language models (LLMs) and data retrieval tools, and (3) multi-agent systems with in-situ learning capabilities. Applied to biologically inspired materials, SciAgents reveals hidden interdisciplinary relationships that were previously considered unrelated, achieving a scale, precision, and exploratory power that surpasses traditional human-driven research methods. The framework autonomously generates and refines research hypotheses, elucidating underlying mechanisms, design principles, and unexpected material properties. By integrating these capabilities in a modular fashion, the intelligent system yields material discoveries, critique and improve existing hypotheses, retrieve up-to-date data about existing research, and highlights their strengths and limitations. Our case studies demonstrate scalable capabilities to combine generative AI, ontological representations, and multi-agent modeling, harnessing a `swarm of intelligence' similar to biological systems. This provides new avenues for materials discovery and accelerates the development of advanced materials by unlocking Nature's design principles.

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.

Multimodal agents repeatedly re-examine the same video frames, UI screenshots, and rendered artifacts as their context window slides and reasoning iterates, yet every look-back re-encodes from scratch, because prefix caches serve reuse only at a fixed leading position. We show this recompute is avoidable, and identify exactly what naive KV reuse loses: the cross-chunk conditioning a chunk absorbs from its neighbours. This loss is asymmetric. The direct readout of a cached chunk is recovered exactly and for free by the standard state-merge. What remains is a diffuse, low-rank residue concentrated in deep layers, invisible to single-hop retrieval but precisely what multi-hop reasoning binds on. Blind reuse therefore leaves single-hop recall intact while halving multi-hop accuracy; this is the failure mode prior position-independent caches, designed for single-context or single-image reuse, do not address. We repair it with a small, training-free low-rank conditioning patch stored alongside each position-free chunk. Reuse reduces to one operator across MLA, GQA, and MHA: exact RoPE re-rotation to any target position, plus the patch that restores cross-chunk binding. This makes three window operations cheap: reorder (one patch serves every ordering of a cached set), sliding-window survival (surviving chunks relocate via rotation only, zero re-encode), and recall (an evicted chunk is rehydrated by its patch, never re-encoded). A rank-m patch recovers full task accuracy on cross-chunk-binding benchmarks, MM-NIAH across two attention families and two-page doc-QA, at a fraction of the KV footprint, and reconstructs re-prefill KV to within bf16 rounding in a production SGLang kernel across six backbones. The conditioning signal is strongest in redundant vision and video streams, making our solution most impactful where multimodal agents spend their recompute budget.

Understanding the changing structure of science over time is essential to elucidating how science evolves. We develop diachronic embeddings of scholarly periodicals to quantify "semantic changes" of periodicals across decades, allowing us to track the evolution of research topics and identify rapidly developing fields. By mapping periodicals within a physical-life-health triangle, we reveal an evolving interdisciplinary science landscape, finding an overall trend toward specialization for most periodicals but increasing interdisciplinarity for bioscience periodicals. Analyzing a periodical's trajectory within this triangle over time allows us to visualize how its research focus shifts. Furthermore, by monitoring the formation of local clusters of periodicals, we can identify emerging research topics such as AIDS research and nanotechnology in the 1980s. Our work offers novel quantification in the science of science and provides a quantitative lens to examine the evolution of science, which may facilitate future investigations into the emergence and development of research fields.

The proliferation of open large language models (LLMs) is fostering a vibrant ecosystem of research and innovation in artificial intelligence (AI). However, the methods of collaboration used to develop open LLMs both before and after their public release have not yet been comprehensively studied, limiting our understanding of how open LLM projects are initiated, organized, and governed as well as what opportunities there are to foster this ecosystem even further. We address this gap through an exploratory analysis of open collaboration throughout the development and reuse lifecycle of open LLMs, drawing on semi-structured interviews with the developers of 14 open LLMs from grassroots projects, research institutes, startups, and Big Tech companies in North America, Europe, Africa, and Asia. We make three key contributions to research and practice. First, collaboration in open LLM projects extends far beyond the LLMs themselves, encompassing datasets, benchmarks, open source frameworks, leaderboards, knowledge sharing and discussion forums, and compute partnerships, among others. Second, open LLM developers have a variety of social, economic, and technological motivations, from democratizing AI access and promoting open science to building regional ecosystems and expanding language representation. Third, the sampled open LLM projects exhibit five distinct organizational models, ranging from single company projects to non-profit-sponsored grassroots projects, which vary in their centralization of control and community engagement strategies used throughout the open LLM lifecycle. We conclude with practical recommendations for stakeholders seeking to support the global community building a more open future for AI.

As computational work becomes more and more integral to many aspects of scientific research, computational reproducibility has become an issue of increasing importance to computer systems researchers and domain scientists alike. Though computational reproducibility seems more straight forward than replicating physical experiments, the complex and rapidly changing nature of computer environments makes being able to reproduce and extend such work a serious challenge. In this paper, I explore common reasons that code developed for one research project cannot be successfully executed or extended by subsequent researchers. I review current approaches to these issues, including virtual machines and workflow systems, and their limitations. I then examine how the popular emerging technology Docker combines several areas from systems research - such as operating system virtualization, cross-platform portability, modular re-usable elements, versioning, and a `DevOps' philosophy, to address these challenges. I illustrate this with several examples of Docker use with a focus on the R statistical environment.

Pre-trained models (PTMs) are machine learning models that have been trained in advance, often on large-scale data, and can be reused for new tasks, thereby reducing the need for costly training from scratch. Their widespread adoption introduces a new class of software dependency, which we term Software Dependencies 2.0, extending beyond conventional libraries to learned behaviors embodied in trained models and their associated artifacts. The integration of PTMs as software dependencies in real projects remains unclear, potentially threatening maintainability and reliability of modern software systems that increasingly rely on them. Objective: In this study, we investigate Software Dependencies 2.0 in open-source software (OSS) projects by examining the reuse of PTMs, with a focus on how developers manage and integrate these models. Specifically, we seek to understand: (1) how OSS projects structure and document their PTM dependencies; (2) what stages and organizational patterns emerge in the reuse pipelines of PTMs within these projects; and (3) the interactions among PTMs and other learned components across pipeline stages. We conduct a mixed-methods analysis of a statistically significant random sample of 401 GitHub repositories from the PeaTMOSS dataset (28,575 repositories reusing PTMs from Hugging Face and PyTorch Hub). We quantitatively examine PTM reuse by identifying patterns and qualitatively investigate how developers integrate and manage these models in practice.

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

We propose Collab-REC, a multi-agent framework designed to counteract popularity bias and enhance diversity in tourism recommendations. In our setting, three LLM-based agents: Personalization, Popularity, and Sustainability, generate city suggestions from complementary perspectives. A non-LLM moderator then merges and refines these proposals via multi-round negotiation, ensuring each agent's viewpoint is incorporated while penalizing spurious or repeated responses. Extensive experiments on European city queries using LLMs from different sizes and model families demonstrate that Collab-REC enhances diversity and overall relevance compared to a single-agent baseline, surfacing lesser-visited locales that are often overlooked. This balanced, context-aware approach addresses over-tourism and better aligns with user-provided constraints, highlighting the promise of multi-stakeholder collaboration in LLM-driven recommender systems. Code, data, and other artifacts are available here: https://github.com/ashmibanerjee/collab-rec, while the prompts used are included in the appendix.

Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However, interdisciplinary adoption remains limited due to challenges in data collection, task benchmarking, and application. This work presents VenusFactory, a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular fine-tuning of PLMs. VenusFactory supports both computer science and biology communities with choices of both a command-line execution and a Gradio-based no-code interface, integrating 40+ protein-related datasets and 40+ popular PLMs. All implementations are open-sourced on https://github.com/tyang816/VenusFactory.

AI is undergoing a paradigm shift with the rise of models (e.g., BERT, DALL-E, GPT-3) that are trained on broad data at scale and are adaptable to a wide range of downstream tasks. We call these models foundation models to underscore their critically central yet incomplete character. This report provides a thorough account of the opportunities and risks of foundation models, ranging from their capabilities (e.g., language, vision, robotics, reasoning, human interaction) and technical principles(e.g., model architectures, training procedures, data, systems, security, evaluation, theory) to their applications (e.g., law, healthcare, education) and societal impact (e.g., inequity, misuse, economic and environmental impact, legal and ethical considerations). Though foundation models are based on standard deep learning and transfer learning, their scale results in new emergent capabilities,and their effectiveness across so many tasks incentivizes homogenization. Homogenization provides powerful leverage but demands caution, as the defects of the foundation model are inherited by all the adapted models downstream. Despite the impending widespread deployment of foundation models, we currently lack a clear understanding of how they work, when they fail, and what they are even capable of due to their emergent properties. To tackle these questions, we believe much of the critical research on foundation models will require deep interdisciplinary collaboration commensurate with their fundamentally sociotechnical nature.

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

High-quality pretraining data is the fossil fuel of large language models (LLMs), yet its reserves are running low for frontier models. In this paper, we introduce RePro, a novel web recycling method that trains a relatively small LM with reinforcement learning to generate effective and faithful rephrasings of pretraining data. Specifically, we design one quality reward and three faithfulness rewards, optimizing the LM rephraser to convert organic data into high-quality rephrasings while maintaining its core semantics and structure. In our experiment, we train a 4B rephraser to recycle 72B tokens sampled from DCLM-RefinedWeb. Pretraining results on 400M and 1.4B models demonstrate that RePro delivers 4.7%-14.0% relative accuracy gains over organic-only baseline on 22 downstream tasks. RePro also outperforms ReWire, the state-of-the-art web recycling method that prompts a 70B rephraser, as well as the organic baseline with a 4x larger data pool. Experiments with different amounts of recycled data highlight that RePro improves organic data efficiency by 2-3x. Individual and distributional analyses validate that RePro preserves more critical information and faithfully reflects the characteristics of organic data compared to prompting-based methods. Together, these results show that RePro provides an efficient and controllable path to effectively harness the fossil fuel of LLM pretraining. We open-source our code, rephraser, and recycled data at https://github.com/cxcscmu/RePro.

The CAD design process includes a number of repetitive steps when creating assemblies. This issue is compounded when engineering whole product lines or design families, as steps like inserting parts common to all variations, such as fasteners and product-integral base parts, get repeated numerous times. This makes creating designs time-, and as a result, cost-intensive. While many CAD software packages have APIs, the effort of creating use-case specific plugins to automate creation of assemblies usually outweighs the benefit. We developed a plugin for the CAD software package "Fusion 360" which tackles this issue. The plugin adds several graphical interfaces to Fusion 360 that allow parts to be annotated with types, subtype hierarchies to be managed, and requests to synthesize assembly programs for assemblies to be posed. The plugin is use-case agnostic and is able to generate arbitrary open kinematic chain structures. We envision engineers working with CAD software being able to make designed parts reusable and automate the generation of different design alternatives as well as whole product lines.

The convergence of artificial intelligence and materials science presents a transformative opportunity, but achieving true acceleration in discovery requires moving beyond task-isolated, fine-tuned models toward agentic systems that plan, act, and learn across the full discovery loop. This survey advances a unique pipeline-centric view that spans from corpus curation and pretraining, through domain adaptation and instruction tuning, to goal-conditioned agents interfacing with simulation and experimental platforms. Unlike prior reviews, we treat the entire process as an end-to-end system to be optimized for tangible discovery outcomes rather than proxy benchmarks. This perspective allows us to trace how upstream design choices-such as data curation and training objectives-can be aligned with downstream experimental success through effective credit assignment. To bridge communities and establish a shared frame of reference, we first present an integrated lens that aligns terminology, evaluation, and workflow stages across AI and materials science. We then analyze the field through two focused lenses: From the AI perspective, the survey details LLM strengths in pattern recognition, predictive analytics, and natural language processing for literature mining, materials characterization, and property prediction; from the materials science perspective, it highlights applications in materials design, process optimization, and the acceleration of computational workflows via integration with external tools (e.g., DFT, robotic labs). Finally, we contrast passive, reactive approaches with agentic design, cataloging current contributions while motivating systems that pursue long-horizon goals with autonomy, memory, and tool use. This survey charts a practical roadmap towards autonomous, safety-aware LLM agents aimed at discovering novel and useful materials.

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

Multimodal interleaved datasets featuring free-form interleaved sequences of images and text are crucial for training frontier large multimodal models (LMMs). Despite the rapid progression of open-source LMMs, there remains a pronounced scarcity of large-scale, diverse open-source multimodal interleaved datasets. In response, we introduce MINT-1T, the most extensive and diverse open-source Multimodal INTerleaved dataset to date. MINT-1T comprises one trillion text tokens and three billion images, a 10x scale-up from existing open-source datasets. Additionally, we include previously untapped sources such as PDFs and ArXiv papers. As scaling multimodal interleaved datasets requires substantial engineering effort, sharing the data curation process and releasing the dataset greatly benefits the community. Our experiments show that LMMs trained on MINT-1T rival the performance of models trained on the previous leading dataset, OBELICS. Our data and code will be released at https://github.com/mlfoundations/MINT-1T.

Existing foundation models are trained on copyrighted material. Deploying these models can pose both legal and ethical risks when data creators fail to receive appropriate attribution or compensation. In the United States and several other countries, copyrighted content may be used to build foundation models without incurring liability due to the fair use doctrine. However, there is a caveat: If the model produces output that is similar to copyrighted data, particularly in scenarios that affect the market of that data, fair use may no longer apply to the output of the model. In this work, we emphasize that fair use is not guaranteed, and additional work may be necessary to keep model development and deployment squarely in the realm of fair use. First, we survey the potential risks of developing and deploying foundation models based on copyrighted content. We review relevant U.S. case law, drawing parallels to existing and potential applications for generating text, source code, and visual art. Experiments confirm that popular foundation models can generate content considerably similar to copyrighted material. Second, we discuss technical mitigations that can help foundation models stay in line with fair use. We argue that more research is needed to align mitigation strategies with the current state of the law. Lastly, we suggest that the law and technical mitigations should co-evolve. For example, coupled with other policy mechanisms, the law could more explicitly consider safe harbors when strong technical tools are used to mitigate infringement harms. This co-evolution may help strike a balance between intellectual property and innovation, which speaks to the original goal of fair use. But we emphasize that the strategies we describe here are not a panacea and more work is needed to develop policies that address the potential harms of foundation models.

The emergent phenomena of large foundation models have revolutionized natural language processing. However, evaluating these models presents significant challenges due to their size, capabilities, and deployment across diverse applications. Existing literature often focuses on individual aspects, such as benchmark performance or specific tasks, but fails to provide a cohesive process that integrates the nuances of diverse use cases with broader ethical and operational considerations. This work focuses on three key aspects: (1) Formalizing the Evaluation Process by providing a structured framework tailored to specific use-case contexts, (2) Offering Actionable Tools and Frameworks such as checklists and templates to ensure thorough, reproducible, and practical evaluations, and (3) Surveying Recent Work with a targeted review of advancements in LLM evaluation, emphasizing real-world applications.

We present Innovator-VL, a scientific multimodal large language model designed to advance understanding and reasoning across diverse scientific domains while maintaining excellent performance on general vision tasks. Contrary to the trend of relying on massive domain-specific pretraining and opaque pipelines, our work demonstrates that principled training design and transparent methodology can yield strong scientific intelligence with substantially reduced data requirements. (i) First, we provide a fully transparent, end-to-end reproducible training pipeline, covering data collection, cleaning, preprocessing, supervised fine-tuning, reinforcement learning, and evaluation, along with detailed optimization recipes. This facilitates systematic extension by the community. (ii) Second, Innovator-VL exhibits remarkable data efficiency, achieving competitive performance on various scientific tasks using fewer than five million curated samples without large-scale pretraining. These results highlight that effective reasoning can be achieved through principled data selection rather than indiscriminate scaling. (iii) Third, Innovator-VL demonstrates strong generalization, achieving competitive performance on general vision, multimodal reasoning, and scientific benchmarks. This indicates that scientific alignment can be integrated into a unified model without compromising general-purpose capabilities. Our practices suggest that efficient, reproducible, and high-performing scientific multimodal models can be built even without large-scale data, providing a practical foundation for future research.

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

As modern software systems continue to grow in complexity, triage has become a fundamental process in system operations and maintenance. Triage aims to efficiently prioritize, assign, and assess issues to ensure the reliability of complex environments. The vast amount of heterogeneous data generated by software systems has made effective triage indispensable for maintaining reliability, facilitating maintainability, and enabling rapid issue response. Motivated by these challenges, researchers have devoted extensive effort to advancing triage automation and have achieved significant progress over the past two decades. This survey provides a comprehensive review of 234 papers from 2004 to the present, offering an in-depth examination of the fundamental concepts, system architecture, and problem statement. By comparing the distinct goals of academic and industrial research and by analyzing empirical studies of industrial practices, we identify the major obstacles that limit the practical deployment of triage systems. To assist practitioners in method selection and performance evaluation, we summarize widely adopted open-source datasets and evaluation metrics, providing a unified perspective on the measurement of triage effectiveness. Finally, we outline potential future directions and emerging opportunities to foster a closer integration between academic innovation and industrial application. All reviewed papers and projects are available at https://github.com/AIOps-Lab-NKU/TriageSurvey.

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

Continual Learning is an important and challenging problem in machine learning, where models must adapt to a continuous stream of new data without forgetting previously acquired knowledge. While existing frameworks are built on PyTorch, the rising popularity of JAX might lead to divergent codebases, ultimately hindering reproducibility and progress. To address this problem, we introduce SequeL, a flexible and extensible library for Continual Learning that supports both PyTorch and JAX frameworks. SequeL provides a unified interface for a wide range of Continual Learning algorithms, including regularization-based approaches, replay-based approaches, and hybrid approaches. The library is designed towards modularity and simplicity, making the API suitable for both researchers and practitioners. We release SequeL\url{https://github.com/nik-dim/sequel} as an open-source library, enabling researchers and developers to easily experiment and extend the library for their own purposes.

Drawing from discussions at the inaugural DMLR workshop at ICML 2023 and meetings prior, in this report we outline the relevance of community engagement and infrastructure development for the creation of next-generation public datasets that will advance machine learning science. We chart a path forward as a collective effort to sustain the creation and maintenance of these datasets and methods towards positive scientific, societal and business impact.

LLMs have demonstrated significant potential in code generation tasks, achieving promising results at the function or statement level across various benchmarks. However, the complexities associated with creating code artifacts like classes, particularly within the context of real-world software repositories, remain underexplored. Prior research treats class-level generation as an isolated task, neglecting the intricate dependencies & interactions that characterize real-world software environments. To address this gap, we introduce RepoClassBench, a comprehensive benchmark designed to rigorously evaluate LLMs in generating complex, class-level code within real-world repositories. RepoClassBench includes "Natural Language to Class generation" tasks across Java, Python & C# from a selection of repositories. We ensure that each class in our dataset not only has cross-file dependencies within the repository but also includes corresponding test cases to verify its functionality. We find that current models struggle with the realistic challenges posed by our benchmark, primarily due to their limited exposure to relevant repository contexts. To address this shortcoming, we introduce Retrieve-Repotools-Reflect (RRR), a novel approach that equips LLMs with static analysis tools to iteratively navigate & reason about repository-level context in an agent-based framework. Our experiments demonstrate that RRR significantly outperforms existing baselines on RepoClassBench, showcasing its effectiveness across programming languages & under various settings. Our findings emphasize the critical need for code-generation benchmarks to incorporate repo-level dependencies to more accurately reflect the complexities of software development. Our work shows the benefits of leveraging specialized tools to enhance LLMs' understanding of repository context. We plan to make our dataset & evaluation harness public.

The widespread availability of fine-tuned LoRA modules for open pre-trained models has led to an interest in methods that can adaptively merge LoRAs to improve performance. These methods typically include some way of selecting LoRAs from a pool and tune merging coefficients based on a task-specific dataset. While adaptive merging methods have demonstrated improvements in some settings, no past work has attempted to recycle LoRAs found "in the wild" on model repositories like the Hugging Face Hub. To address this gap, we consider recycling from a pool of nearly 1,000 user-contributed LoRAs trained from the Llama 3.1 8B-Instruct language model. Our empirical study includes a range of adaptive and non-adaptive merging methods in addition to a new method designed via a wide search over the methodological design space. We demonstrate that adaptive merging methods can improve performance over the base model but provide limited benefit over training a new LoRA on the same data used to set merging coefficients. We additionally find not only that the specific choice of LoRAs to merge has little importance, but that using LoRAs with randomly initialized parameter values yields similar performance. This raises the possibility that adaptive merging from recycled LoRAs primarily works via some kind of regularization effect, rather than by enabling positive cross-task transfer. To better understand why past work has proven successful, we confirm that positive transfer is indeed possible when there are highly relevant LoRAs in the pool. We release the model checkpoints and code online.

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.

Foundation models are redefining how AI systems are built. Practitioners now follow a standard procedure to build their machine learning solutions: from a pre-trained foundation model, they fine-tune the weights on the target task of interest. So, the Internet is swarmed by a handful of foundation models fine-tuned on many diverse tasks: these individual fine-tunings exist in isolation without benefiting from each other. In our opinion, this is a missed opportunity, as these specialized models contain rich and diverse features. In this paper, we thus propose model ratatouille, a new strategy to recycle the multiple fine-tunings of the same foundation model on diverse auxiliary tasks. Specifically, we repurpose these auxiliary weights as initializations for multiple parallel fine-tunings on the target task; then, we average all fine-tuned weights to obtain the final model. This recycling strategy aims at maximizing the diversity in weights by leveraging the diversity in auxiliary tasks. Empirically, it improves the state of the art on the reference DomainBed benchmark for out-of-distribution generalization. Looking forward, this work contributes to the emerging paradigm of updatable machine learning where, akin to open-source software development, the community collaborates to reliably update machine learning models.

Continual learning (CL) aims to empower machine learning models to learn continually from new data, while building upon previously acquired knowledge without forgetting. As machine learning models have evolved from small to large pre-trained architectures, and from supporting unimodal to multimodal data, multimodal continual learning (MMCL) methods have recently emerged. The primary challenge of MMCL is that it goes beyond a simple stacking of unimodal CL methods, as such straightforward approaches often yield unsatisfactory performance. In this work, we present the first comprehensive survey on MMCL. We provide essential background knowledge and MMCL settings, as well as a structured taxonomy of MMCL methods. We categorize existing MMCL methods into four categories, i.e., regularization-based, architecture-based, replay-based, and prompt-based methods, explaining their methodologies and highlighting their key innovations. Additionally, to prompt further research in this field, we summarize open MMCL datasets and benchmarks, and discuss several promising future directions for investigation and development. We have also created a GitHub repository for indexing relevant MMCL papers and open resources available at https://github.com/LucyDYu/Awesome-Multimodal-Continual-Learning.

Designing effective agentic systems requires the seamless composition and integration of agents, tools, and models within dynamic and uncertain environments. Most existing methods rely on static, semantic retrieval approaches for tool or agent discovery. However, effective reuse and composition of existing components remain challenging due to incomplete capability descriptions and the limitations of retrieval methods. Component selection suffers because the decisions are not based on capability, cost, and real-time utility. To address these challenges, we introduce a structured, automated framework for agentic system composition that is inspired by the knapsack problem. Our framework enables a composer agent to systematically identify, select, and assemble an optimal set of agentic components by jointly considering performance, budget constraints, and compatibility. By dynamically testing candidate components and modeling their utility in real-time, our approach streamlines the assembly of agentic systems and facilitates scalable reuse of resources. Empirical evaluation with Claude 3.5 Sonnet across five benchmarking datasets shows that our online-knapsack-based composer consistently lies on the Pareto frontier, achieving higher success rates at significantly lower component costs compared to our baselines. In the single-agent setup, the online knapsack composer shows a success rate improvement of up to 31.6% in comparison to the retrieval baselines. In multi-agent systems, the online knapsack composer increases success rate from 37% to 87% when agents are selected from an agent inventory of 100+ agents. The substantial performance gap confirms the robust adaptability of our method across diverse domains and budget constraints.

In the proposed demo, we will present a new software - Linguistic Field Data Management and Analysis System - LiFE (https://github.com/kmi-linguistics/life) - an open-source, web-based linguistic data management and analysis application that allows for systematic storage, management, sharing and usage of linguistic data collected from the field. The application allows users to store lexical items, sentences, paragraphs, audio-visual content with rich glossing / annotation; generate interactive and print dictionaries; and also train and use natural language processing tools and models for various purposes using this data. Since its a web-based application, it also allows for seamless collaboration among multiple persons and sharing the data, models, etc with each other. The system uses the Python-based Flask framework and MongoDB in the backend and HTML, CSS and Javascript at the frontend. The interface allows creation of multiple projects that could be shared with the other users. At the backend, the application stores the data in RDF format so as to allow its release as Linked Data over the web using semantic web technologies - as of now it makes use of the OntoLex-Lemon for storing the lexical data and Ligt for storing the interlinear glossed text and then internally linking it to the other linked lexicons and databases such as DBpedia and WordNet. Furthermore it provides support for training the NLP systems using scikit-learn and HuggingFace Transformers libraries as well as make use of any model trained using these libraries - while the user interface itself provides limited options for tuning the system, an externally-trained model could be easily incorporated within the application; similarly the dataset itself could be easily exported into a standard machine-readable format like JSON or CSV that could be consumed by other programs and pipelines.

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.

Context: Jupyter Notebook has emerged as a versatile tool that transforms how researchers, developers, and data scientists conduct and communicate their work. As the adoption of Jupyter notebooks continues to rise, so does the interest from the software engineering research community in improving the software engineering practices for Jupyter notebooks. Objective: The purpose of this study is to analyze trends, gaps, and methodologies used in software engineering research on Jupyter notebooks. Method: We selected 146 relevant publications from the DBLP Computer Science Bibliography up to the end of 2024, following established systematic literature review guidelines. We explored publication trends, categorized them based on software engineering topics, and reported findings based on those topics. Results: The most popular venues for publishing software engineering research on Jupyter notebooks are related to human-computer interaction instead of traditional software engineering venues. Researchers have addressed a wide range of software engineering topics on notebooks, such as code reuse, readability, and execution environment. Although reusability is one of the research topics for Jupyter notebooks, only 64 of the 146 studies can be reused based on their provided URLs. Additionally, most replication packages are not hosted on permanent repositories for long-term availability and adherence to open science principles. Conclusion: Solutions specific to notebooks for software engineering issues, including testing, refactoring, and documentation, are underexplored. Future research opportunities exist in automatic testing frameworks, refactoring clones between notebooks, and generating group documentation for coherent code cells.

Background: Collaborative Software Package Registries (SPRs) are an integral part of the software supply chain. Much engineering work synthesizes SPR package into applications. Prior research has examined SPRs for traditional software, such as NPM (JavaScript) and PyPI (Python). Pre-Trained Model (PTM) Registries are an emerging class of SPR of increasing importance, because they support the deep learning supply chain. Aims: Recent empirical research has examined PTM registries in ways such as vulnerabilities, reuse processes, and evolution. However, no existing research synthesizes them to provide a systematic understanding of the current knowledge. Some of the existing research includes qualitative claims lacking quantitative analysis. Our research fills these gaps by providing a knowledge synthesis and quantitative analyses. Methods: We first conduct a systematic literature review (SLR). We then observe that some of the claims are qualitative. We identify quantifiable metrics associated with those claims, and measure in order to substantiate these claims. Results: From our SLR, we identify 12 claims about PTM reuse on the HuggingFace platform, 4 of which lack quantitative validation. We successfully test 3 of these claims through a quantitative analysis, and directly compare one with traditional software. Our findings corroborate qualitative claims with quantitative measurements. Our findings are: (1) PTMs have a much higher turnover rate than traditional software, indicating a dynamic and rapidly evolving reuse environment within the PTM ecosystem; and (2) There is a strong correlation between documentation quality and PTM popularity. Conclusions: We confirm qualitative research claims with concrete metrics, supporting prior qualitative and case study research. Our measures show further dynamics of PTM reuse, inspiring research infrastructure and new measures.

Split and rephrase is the task of breaking down a sentence into shorter ones that together convey the same meaning. We extract a rich new dataset for this task by mining Wikipedia's edit history: WikiSplit contains one million naturally occurring sentence rewrites, providing sixty times more distinct split examples and a ninety times larger vocabulary than the WebSplit corpus introduced by Narayan et al. (2017) as a benchmark for this task. Incorporating WikiSplit as training data produces a model with qualitatively better predictions that score 32 BLEU points above the prior best result on the WebSplit benchmark.

Datasets are central to training machine learning (ML) models. The ML community has recently made significant improvements to data stewardship and documentation practices across the model development life cycle. However, the act of deprecating, or deleting, datasets has been largely overlooked, and there are currently no standardized approaches for structuring this stage of the dataset life cycle. In this paper, we study the practice of dataset deprecation in ML, identify several cases of datasets that continued to circulate despite having been deprecated, and describe the different technical, legal, ethical, and organizational issues raised by such continuations. We then propose a Dataset Deprecation Framework that includes considerations of risk, mitigation of impact, appeal mechanisms, timeline, post-deprecation protocols, and publication checks that can be adapted and implemented by the ML community. Finally, we propose creating a centralized, sustainable repository system for archiving datasets, tracking dataset modifications or deprecations, and facilitating practices of care and stewardship that can be integrated into research and publication processes.

Data mixing -- determining the ratios of data from different domains -- is a first-order concern for training language models (LMs). While existing mixing methods show promise, they fall short when applied during real-world LM development. We present Olmix, a framework that addresses two such challenges. First, the configuration space for developing a mixing method is not well understood -- design choices across existing methods lack justification or consensus and overlook practical issues like data constraints. We conduct a comprehensive empirical study of this space, identifying which design choices lead to a strong mixing method. Second, in practice, the domain set evolves throughout LM development as datasets are added, removed, partitioned, and revised -- a problem setting largely unaddressed by existing works, which assume fixed domains. We study how to efficiently recompute the mixture after the domain set is updated, leveraging information from past mixtures. We introduce mixture reuse, a mechanism that reuses existing ratios and recomputes ratios only for domains affected by the update. Over a sequence of five domain-set updates mirroring real-world LM development, mixture reuse matches the performance of fully recomputing the mix after each update with 74% less compute and improves over training without mixing by 11.6% on downstream tasks.

Addressing the critical theme of recycling electronic waste (E-waste), this contribution is dedicated to developing advanced automated data processing pipelines as a basis for decision-making and process control. Aligning with the broader goals of the circular economy and the United Nations (UN) Sustainable Development Goals (SDG), our work leverages non-invasive analysis methods utilizing RGB and hyperspectral imaging data to provide both quantitative and qualitative insights into the E-waste stream composition for optimizing recycling efficiency. In this paper, we introduce 'PCB-Vision'; a pioneering RGB-hyperspectral printed circuit board (PCB) benchmark dataset, comprising 53 RGB images of high spatial resolution paired with their corresponding high spectral resolution hyperspectral data cubes in the visible and near-infrared (VNIR) range. Grounded in open science principles, our dataset provides a comprehensive resource for researchers through high-quality ground truths, focusing on three primary PCB components: integrated circuits (IC), capacitors, and connectors. We provide extensive statistical investigations on the proposed dataset together with the performance of several state-of-the-art (SOTA) models, including U-Net, Attention U-Net, Residual U-Net, LinkNet, and DeepLabv3+. By openly sharing this multi-scene benchmark dataset along with the baseline codes, we hope to foster transparent, traceable, and comparable developments of advanced data processing across various scientific communities, including, but not limited to, computer vision and remote sensing. Emphasizing our commitment to supporting a collaborative and inclusive scientific community, all materials, including code, data, ground truth, and masks, will be accessible at https://github.com/hifexplo/PCBVision.

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.

The recent advances in diffusion models have set an impressive milestone in many generation tasks. Trending works such as DALL-E2, Imagen, and Stable Diffusion have attracted great interest in academia and industry. Despite the rapid landscape changes, recent new approaches focus on extensions and performance rather than capacity, thus requiring separate models for separate tasks. In this work, we expand the existing single-flow diffusion pipeline into a multi-flow network, dubbed Versatile Diffusion (VD), that handles text-to-image, image-to-text, image-variation, and text-variation in one unified model. Moreover, we generalize VD to a unified multi-flow multimodal diffusion framework with grouped layers, swappable streams, and other propositions that can process modalities beyond images and text. Through our experiments, we demonstrate that VD and its underlying framework have the following merits: a) VD handles all subtasks with competitive quality; b) VD initiates novel extensions and applications such as disentanglement of style and semantic, image-text dual-guided generation, etc.; c) Through these experiments and applications, VD provides more semantic insights of the generated outputs. Our code and models are open-sourced at https://github.com/SHI-Labs/Versatile-Diffusion.

Reproducibility in scientific work has been becoming increasingly important in research communities such as machine learning, natural language processing, and computer vision communities due to the rapid development of the research domains supported by recent advances in deep learning. In this work, we present a significantly upgraded version of torchdistill, a modular-driven coding-free deep learning framework significantly upgraded from the initial release, which supports only image classification and object detection tasks for reproducible knowledge distillation experiments. To demonstrate that the upgraded framework can support more tasks with third-party libraries, we reproduce the GLUE benchmark results of BERT models using a script based on the upgraded torchdistill, harmonizing with various Hugging Face libraries. All the 27 fine-tuned BERT models and configurations to reproduce the results are published at Hugging Face, and the model weights have already been widely used in research communities. We also reimplement popular small-sized models and new knowledge distillation methods and perform additional experiments for computer vision tasks.

Artificial Intelligence (AI) can augment and sometimes even replace human cognition. Inspired by efforts to value human agency alongside productivity, we discuss the benefits of solving Citizen Science (CS) tasks with Hybrid Intelligence (HI), a synergetic mixture of human and artificial intelligence. Currently there is no clear framework or methodology on how to create such an effective mixture. Due to the unique participant-centered set of values and the abundance of tasks drawing upon both human common sense and complex 21st century skills, we believe that the field of CS offers an invaluable testbed for the development of HI and human-centered AI of the 21st century, while benefiting CS as well. In order to investigate this potential, we first relate CS to adjacent computational disciplines. Then, we demonstrate that CS projects can be grouped according to their potential for HI-enhancement by examining two key dimensions: the level of digitization and the amount of knowledge or experience required for participation. Finally, we propose a framework for types of human-AI interaction in CS based on established criteria of HI. This "HI lens" provides the CS community with an overview of several ways to utilize the combination of AI and human intelligence in their projects. It also allows the AI community to gain ideas on how developing AI in CS projects can further their own field.

We propose LLM-Interleaved (LLM-I), a flexible and dynamic framework that reframes interleaved image-text generation as a tool-use problem. LLM-I is designed to overcome the "one-tool" bottleneck of current unified models, which are limited to synthetic imagery and struggle with tasks requiring factual grounding or programmatic precision. Our framework empowers a central LLM or MLLM agent to intelligently orchestrate a diverse toolkit of specialized visual tools, including online image search, diffusion-based generation, code execution, and image editing. The agent is trained to select and apply these tools proficiently via a Reinforcement Learning (RL) framework that features a hybrid reward system combining rule-based logic with judgments from LLM and MLLM evaluators. Trained on a diverse new dataset using four different model backbones, LLM-I demonstrates state-of-the-art performance, outperforming existing methods by a large margin across four benchmarks. We also introduce a novel test-time scaling strategy that provides further performance gains. Project Page: https://github.com/ByteDance-BandAI/LLM-I.

Artificial Intelligence (AI)-driven defect inspection is pivotal in industrial manufacturing. Yet, many methods, tailored to specific pipelines, grapple with diverse product portfolios and evolving processes. Addressing this, we present the Incremental Unified Framework (IUF), which can reduce the feature conflict problem when continuously integrating new objects in the pipeline, making it advantageous in object-incremental learning scenarios. Employing a state-of-the-art transformer, we introduce Object-Aware Self-Attention (OASA) to delineate distinct semantic boundaries. Semantic Compression Loss (SCL) is integrated to optimize non-primary semantic space, enhancing network adaptability for novel objects. Additionally, we prioritize retaining the features of established objects during weight updates. Demonstrating prowess in both image and pixel-level defect inspection, our approach achieves state-of-the-art performance, proving indispensable for dynamic and scalable industrial inspections. Our code will be released at https://github.com/jqtangust/IUF.

While knowledge distillation (transfer) has been attracting attentions from the research community, the recent development in the fields has heightened the need for reproducible studies and highly generalized frameworks to lower barriers to such high-quality, reproducible deep learning research. Several researchers voluntarily published frameworks used in their knowledge distillation studies to help other interested researchers reproduce their original work. Such frameworks, however, are usually neither well generalized nor maintained, thus researchers are still required to write a lot of code to refactor/build on the frameworks for introducing new methods, models, datasets and designing experiments. In this paper, we present our developed open-source framework built on PyTorch and dedicated for knowledge distillation studies. The framework is designed to enable users to design experiments by declarative PyYAML configuration files, and helps researchers complete the recently proposed ML Code Completeness Checklist. Using the developed framework, we demonstrate its various efficient training strategies, and implement a variety of knowledge distillation methods. We also reproduce some of their original experimental results on the ImageNet and COCO datasets presented at major machine learning conferences such as ICLR, NeurIPS, CVPR and ECCV, including recent state-of-the-art methods. All the source code, configurations, log files and trained model weights are publicly available at https://github.com/yoshitomo-matsubara/torchdistill .

This white paper introduces my educational community initiative to learn how to run AI, ML and other emerging workloads in the most efficient and cost-effective way across diverse models, data sets, software and hardware. This project leverages Collective Mind (CM), virtualized MLOps and DevOps (CM4MLOps), MLPerf benchmarks, and the Collective Knowledge playground (CK), which I have developed in collaboration with the community and MLCommons. I created Collective Mind as a small and portable Python package with minimal dependencies, a unified CLI and Python API to help researchers and engineers automate repetitive, tedious, and time-consuming tasks. I also designed CM as a distributed framework, continuously enhanced by the community through the CM4* repositories, which function as the unified interface for organizing and managing various collections of automations and artifacts. For example, CM4MLOps repository includes many automations, also known as CM scripts, to streamline the process of building, running, benchmarking, and optimizing AI, ML, and other workflows across ever-evolving models, data, and systems. I donated CK, CM and CM4MLOps to MLCommons to foster collaboration between academia and industry to learn how to co-design more efficient and cost-effective AI systems while capturing and encoding knowledge within Collective Mind, protecting intellectual property, enabling portable skills, and accelerating the transition of the state-of-the-art research into production. My ultimate goal is to collaborate with the community to complete my two-decade journey toward creating self-optimizing software and hardware that can automatically learn how to run any workload in the most efficient and cost-effective manner based on user requirements and constraints such as cost, latency, throughput, accuracy, power consumption, size, and other critical factors.

We present a detailed replication study of the BASS framework, an abstractive summarization system based on the notion of Unified Semantic Graphs. Our investigation includes challenges in replicating key components and an ablation study to systematically isolate error sources rooted in replicating novel components. Our findings reveal discrepancies in performance compared to the original work. We highlight the significance of paying careful attention even to reasonably omitted details for replicating advanced frameworks like BASS, and emphasize key practices for writing replicable papers.

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

Software repositories is one of the sources of data in Empirical Software Engineering, primarily in the Mining Software Repositories field, aimed at extracting knowledge from the dynamics and practice of software projects. With the emergence of social coding platforms such as GitHub, researchers have now access to millions of software repositories to use as source data for their studies. With this massive amount of data, sampling techniques are needed to create more manageable datasets. The creation of these datasets is a crucial step, and researchers have to carefully select the repositories to create representative samples according to a set of variables of interest. However, current sampling methods are often based on random selection or rely on variables which may not be related to the research study (e.g., popularity or activity). In this paper, we present a methodology for creating representative samples of software repositories, where such representativeness is properly aligned with both the characteristics of the population of repositories and the requirements of the empirical study. We illustrate our approach with use cases based on Hugging Face repositories.

Developers gain productivity by reusing readily available Free and Open Source Software (FOSS) components. Such practices also bring some difficulties, such as managing licensing, components and related security. One approach to handle those difficulties is to use Software Bill of Materials (SBOMs). While there have been studies on the readiness of practitioners to embrace SBOMs and on the SBOM tools ecosystem, a large scale study on SBOM practices based on SBOM files produced in the wild is still lacking. A starting point for such a study is a large dataset of SBOM files found in the wild. We introduce such a dataset, consisting of over 78 thousand unique SBOM files, deduplicated from those found in over 94 million repositories. We include metadata that contains the standard and format used, quality score generated by the tool sbomqs, number of revisions, filenames and provenance information. Finally, we give suggestions and examples of research that could bring new insights on assessing and improving SBOM real practices.

Retrieval, re-ranking, and retrieval-augmented generation (RAG) are critical components of modern applications in information retrieval, question answering, or knowledge-based text generation. However, existing solutions are often fragmented, lacking a unified framework that easily integrates these essential processes. The absence of a standardized implementation, coupled with the complexity of retrieval and re-ranking workflows, makes it challenging for researchers to compare and evaluate different approaches in a consistent environment. While existing toolkits such as Rerankers and RankLLM provide general-purpose reranking pipelines, they often lack the flexibility required for fine-grained experimentation and benchmarking. In response to these challenges, we introduce Rankify, a powerful and modular open-source toolkit designed to unify retrieval, re-ranking, and RAG within a cohesive framework. Rankify supports a wide range of retrieval techniques, including dense and sparse retrievers, while incorporating state-of-the-art re-ranking models to enhance retrieval quality. Additionally, Rankify includes a collection of pre-retrieved datasets to facilitate benchmarking, available at Huggingface (https://huggingface.co/datasets/abdoelsayed/reranking-datasets-light). To encourage adoption and ease of integration, we provide comprehensive documentation (http://rankify.readthedocs.io/), an open-source implementation on GitHub (https://github.com/DataScienceUIBK/rankify), and a PyPI package for easy installation (https://pypi.org/project/rankify/). As a unified and lightweight framework, Rankify allows researchers and practitioners to advance retrieval and re-ranking methodologies while ensuring consistency, scalability, and ease of use.

Redundant code is a persistent challenge in software development that makes systems harder to maintain, scale, and update. It adds unnecessary complexity, hinders bug fixes, and increases technical debt. Despite their impact, removing redundant code manually is risky and error-prone, often introducing new bugs or missing dependencies. While studies highlight the prevalence and negative impact of redundant code, little focus has been given to Artificial Intelligence (AI) system codebases and the common patterns that cause redundancy. Additionally, the reasons behind developers unintentionally introducing redundant code remain largely unexplored. This research addresses these gaps by leveraging large language models (LLMs) to automatically detect and optimize redundant code in AI projects. Our research aims to identify recurring patterns of redundancy and analyze their underlying causes, such as outdated practices or insufficient awareness of best coding principles. Additionally, we plan to propose an LLM agent that will facilitate the detection and refactoring of redundancies on a large scale while preserving original functionality. This work advances the application of AI in identifying and optimizing redundant code, ultimately helping developers maintain cleaner, more readable, and scalable codebases.

Language models may memorize more than just facts, including entire chunks of texts seen during training. Fair use exemptions to copyright laws typically allow for limited use of copyrighted material without permission from the copyright holder, but typically for extraction of information from copyrighted materials, rather than {\em verbatim} reproduction. This work explores the issue of copyright violations and large language models through the lens of verbatim memorization, focusing on possible redistribution of copyrighted text. We present experiments with a range of language models over a collection of popular books and coding problems, providing a conservative characterization of the extent to which language models can redistribute these materials. Overall, this research highlights the need for further examination and the potential impact on future developments in natural language processing to ensure adherence to copyright regulations. Code is at https://github.com/coastalcph/CopyrightLLMs.

Open-source AI is scaling rapidly, and model hubs now host millions of artifacts. Each foundation model can spawn large numbers of fine-tunes, adapters, quantizations, merges, and forks. We take the position that compute efficiency alone is insufficient for sustainability in open-source AI: lower per-run costs can accelerate experimentation and deployment, increasing aggregate environmental footprint unless impacts are measurable and comparable across derivative lineages. However, the energy use, water consumption, and emissions of these derivative lineages are rarely measured or disclosed in a consistent, comparable manner, leaving ecosystem-level impact largely invisible. We argue that sustainable open-source AI requires coordination infrastructure that tracks impacts across model lineages, not only base models. We propose Data and Impact Accounting (DIA), a lightweight, non-restrictive transparency layer that (i) standardizes carbon and water reporting metadata, (ii) integrates low-friction measurement into common training and inference pipelines, and (iii) aggregates reports through public dashboards to summarize cumulative impacts across releases and derivatives. DIA makes derivative costs visible and supports ecosystem-level accountability while preserving openness. https://vectorinstitute.github.io/ai-impact-accounting/

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.

Large Language Models (LLMs) have demonstrated remarkable capabilities in important tasks such as natural language understanding, language generation, and complex reasoning and have the potential to make a substantial impact on our society. Such capabilities, however, come with the considerable resources they demand, highlighting the strong need to develop effective techniques for addressing their efficiency challenges. In this survey, we provide a systematic and comprehensive review of efficient LLMs research. We organize the literature in a taxonomy consisting of three main categories, covering distinct yet interconnected efficient LLMs topics from model-centric, data-centric, and framework-centric perspective, respectively. We have also created a GitHub repository where we compile the papers featured in this survey at https://github.com/AIoT-MLSys-Lab/EfficientLLMs, and will actively maintain this repository and incorporate new research as it emerges. We hope our survey can serve as a valuable resource to help researchers and practitioners gain a systematic understanding of the research developments in efficient LLMs and inspire them to contribute to this important and exciting field.

Modern LLM training pipelines increasingly rely on other models to generate data, filter corpora, judge outputs, and guide development decisions. These dependencies are recursive: a model may depend on an upstream artifact whose own dependencies are documented only in separate releases and artifacts. As a result, the full dependency structure is fragmented across heterogeneous public artifacts, with complexity and recursive depth far outpacing humans' ability to trace. We introduce ModSleuth, an agentic system that recursively reconstructs LLM dependency graphs from public artifacts with source-grounded evidence. We find that the primary challenge is no longer information extraction, but defining what constitutes a dependency and reconciling artifact references across inconsistent documentation. We address these challenges through a formalization that distinguishes direct and indirect dependencies, represents heterogeneous pipeline roles through operation-centered relationships, and resolves artifact identities across names, versions, and repositories. Applying ModSleuth to four public-artifact-rich LLM releases, we recover 1,060 source-verified dependencies and construct large-scale dependency graphs of modern LLM development. These graphs reveal multi-hop license obligations, train-evaluation coupling, discrepancies between released and training-time artifacts, and documentation inconsistencies that would otherwise be difficult to uncover. We release ModSleuth and the resulting dependency graphs to support transparent analysis of the increasingly complex ecosystems underlying modern LLMs.

Interleaved text-and-image generation represents a significant frontier for Multimodal Large Language Models (MLLMs), offering a more intuitive way to convey complex information. Current paradigms rely on either image generation or retrieval augmentation, yet they typically treat the two as mutually exclusive paths, failing to unify factuality with creativity. We argue that the next milestone in this field is Agentic Tool Planning, where the model serves as a central controller that autonomously determines when, where, and which tools to invoke to produce interleaved responses for visual-critical queries. To systematically evaluate this paradigm, we introduce ATP-Bench, a novel benchmark comprising 7,702 QA pairs (including 1,592 VQA pairs) across eight categories and 25 visual-critical intents, featuring human-verified queries and ground truths. Furthermore, to evaluate agentic planning independent of end-to-end execution and changing tool backends, we propose a Multi-Agent MLLM-as-a-Judge (MAM) system. MAM evaluates tool-call precision, identifies missed opportunities for tool use, and assesses overall response quality without requiring ground-truth references. Our extensive experiments on 10 state-of-the-art MLLMs reveal that models struggle with coherent interleaved planning and exhibit significant variations in tool-use behavior, highlighting substantial room for improvement and providing actionable guidance for advancing interleaved generation. Dataset and code are available at https://github.com/Qwen-Applications/ATP-Bench.

Many environmental remediation and energy applications (conversion and storage) for sustainability need design and development of green novel materials. Discovery processes of such novel materials are time taking and cumbersome due to large number of possible combinations and permutations of materials structures. Often theoretical studies based on Density Functional Theory (DFT) and other theories, coupled with Simulations are conducted to narrow down sample space of candidate materials, before conducting laboratory-based synthesis and analytical process. With the emergence of artificial intelligence (AI), AI techniques are being tried in this process too to ease out simulation time and cost. However tremendous values of previously published research from various parts of the world are still left as labor-intensive manual effort and discretion of individual researcher and prone to human omissions. AIMS-EREA is our novel framework to blend best of breed of Material Science theory with power of Generative AI to give best impact and smooth and quickest discovery of material for sustainability. This also helps to eliminate the possibility of production of hazardous residues and bye-products of the reactions. AIMS-EREA uses all available resources -- Predictive and Analytical AI on large collection of chemical databases along with automated intelligent assimilation of deep materials knowledge from previously published research works through Generative AI. We demonstrate use of our own novel framework with an example, how this framework can be successfully applied to achieve desired success in development of thermoelectric material for waste heat conversion.

In this work, we present the ChemNLP library that can be used for 1) curating open access datasets for materials and chemistry literature, developing and comparing traditional machine learning, transformers and graph neural network models for 2) classifying and clustering texts, 3) named entity recognition for large-scale text-mining, 4) abstractive summarization for generating titles of articles from abstracts, 5) text generation for suggesting abstracts from titles, 6) integration with density functional theory dataset for identifying potential candidate materials such as superconductors, and 7) web-interface development for text and reference query. We primarily use the publicly available arXiv and Pubchem datasets but the tools can be used for other datasets as well. Moreover, as new models are developed, they can be easily integrated in the library. ChemNLP is available at the websites: https://github.com/usnistgov/chemnlp and https://jarvis.nist.gov/jarvischemnlp.

While the history of machine learning so far largely encompasses a series of problems posed by researchers and algorithms that learn their solutions, an important question is whether the problems themselves can be generated by the algorithm at the same time as they are being solved. Such a process would in effect build its own diverse and expanding curricula, and the solutions to problems at various stages would become stepping stones towards solving even more challenging problems later in the process. The Paired Open-Ended Trailblazer (POET) algorithm introduced in this paper does just that: it pairs the generation of environmental challenges and the optimization of agents to solve those challenges. It simultaneously explores many different paths through the space of possible problems and solutions and, critically, allows these stepping-stone solutions to transfer between problems if better, catalyzing innovation. The term open-ended signifies the intriguing potential for algorithms like POET to continue to create novel and increasingly complex capabilities without bound. Our results show that POET produces a diverse range of sophisticated behaviors that solve a wide range of environmental challenges, many of which cannot be solved by direct optimization alone, or even through a direct-path curriculum-building control algorithm introduced to highlight the critical role of open-endedness in solving ambitious challenges. The ability to transfer solutions from one environment to another proves essential to unlocking the full potential of the system as a whole, demonstrating the unpredictable nature of fortuitous stepping stones. We hope that POET will inspire a new push towards open-ended discovery across many domains, where algorithms like POET can blaze a trail through their interesting possible manifestations and solutions.

A growing body of work shows that many problems in fairness, accountability, transparency, and ethics in machine learning systems are rooted in decisions surrounding the data collection and annotation process. In spite of its fundamental nature however, data collection remains an overlooked part of the machine learning (ML) pipeline. In this paper, we argue that a new specialization should be formed within ML that is focused on methodologies for data collection and annotation: efforts that require institutional frameworks and procedures. Specifically for sociocultural data, parallels can be drawn from archives and libraries. Archives are the longest standing communal effort to gather human information and archive scholars have already developed the language and procedures to address and discuss many challenges pertaining to data collection such as consent, power, inclusivity, transparency, and ethics & privacy. We discuss these five key approaches in document collection practices in archives that can inform data collection in sociocultural ML. By showing data collection practices from another field, we encourage ML research to be more cognizant and systematic in data collection and draw from interdisciplinary expertise.

To advance the circular economy (CE), it is crucial to gain insights into the evolution of public attention, cognitive pathways of the masses concerning circular products, and to identify primary concerns. To achieve this, we collected data from diverse platforms, including Twitter, Reddit, and The Guardian, and utilised three topic models to analyse the data. Given the performance of topic modelling may vary depending on hyperparameter settings, this research proposed a novel framework that integrates twin (single and multi-objective) hyperparameter optimisation for the CE. We conducted systematic experiments to ensure that topic models are set with appropriate hyperparameters under different constraints, providing valuable insights into the correlations between CE and public attention. In summary, our optimised model reveals that public remains concerned about the economic impacts of sustainability and circular practices, particularly regarding recyclable materials and environmentally sustainable technologies. The analysis shows that the CE has attracted significant attention on The Guardian, especially in topics related to sustainable development and environmental protection technologies, while discussions are comparatively less active on Twitter. These insights highlight the need for policymakers to implement targeted education programs, create incentives for businesses to adopt CE principles, and enforce more stringent waste management policies alongside improved recycling processes.

We introduce Adapters, an open-source library that unifies parameter-efficient and modular transfer learning in large language models. By integrating 10 diverse adapter methods into a unified interface, Adapters offers ease of use and flexible configuration. Our library allows researchers and practitioners to leverage adapter modularity through composition blocks, enabling the design of complex adapter setups. We demonstrate the library's efficacy by evaluating its performance against full fine-tuning on various NLP tasks. Adapters provides a powerful tool for addressing the challenges of conventional fine-tuning paradigms and promoting more efficient and modular transfer learning. The library is available via https://adapterhub.ml/adapters.

Recently, large language models (LLMs) have shown promising abilities to generate novel research ideas in science, a direction which coincides with many foundational principles in computational creativity (CC). In light of these developments, we present an idea generation system named Spark that couples retrieval-augmented idea generation using LLMs with a reviewer model named Judge trained on 600K scientific reviews from OpenReview. Our work is both a system demonstration and intended to inspire other CC researchers to explore grounding the generation and evaluation of scientific ideas within foundational CC principles. To this end, we release the annotated dataset used to train Judge, inviting other researchers to explore the use of LLMs for idea generation and creative evaluations.

The integration of Large Language Models (LLMs) into the scientific ecosystem raises fundamental questions about the creativity and originality of AI-generated research. Recent work has identified ``smart plagiarism'' as a concern in single-step prompting approaches, where models reproduce existing ideas with terminological shifts. This paper investigates whether agentic workflows -- multi-step systems employing iterative reasoning, evolutionary search, and recursive decomposition -- can generate more novel and feasible research plans. We benchmark five reasoning architectures: Reflection-based iterative refinement, Sakana AI v2 evolutionary algorithms, Google Co-Scientist multi-agent framework, GPT Deep Research (GPT-5.1) recursive decomposition, and Gemini~3 Pro multimodal long-context pipeline. Using evaluations from thirty proposals each on novelty, feasibility, and impact, we find that decomposition-based and long-context workflows achieve mean novelty of 4.17/5, while reflection-based approaches score significantly lower (2.33/5). Results reveal varied performance across research domains, with high-performing workflows maintaining feasibility without sacrificing creativity. These findings support the view that carefully designed multi-stage agentic workflows can advance AI-assisted research ideation.

Conducting literature reviews for scientific papers is essential for understanding research, its limitations, and building on existing work. It is a tedious task which makes an automatic literature review generator appealing. Unfortunately, many existing works that generate such reviews using Large Language Models (LLMs) have significant limitations. They tend to hallucinate-generate non-factual information-and ignore the latest research they have not been trained on. To address these limitations, we propose a toolkit that operates on Retrieval Augmented Generation (RAG) principles, specialized prompting and instructing techniques with the help of LLMs. Our system first initiates a web search to retrieve relevant papers by summarizing user-provided abstracts into keywords using an off-the-shelf LLM. Authors can enhance the search by supplementing it with relevant papers or keywords, contributing to a tailored retrieval process. Second, the system re-ranks the retrieved papers based on the user-provided abstract. Finally, the related work section is generated based on the re-ranked results and the abstract. There is a substantial reduction in time and effort for literature review compared to traditional methods, establishing our toolkit as an efficient alternative. Our project page including the demo and toolkit can be accessed here: https://litllm.github.io

Next-generation multimodal foundation models capable of any-to-any cross-modal generation and multi-turn interaction will serve as core components of artificial general intelligence systems, playing a pivotal role in human-machine interaction. However, most existing multimodal models remain constrained by autoregressive architectures, whose inherent limitations prevent a balanced integration of understanding and generation capabilities. Although hybrid and decoupling strategies have been explored to address these tasks within unified frameworks separately, their redundant, non-integrated designs limit their applicability to broader scenarios, such as cross-modal retrieval. In this work, we introduce NExT-OMNI, an open-source omnimodal foundation model that achieves unified modeling through discrete flow paradigms. By leveraging metric-induced probability paths and kinetic optimal velocities, NExT-OMNI natively supports any-to-any understanding and generation with enhanced response efficiency, while enabling broader application scenarios through concise unified representations rather than task-decoupled designs. Trained on large-scale interleaved text, image, video, and audio data, NExT-OMNI delivers competitive performance on multimodal generation and understanding benchmarks, while outperforming prior unified models in multi-turn multimodal interaction and cross-modal retrieval, highlighting its architectural advantages as a next-generation multimodal foundation model. To advance further research, we release training details, data protocols, and open-source both the code and model checkpoints.

We present a scientific reasoning foundation model that aligns natural language with heterogeneous scientific representations. The model is pretrained on a 206B-token corpus spanning scientific text, pure sequences, and sequence-text pairs, then aligned via SFT on 40M instructions, annealed cold-start bootstrapping to elicit long-form chain-of-thought, and reinforcement learning with task-specific reward shaping, which instills deliberate scientific reasoning. It supports four capability families, covering up to 103 tasks across workflows: (i) faithful translation between text and scientific formats, (ii) text/knowledge extraction, (iii) property prediction, (iv) property classification, (v) unconditional and conditional sequence generation and design. Compared with specialist systems, our approach broadens instruction coverage, improves cross-domain generalization, and enhances fidelity. We detail data curation and training and show that cross-discipline learning strengthens transfer and downstream reliability. The model, instruct tuning datasets and the evaluation code are open-sourced at https://huggingface.co/SciReason and https://github.com/open-sciencelab/SciReason.

Understanding the creation, evolution, and dissemination of scientific knowledge is crucial for bridging diverse subject areas and addressing complex global challenges such as pandemics, climate change, and ethical AI. Scientometrics, the quantitative and qualitative study of scientific literature, provides valuable insights into these processes. We introduce Scito2M, a longitudinal scientometric dataset with over two million academic publications, providing comprehensive contents information and citation graphs to support cross-disciplinary analyses. Using Scito2M, we conduct a temporal study spanning over 30 years to explore key questions in scientometrics: the evolution of academic terminology, citation patterns, and interdisciplinary knowledge exchange. Our findings reveal critical insights, such as disparities in epistemic cultures, knowledge production modes, and citation practices. For example, rapidly developing, application-driven fields like LLMs exhibit significantly shorter citation age (2.48 years) compared to traditional theoretical disciplines like oral history (9.71 years).

One of the central tasks in software maintenance is being able to understand and develop code changes. Thus, given a natural language description of the desired new operation of a function, an agent (human or AI) might be asked to generate the set of edits to that function to implement the desired new operation; likewise, given a set of edits to a function, an agent might be asked to generate a changed description, of that function's new workings. Thus, there is an incentive to train a neural model for change-related tasks. Motivated by this, we offer a new, "natural", large dataset of coupled changes to code and documentation mined from actual high-quality GitHub projects, where each sample represents a single commit where the code and the associated docstring were changed together. We present the methodology for gathering the dataset, and some sample, challenging (but realistic) tasks where our dataset provides opportunities for both learning and evaluation. We find that current models (specifically Llama-3.1 405B, Mixtral 8times22B) do find these maintenance-related tasks challenging.

Current LLM-based research agents have advanced through agent orchestration, yet largely overlook scientific knowledge orchestration. Existing works often reduce papers to abstracts, surface mentions, and flat cites edges, omitting key entities, claims, evidence, mechanisms, and method lineages essential for scientific reasoning. To this end, we introduce Agents-K1, an end-to-end knowledge orchestration pipeline that converts raw documents into agent-native scientific knowledge graphs. Agents-K1 integrates three components under a unifying theoretical foundation: a multimodal parser whose five-module schema captures entities, multimodal evidence, citations, and typed inter-entity relations across the full paper rather than abstracts alone; a 4B information-extraction backbone trained with GRPO under a rule-based reward; and a graphanything CLI, a tri-source agent interface that unifies web search, multimodal graph retrieval, and cross-document traversal. On top of this, we process 2.46 million scientific papers across six subjects to produce Scholar-KG, of which we release a one-million-paper subset, and the full Scholar-KG is accessible via the SCP link below. The same pipeline can be extended to general-domain corpora and to schema-conformant data synthesis. Extensive experiments demonstrate that Agents-K1 achieves superior performance in scientific information extraction, knowledge graph construction, and multi-hop scientific reasoning.