Daily Papers

Federated Learning (FL) has emerged as a promising technique for edge devices to collaboratively learn a shared prediction model, while keeping their training data on the device, thereby decoupling the ability to do machine learning from the need to store the data in the cloud. However, FL is difficult to implement realistically, both in terms of scale and systems heterogeneity. Although there are a number of research frameworks available to simulate FL algorithms, they do not support the study of scalable FL workloads on heterogeneous edge devices. In this paper, we present Flower -- a comprehensive FL framework that distinguishes itself from existing platforms by offering new facilities to execute large-scale FL experiments and consider richly heterogeneous FL device scenarios. Our experiments show Flower can perform FL experiments up to 15M in client size using only a pair of high-end GPUs. Researchers can then seamlessly migrate experiments to real devices to examine other parts of the design space. We believe Flower provides the community with a critical new tool for FL study and development.

Multimodal Large Language Models (MLLMs) excel in tasks like multimodal reasoning and cross-modal retrieval but face deployment challenges in real-world scenarios due to distributed multimodal data and strict privacy requirements. Federated Learning (FL) offers a solution by enabling collaborative model training without centralizing data. However, realizing FL for MLLMs presents significant challenges, including high computational demands, limited client capacity, substantial communication costs, and heterogeneous client data. Existing FL methods assume client-side deployment of full models, an assumption that breaks down for large-scale MLLMs due to their massive size and communication demands. To address these limitations, we propose FedNano, the first FL framework that centralizes the LLM on the server while introducing NanoEdge, a lightweight module for client-specific adaptation. NanoEdge employs modality-specific encoders, connectors, and trainable NanoAdapters with low-rank adaptation. This design eliminates the need to deploy LLM on clients, reducing client-side storage by 95%, and limiting communication overhead to only 0.01% of the model parameters. By transmitting only compact NanoAdapter updates, FedNano handles heterogeneous client data and resource constraints while preserving privacy. Experiments demonstrate that FedNano outperforms prior FL baselines, bridging the gap between MLLM scale and FL feasibility, and enabling scalable, decentralized multimodal AI systems.

Foundation models (FMs) achieve strong performance across diverse tasks with task-specific fine-tuning, yet full parameter fine-tuning is often computationally prohibitive for large models. Parameter-efficient fine-tuning (PEFT) methods like Low-Rank Adaptation (LoRA) reduce this cost by introducing low-rank matrices for tuning fewer parameters. While LoRA allows for efficient fine-tuning, it requires significant data for adaptation, making Federated Learning (FL) an appealing solution due to its privacy-preserving collaborative framework. However, combining LoRA with FL introduces two key challenges: the Server-Side LoRA Aggregation Bias, where server-side averaging of LoRA matrices diverges from the ideal global update, and the Client-Side LoRA Initialization Drift, emphasizing the need for consistent initialization across rounds. Existing approaches address these challenges individually, limiting their effectiveness. We propose LoRA-FAIR, a novel method that tackles both issues by introducing a correction term on the server while keeping the original LoRA modules, enhancing aggregation efficiency and accuracy. LoRA-FAIR maintains computational and communication efficiency, yielding superior performance over state-of-the-art methods. Experimental results on ViT and MLP-Mixer models across large-scale datasets demonstrate that LoRA-FAIR consistently achieves performance improvements in FL settings.

While Federated Learning (FL) is gaining popularity for training machine learning models in a decentralized fashion, numerous challenges persist, such as asynchronization, computational expenses, data heterogeneity, and gradient and membership privacy attacks. Lately, dataset distillation has emerged as a promising solution for addressing the aforementioned challenges by generating a compact synthetic dataset that preserves a model's training efficacy. However, we discover that using distilled local datasets can amplify the heterogeneity issue in FL. To address this, we propose Federated Learning on Virtual Heterogeneous Data with Local-Global Dataset Distillation (FedLGD), where we seamlessly integrate dataset distillation algorithms into FL pipeline and train FL using a smaller synthetic dataset (referred as virtual data). Specifically, to harmonize the domain shifts, we propose iterative distribution matching to inpaint global information to local virtual data and use federated gradient matching to distill global virtual data that serve as anchor points to rectify heterogeneous local training, without compromising data privacy. We experiment on both benchmark and real-world datasets that contain heterogeneous data from different sources, and further scale up to an FL scenario that contains a large number of clients with heterogeneous and class-imbalanced data. Our method outperforms state-of-the-art heterogeneous FL algorithms under various settings. Our code is available at https://github.com/ubc-tea/FedLGD.

Large Language Models (LLMs) represent a significant stride toward Artificial General Intelligence. As scaling laws underscore the potential of increasing model sizes, the academic community has intensified its investigations into LLMs with capacities exceeding 50 billion parameters. This technical report builds on our prior work with Tele-FLM (also known as FLM-2), a publicly available 52-billion-parameter model. We delve into two primary areas: we first discuss our observation of Supervised Fine-tuning (SFT) on Tele-FLM-52B, which supports the "less is more" approach for SFT data construction; second, we demonstrate our experiments and analyses on the best practices for progressively growing a model from 52 billion to 102 billion, and subsequently to 1 trillion parameters. We will open-source a 1T model checkpoint, namely Tele-FLM-1T, to advance further training and research.

Federated learning (FL) is an emerging machine learning (ML) training paradigm where clients own their data and collaborate to train a global model, without revealing any data to the server and other participants. Researchers commonly perform experiments in a simulation environment to quickly iterate on ideas. However, existing open-source tools do not offer the efficiency required to simulate FL on larger and more realistic FL datasets. We introduce pfl-research, a fast, modular, and easy-to-use Python framework for simulating FL. It supports TensorFlow, PyTorch, and non-neural network models, and is tightly integrated with state-of-the-art privacy algorithms. We study the speed of open-source FL frameworks and show that pfl-research is 7-72times faster than alternative open-source frameworks on common cross-device setups. Such speedup will significantly boost the productivity of the FL research community and enable testing hypotheses on realistic FL datasets that were previously too resource intensive. We release a suite of benchmarks that evaluates an algorithm's overall performance on a diverse set of realistic scenarios. The code is available on GitHub at https://github.com/apple/pfl-research.

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

Multimodal Large Language Models (MLLMs) have made significant advancements, demonstrating powerful capabilities in processing and understanding multimodal data. Fine-tuning MLLMs with Federated Learning (FL) allows for expanding the training data scope by including private data sources, thereby enhancing their practical applicability in privacy-sensitive domains. However, current research remains in the early stage, particularly in addressing the multimodal heterogeneities in real-world applications. In this paper, we introduce a benchmark to evaluate the performance of federated fine-tuning of MLLMs across various multimodal heterogeneous scenarios, laying the groundwork for future research in the field. Our benchmark includes two lightweight MLLMs, two downstream tasks, three evaluation metrics, and five datasets across three domains, along with six comparison baselines, covering over ten types of modality heterogeneities across four multimodal scenarios. To address the challenges posed by multimodal heterogeneity, we develop a general FedMLLM framework that integrates classic FL methods alongside two modality-agnostic strategies. Extensive experimental results show that our proposed FL paradigm improves the performance of MLLMs by broadening the range of training data and mitigating multimodal heterogeneity. Code is available in supplementary materials.

Large Language Models (LLMs) are often described as being instances of foundation models - that is, models that transfer strongly across various tasks and conditions in few-show or zero-shot manner, while exhibiting scaling laws that predict function improvement when increasing the pre-training scale. These claims of excelling in different functions and tasks rely on measurements taken across various sets of standardized benchmarks showing high scores for such models. We demonstrate here a dramatic breakdown of function and reasoning capabilities of state-of-the-art models trained at the largest available scales which claim strong function, using a simple, short, conventional common sense problem formulated in concise natural language, easily solvable by humans. The breakdown is dramatic, as models also express strong overconfidence in their wrong solutions, while providing often non-sensical "reasoning"-like explanations akin to confabulations to justify and backup the validity of their clearly failed responses, making them sound plausible. Various standard interventions in an attempt to get the right solution, like various type of enhanced prompting, or urging the models to reconsider the wrong solutions again by multi step re-evaluation, fail. We take these initial observations to the scientific and technological community to stimulate urgent re-assessment of the claimed capabilities of current generation of LLMs, Such re-assessment also requires common action to create standardized benchmarks that would allow proper detection of such basic reasoning deficits that obviously manage to remain undiscovered by current state-of-the-art evaluation procedures and benchmarks. Code for reproducing experiments in the paper and raw experiments data can be found at https://github.com/LAION-AI/AIW

Scaling up neural networks has led to remarkable performance across a wide range of tasks. Moreover, performance often follows reliable scaling laws as a function of training set size, model size, and compute, which offers valuable guidance as large-scale experiments are becoming increasingly expensive. However, previous work on scaling laws has primarily used private data \& models or focused on uni-modal language or vision learning. To address these limitations, we investigate scaling laws for contrastive language-image pre-training (CLIP) with the public LAION dataset and the open-source OpenCLIP repository. Our large-scale experiments involve models trained on up to two billion image-text pairs and identify power law scaling for multiple downstream tasks including zero-shot classification, retrieval, linear probing, and end-to-end fine-tuning. We find that the training distribution plays a key role in scaling laws as the OpenAI and OpenCLIP models exhibit different scaling behavior despite identical model architectures and similar training recipes. We open-source our evaluation workflow and all models, including the largest public CLIP models, to ensure reproducibility and make scaling laws research more accessible. Source code and instructions to reproduce this study will be available at https://github.com/LAION-AI/scaling-laws-openclip

We investigate the predictability of large language model (LLM) capabilities: given records of past experiments using different model families, numbers of parameters, tasks, and numbers of in-context examples, can we accurately predict LLM performance on new experiment configurations? Answering this question has practical implications for LLM users (e.g., deciding which models to try), developers (e.g., prioritizing evaluation on representative tasks), and the research community (e.g., identifying hard-to-predict capabilities that warrant further investigation). We study the performance prediction problem on experiment records from BIG-bench. On a random train-test split, an MLP-based predictor achieves an R^2 score greater than 95%, indicating the presence of learnable patterns within the experiment records. We then formulate the problem of searching for "small-bench," an informative subset of BIG-bench tasks from which the performance on the full set can be maximally recovered. We find a subset as informative as BIG-bench Hard for evaluating new model families, while being 3times smaller. Additionally, we find competitive subsets by clustering task representations learned by our MLP-based predictor and selecting tasks close to cluster centroids, highlighting the importance of task diversity in constructing "small-bench."

We introduce LongCat-Flash, a 560-billion-parameter Mixture-of-Experts (MoE) language model designed for both computational efficiency and advanced agentic capabilities. Stemming from the need for scalable efficiency, LongCat-Flash adopts two novel designs: (a) Zero-computation Experts, which enables dynamic computational budget allocation and activates 18.6B-31.3B (27B on average) per token depending on contextual demands, optimizing resource usage. (b) Shortcut-connected MoE, which enlarges the computation-communication overlap window, demonstrating notable gains in inference efficiency and throughput compared to models of a comparable scale. We develop a comprehensive scaling framework for large models that combines hyperparameter transfer, model-growth initialization, a multi-pronged stability suite, and deterministic computation to achieve stable and reproducible training. Notably, leveraging the synergy among scalable architectural design and infrastructure efforts, we complete model training on more than 20 trillion tokens within 30 days, while achieving over 100 tokens per second (TPS) for inference at a cost of \$0.70 per million output tokens. To cultivate LongCat-Flash towards agentic intelligence, we conduct a large-scale pre-training on optimized mixtures, followed by targeted mid- and post-training on reasoning, code, and instructions, with further augmentation from synthetic data and tool use tasks. Comprehensive evaluations demonstrate that, as a non-thinking foundation model, LongCat-Flash delivers highly competitive performance among other leading models, with exceptional strengths in agentic tasks. The model checkpoint of LongCat-Flash is open-sourced to foster community research. LongCat Chat: https://longcat.ai Hugging Face: https://huggingface.co/meituan-longcat GitHub: https://github.com/meituan-longcat

Large language models (LLMs) have showcased profound capabilities in language understanding and generation, facilitating a wide array of applications. However, there is a notable paucity of detailed, open-sourced methodologies on efficiently scaling LLMs beyond 50 billion parameters with minimum trial-and-error cost and computational resources. In this report, we introduce Tele-FLM (aka FLM-2), a 52B open-sourced multilingual large language model that features a stable, efficient pre-training paradigm and enhanced factual judgment capabilities. Tele-FLM demonstrates superior multilingual language modeling abilities, measured by BPB on textual corpus. Besides, in both English and Chinese foundation model evaluation, it is comparable to strong open-sourced models that involve larger pre-training FLOPs, such as Llama2-70B and DeepSeek-67B. In addition to the model weights, we share the core designs, engineering practices, and training details, which we expect to benefit both the academic and industrial communities.

Large language models (LLMs) have emerged as a cornerstone in real-world applications with lengthy streaming inputs, such as LLM-driven agents. However, existing LLMs, pre-trained on sequences with restricted maximum length, cannot generalize to longer sequences due to the out-of-domain and distraction issues. To alleviate these issues, existing efforts employ sliding attention windows and discard distant tokens to achieve the processing of extremely long sequences. Unfortunately, these approaches inevitably fail to capture long-distance dependencies within sequences to deeply understand semantics. This paper introduces a training-free memory-based method, InfLLM, to unveil the intrinsic ability of LLMs to process streaming long sequences. Specifically, InfLLM stores distant contexts into additional memory units and employs an efficient mechanism to lookup token-relevant units for attention computation. Thereby, InfLLM allows LLMs to efficiently process long sequences while maintaining the ability to capture long-distance dependencies. Without any training, InfLLM enables LLMs pre-trained on sequences of a few thousand tokens to achieve superior performance than competitive baselines continually training these LLMs on long sequences. Even when the sequence length is scaled to 1,024K, InfLLM still effectively captures long-distance dependencies.

Pre-trained large language models (LLMs) require fine-tuning to improve their responsiveness to natural language instructions. Federated learning (FL) offers a way to perform fine-tuning using the abundant data on end devices without compromising data privacy. Most existing federated fine-tuning methods for LLMs rely on parameter-efficient fine-tuning techniques, which may not reach the performance heights possible with full-parameter tuning. However, the communication overhead associated with full-parameter tuning is prohibitively high for both servers and clients. This work introduces FedKSeed, a novel approach that employs zeroth-order optimization (ZOO) with a set of random seeds. It enables federated full-parameter tuning of billion-sized LLMs directly on devices. Our method significantly reduces transmission requirements between the server and clients to just a few scalar gradients and random seeds, amounting to only a few thousand bytes. Building on this, we develop a strategy to assess the significance of ZOO perturbations for FL, allowing for probability-differentiated seed sampling. This prioritizes perturbations that have a greater impact on model accuracy. Experiments across six scenarios with different LLMs, datasets and data partitions demonstrate that our approach outperforms existing federated LLM fine-tuning methods in terms of both communication efficiency and new task generalization.

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal inputs. To advance the new field of LLM for molecular discovery, this survey provides an up-to-date and forward-looking review of the emerging use of LLMs for two central tasks: molecule generation and molecule optimization. Based on our proposed taxonomy for both problems, we analyze representative techniques in each category, highlighting how LLM capabilities are leveraged across different learning settings. In addition, we include the commonly used datasets and evaluation protocols. We conclude by discussing key challenges and future directions, positioning this survey as a resource for researchers working at the intersection of LLMs and molecular science. A continuously updated reading list is available at https://github.com/REAL-Lab-NU/Awesome-LLM-Centric-Molecular-Discovery.

Deploying Large Language Models (LLMs) on resource-constrained (or weak) devices presents significant challenges due to limited resources and heterogeneous data distribution. To address the data concern, it is necessary to fine-tune LLMs using on-device private data for various downstream tasks. While Federated Learning (FL) offers a promising privacy-preserving solution, existing fine-tuning methods retain the original LLM size, leaving issues of high inference latency and excessive memory demands unresolved. Hence, we design FedSpine, an FL framework that combines Parameter- Efficient Fine-Tuning (PEFT) with structured pruning for efficient deployment of LLMs on resource-constrained devices. Specifically, FedSpine introduces an iterative process to prune and tune the parameters of LLMs. To mitigate the impact of device heterogeneity, an online Multi-Armed Bandit (MAB) algorithm is employed to adaptively determine different pruning ratios and LoRA ranks for heterogeneous devices without any prior knowledge of their computing and communication capabilities. As a result, FedSpine maintains higher inference accuracy while improving fine-tuning efficiency. Experimental results conducted on a physical platform with 80 devices demonstrate that FedSpine can speed up fine-tuning by 1.4times-6.9times and improve final accuracy by 0.4%-4.5% under the same sparsity level compared to other baselines.

Multimodal Large Language Models (MLLMs) hold promise for accelerating scientific discovery by interpreting complex experimental procedures. However, their true capabilities are poorly understood, as existing benchmarks neglect the fine-grained and long-horizon nature of authentic laboratory work, especially in wet-lab settings. To bridge this gap, we introduce ExpVid, the first benchmark designed to systematically evaluate MLLMs on scientific experiment videos. Curated from peer-reviewed video publications, ExpVid features a new three-level task hierarchy that mirrors the scientific process: (1) Fine-grained Perception of tools, materials, and actions; (2) Procedural Understanding of step order and completeness; and (3) Scientific Reasoning that connects the full experiment to its published conclusions. Our vision-centric annotation pipeline, combining automated generation with multi-disciplinary expert validation, ensures that tasks require visual grounding. We evaluate 19 leading MLLMs on ExpVid and find that while they excel at coarse-grained recognition, they struggle with disambiguating fine details, tracking state changes over time, and linking experimental procedures to scientific outcomes. Our results reveal a notable performance gap between proprietary and open-source models, particularly in high-order reasoning. ExpVid not only provides a diagnostic tool but also charts a roadmap for developing MLLMs capable of becoming trustworthy partners in scientific experimentation.

Large language models (LLMs) are useful in many NLP tasks and become more capable with size, with the best open-source models having over 50 billion parameters. However, using these 50B+ models requires high-end hardware, making them inaccessible to most researchers. In this work, we investigate methods for cost-efficient inference and fine-tuning of LLMs, comparing local and distributed strategies. We observe that a large enough model (50B+) can run efficiently even on geodistributed devices in a consumer-grade network. This could allow running LLM efficiently by pooling together idle compute resources of multiple research groups and volunteers. We address two open problems: (1) how to perform inference and fine-tuning reliably if any device can disconnect abruptly and (2) how to partition LLMs between devices with uneven hardware, joining and leaving at will. In order to do that, we develop special fault-tolerant inference algorithms and load-balancing protocols that automatically assign devices to maximize the total system throughput. We showcase these algorithms in Petals - a decentralized system that runs Llama 2 (70B) and BLOOM (176B) over the Internet up to 10x faster than offloading for interactive generation. We evaluate the performance of our system in simulated conditions and a real-world setup spanning two continents.

LLMs have demonstrated great capabilities in various NLP tasks. Different entities can further improve the performance of those LLMs on their specific downstream tasks by fine-tuning LLMs. When several entities have similar interested tasks, but their data cannot be shared because of privacy concerns regulations, federated learning (FL) is a mainstream solution to leverage the data of different entities. However, fine-tuning LLMs in federated learning settings still lacks adequate support from existing FL frameworks because it has to deal with optimizing the consumption of significant communication and computational resources, data preparation for different tasks, and distinct information protection demands. This paper first discusses these challenges of federated fine-tuning LLMs, and introduces our package FS-LLM as a main contribution, which consists of the following components: (1) we build an end-to-end benchmarking pipeline, automizing the processes of dataset preprocessing, federated fine-tuning execution, and performance evaluation on federated LLM fine-tuning; (2) we provide comprehensive federated parameter-efficient fine-tuning algorithm implementations and versatile programming interfaces for future extension in FL scenarios with low communication and computation costs, even without accessing the full model; (3) we adopt several accelerating and resource-efficient operators for fine-tuning LLMs with limited resources and the flexible pluggable sub-routines for interdisciplinary study. We conduct extensive experiments to validate the effectiveness of FS-LLM and benchmark advanced LLMs with state-of-the-art parameter-efficient fine-tuning algorithms in FL settings, which also yields valuable insights into federated fine-tuning LLMs for the research community. To facilitate further research and adoption, we release FS-LLM at https://github.com/alibaba/FederatedScope/tree/llm.

Foundational Language Models (FLMs) have advanced natural language processing (NLP) research. Current researchers are developing larger FLMs (e.g., XLNet, T5) to enable contextualized language representation, classification, and generation. While developing larger FLMs has been of significant advantage, it is also a liability concerning hallucination and predictive uncertainty. Fundamentally, larger FLMs are built on the same foundations as smaller FLMs (e.g., BERT); hence, one must recognize the potential of smaller FLMs which can be realized through an ensemble. In the current research, we perform a reality check on FLMs and their ensemble on benchmark and real-world datasets. We hypothesize that the ensembling of FLMs can influence the individualistic attention of FLMs and unravel the strength of coordination and cooperation of different FLMs. We utilize BERT and define three other ensemble techniques: {Shallow, Semi, and Deep}, wherein the Deep-Ensemble introduces a knowledge-guided reinforcement learning approach. We discovered that the suggested Deep-Ensemble BERT outperforms its large variation i.e. BERTlarge, by a factor of many times using datasets that show the usefulness of NLP in sensitive fields, such as mental health.

Large Language Models (LLMs) and other large foundation models have achieved noteworthy success, but their size exacerbates existing resource consumption and latency challenges. In particular, the large-scale deployment of these models is hindered by the significant resource requirements during inference. In this paper, we study two approaches for mitigating these challenges: employing a cache to store previous queries and learning a model multiplexer to choose from an ensemble of models for query processing. Theoretically, we provide an optimal algorithm for jointly optimizing both approaches to reduce the inference cost in both offline and online tabular settings. By combining a caching algorithm, namely Greedy Dual Size with Frequency (GDSF) or Least Expected Cost (LEC), with a model multiplexer, we achieve optimal rates in both offline and online settings. Empirically, simulations show that the combination of our caching and model multiplexing algorithms greatly improves over the baselines, with up to 50times improvement over the baseline when the ratio between the maximum cost and minimum cost is 100. Experiments on real datasets show a 4.3times improvement in FLOPs over the baseline when the ratio for FLOPs is 10, and a 1.8times improvement in latency when the ratio for average latency is 1.85.

Large language models (LLMs) are catalyzing the development of autonomous AI research agents for scientific and engineering discovery. We present FM Agent, a novel and general-purpose multi-agent framework that leverages a synergistic combination of LLM-based reasoning and large-scale evolutionary search to address complex real-world challenges. The core of FM Agent integrates several key innovations: 1) a cold-start initialization phase incorporating expert guidance, 2) a novel evolutionary sampling strategy for iterative optimization, 3) domain-specific evaluators that combine correctness, effectiveness, and LLM-supervised feedback, and 4) a distributed, asynchronous execution infrastructure built on Ray. Demonstrating broad applicability, our system has been evaluated across diverse domains, including operations research, machine learning, GPU kernel optimization, and classical mathematical problems. FM Agent reaches state-of-the-art results autonomously, without human interpretation or tuning -- 1976.3 on ALE-Bench (+5.2\%), 43.56\% on MLE-Bench (+4.0pp), up to 20x speedups on KernelBench, and establishes new state-of-the-art(SOTA) results on several classical mathematical problems. Beyond academic benchmarks, FM Agent shows considerable promise for both large-scale enterprise R\&D workflows and fundamental scientific research, where it can accelerate innovation, automate complex discovery processes, and deliver substantial engineering and scientific advances with broader societal impact.

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/.

Fluorescence Lifetime Imaging (FLI) is a critical molecular imaging modality that provides unique information about the tissue microenvironment, which is invaluable for biomedical applications. FLI operates by acquiring and analyzing photon time-of-arrival histograms to extract quantitative parameters associated with temporal fluorescence decay. These histograms are influenced by the intrinsic properties of the fluorophore, instrument parameters, time-of-flight distributions associated with pixel-wise variations in the topographic and optical characteristics of the sample. Recent advancements in Deep Learning (DL) have enabled improved fluorescence lifetime parameter estimation. However, existing models are primarily designed for planar surface samples, limiting their applicability in translational scenarios involving complex surface profiles, such as in-vivo whole-animal or imaged guided surgical applications. To address this limitation, we present MFliNet (Macroscopic FLI Network), a novel DL architecture that integrates the Instrument Response Function (IRF) as an additional input alongside experimental photon time-of-arrival histograms. Leveraging the capabilities of a Differential Transformer encoder-decoder architecture, MFliNet effectively focuses on critical input features, such as variations in photon time-of-arrival distributions. We evaluate MFliNet using rigorously designed tissue-mimicking phantoms and preclinical in-vivo cancer xenograft models. Our results demonstrate the model's robustness and suitability for complex macroscopic FLI applications, offering new opportunities for advanced biomedical imaging in diverse and challenging settings.

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

Because large language models are expensive to pretrain on different datasets, using smaller-scale experiments to decide on data is crucial for reducing costs. Which benchmarks and methods of making decisions from observed performance at small scale most accurately predict the datasets that yield the best large models? To empower open exploration of this question, we release models, data, and evaluations in DataDecide -- the most extensive open suite of models over differences in data and scale. We conduct controlled pretraining experiments across 25 corpora with differing sources, deduplication, and filtering up to 100B tokens, model sizes up to 1B parameters, and 3 random seeds. We find that the ranking of models at a single, small size (e.g., 150M parameters) is a strong baseline for predicting best models at our larger target scale (1B) (~80% of com parisons correct). No scaling law methods among 8 baselines exceed the compute-decision frontier of single-scale predictions, but DataDecide can measure improvement in future scaling laws. We also identify that using continuous likelihood metrics as proxies in small experiments makes benchmarks including MMLU, ARC, HellaSwag, MBPP, and HumanEval >80% predictable at the target 1B scale with just 0.01% of the compute.

Recent advancements in Large Language Models (LLMs) have revealed new capabilities and opportunities across the technological landscape. However, the practicality of very large LLMs is challenged by their high compute cost, which does not justify the benefits given their limited capability compared to humans. While smaller, more practical LLMs have shown potential in financial analysis, though they are not yet fully proficient, as evidenced by their near-passing performance on the Chartered Financial Analyst (CFA) exam. In this work, we present Financial Analyst Extension to our Text Hyperlocally Augmented Large Language Extension (THaLLE), a series of 8B LLMs consistently achieving highest performance on mock CFA exams against models of comparable size. We thoroughly document the fine-tuning techniques used to facilitate future research. Additionally, we introduce the use of Flare CFA, a publicly available dataset for evaluating LLMs as a financial advisor.

Large foundation models are typically trained on data from multiple domains, with the data mixture--the proportion of each domain used--playing a critical role in model performance. The standard approach to selecting this mixture relies on trial and error, which becomes impractical for large-scale pretraining. We propose a systematic method to determine the optimal data mixture for any target domain using scaling laws. Our approach accurately predicts the loss of a model of size N trained with D tokens and a specific domain weight vector h. We validate the universality of these scaling laws by demonstrating their predictive power in three distinct and large-scale settings: large language model (LLM), native multimodal model (NMM), and large vision models (LVM) pretraining. We further show that these scaling laws can extrapolate to new data mixtures and across scales: their parameters can be accurately estimated using a few small-scale training runs, and used to estimate the performance at larger scales and unseen domain weights. The scaling laws allow to derive the optimal domain weights for any target domain under a given training budget (N,D), providing a principled alternative to costly trial-and-error methods.

Developing artificial intelligence (AI) for vertical domains requires a solid data foundation for both training and evaluation. In this work, we introduce TrialPanorama, a large-scale, structured database comprising 1,657,476 clinical trial records aggregated from 15 global sources. The database captures key aspects of trial design and execution, including trial setups, interventions, conditions, biomarkers, and outcomes, and links them to standard biomedical ontologies such as DrugBank and MedDRA. This structured and ontology-grounded design enables TrialPanorama to serve as a unified, extensible resource for a wide range of clinical trial tasks, including trial planning, design, and summarization. To demonstrate its utility, we derive a suite of benchmark tasks directly from the TrialPanorama database. The benchmark spans eight tasks across two categories: three for systematic review (study search, study screening, and evidence summarization) and five for trial design (arm design, eligibility criteria, endpoint selection, sample size estimation, and trial completion assessment). The experiments using five state-of-the-art large language models (LLMs) show that while general-purpose LLMs exhibit some zero-shot capability, their performance is still inadequate for high-stakes clinical trial workflows. We release TrialPanorama database and the benchmark to facilitate further research on AI for clinical trials.

Large language models (LLMs) have attracted significant attention due to their impressive general capabilities across diverse downstream tasks. However, without domain-specific optimization, they often underperform on specialized knowledge benchmarks and even produce hallucination. Recent studies show that strategically infusing domain knowledge during pretraining can substantially improve downstream performance. A critical challenge lies in balancing this infusion trade-off: injecting too little domain-specific data yields insufficient specialization, whereas excessive infusion triggers catastrophic forgetting of previously acquired knowledge. In this work, we focus on the phenomenon of memory collapse induced by over-infusion. Through systematic experiments, we make two key observations, i.e. 1) Critical collapse point: each model exhibits a threshold beyond which its knowledge retention capabilities sharply degrade. 2) Scale correlation: these collapse points scale consistently with the model's size. Building on these insights, we propose a knowledge infusion scaling law that predicts the optimal amount of domain knowledge to inject into large LLMs by analyzing their smaller counterparts. Extensive experiments across different model sizes and pertaining token budgets validate both the effectiveness and generalizability of our scaling law.

Conventional federated learning (FL) frameworks follow a server-driven model where the server determines session initiation and client participation, which faces challenges in accommodating clients' asynchronous needs for model updates. We introduce Client-Driven Federated Learning (CDFL), a novel FL framework that puts clients at the driving role. In CDFL, each client independently and asynchronously updates its model by uploading the locally trained model to the server and receiving a customized model tailored to its local task. The server maintains a repository of cluster models, iteratively refining them using received client models. Our framework accommodates complex dynamics in clients' data distributions, characterized by time-varying mixtures of cluster distributions, enabling rapid adaptation to new tasks with superior performance. In contrast to traditional clustered FL protocols that send multiple cluster models to a client to perform distribution estimation, we propose a paradigm that offloads the estimation task to the server and only sends a single model to a client, and novel strategies to improve estimation accuracy. We provide a theoretical analysis of CDFL's convergence. Extensive experiments across various datasets and system settings highlight CDFL's substantial advantages in model performance and computation efficiency over baselines.

We introduce LongSkywork, a long-context Large Language Model (LLM) capable of processing up to 200,000 tokens. We provide a training recipe for efficiently extending context length of LLMs. We identify that the critical element in enhancing long-context processing capability is to incorporate a long-context SFT stage following the standard SFT stage. A mere 200 iterations can convert the standard SFT model into a long-context model. To reduce the effort in collecting and annotating data for long-context language modeling, we develop two novel methods for creating synthetic data. These methods are applied during the continual pretraining phase as well as the Supervised Fine-Tuning (SFT) phase, greatly enhancing the training efficiency of our long-context LLMs. Our findings suggest that synthetic long-context SFT data can surpass the performance of data curated by humans to some extent. LongSkywork achieves outstanding performance on a variety of long-context benchmarks. In the Needle test, a benchmark for long-context information retrieval, our models achieved perfect accuracy across multiple context spans. Moreover, in realistic application scenarios, LongSkywork-13B demonstrates performance on par with Claude2.1, the leading long-context model, underscoring the effectiveness of our proposed methods.

Amid the ongoing advancements in Federated Learning (FL), a machine learning paradigm that allows collaborative learning with data privacy protection, personalized FL (pFL)has gained significant prominence as a research direction within the FL domain. Whereas traditional FL (tFL) focuses on jointly learning a global model, pFL aims to balance each client's global and personalized goals in FL settings. To foster the pFL research community, we started and built PFLlib, a comprehensive pFL library with an integrated benchmark platform. In PFLlib, we implemented 37 state-of-the-art FL algorithms (8 tFL algorithms and 29 pFL algorithms) and provided various evaluation environments with three statistically heterogeneous scenarios and 24 datasets. At present, PFLlib has gained more than 1600 stars and 300 forks on GitHub.

We study the problem of using low computational cost to automate the choices of learners and hyperparameters for an ad-hoc training dataset and error metric, by conducting trials of different configurations on the given training data. We investigate the joint impact of multiple factors on both trial cost and model error, and propose several design guidelines. Following them, we build a fast and lightweight library FLAML which optimizes for low computational resource in finding accurate models. FLAML integrates several simple but effective search strategies into an adaptive system. It significantly outperforms top-ranked AutoML libraries on a large open source AutoML benchmark under equal, or sometimes orders of magnitude smaller budget constraints.

As scientific research becomes increasingly complex, innovative tools are needed to manage vast data, facilitate interdisciplinary collaboration, and accelerate discovery. Large language models (LLMs) are now evolving into LLM-based scientific agents that automate critical tasks, ranging from hypothesis generation and experiment design to data analysis and simulation. Unlike general-purpose LLMs, these specialized agents integrate domain-specific knowledge, advanced tool sets, and robust validation mechanisms, enabling them to handle complex data types, ensure reproducibility, and drive scientific breakthroughs. This survey provides a focused review of the architectures, design, benchmarks, applications, and ethical considerations surrounding LLM-based scientific agents. We highlight why they differ from general agents and the ways in which they advance research across various scientific fields. By examining their development and challenges, this survey offers a comprehensive roadmap for researchers and practitioners to harness these agents for more efficient, reliable, and ethically sound scientific discovery.

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

Large Language Models (LLMs) have demonstrated impressive capabilities to solve a wide range of tasks without being explicitly fine-tuned on task-specific datasets. However, deploying LLMs in the real world is not trivial, as it requires substantial computing resources. In this paper, we investigate whether smaller, compact LLMs are a good alternative to the comparatively Larger LLMs2 to address significant costs associated with utilizing LLMs in the real world. In this regard, we study the meeting summarization task in a real-world industrial environment and conduct extensive experiments by comparing the performance of fine-tuned compact LLMs (e.g., FLAN-T5, TinyLLaMA, LiteLLaMA) with zero-shot larger LLMs (e.g., LLaMA-2, GPT-3.5, PaLM-2). We observe that most smaller LLMs, even after fine-tuning, fail to outperform larger zero-shot LLMs in meeting summarization datasets. However, a notable exception is FLAN-T5 (780M parameters), which performs on par or even better than many zero-shot Larger LLMs (from 7B to above 70B parameters), while being significantly smaller. This makes compact LLMs like FLAN-T5 a suitable cost-efficient solution for real-world industrial deployment.

The rapid growth of biomedical knowledge has outpaced our ability to efficiently extract insights and generate novel hypotheses. Large language models (LLMs) have emerged as a promising tool to revolutionize knowledge interaction and potentially accelerate biomedical discovery. In this paper, we present a comprehensive evaluation of LLMs as biomedical hypothesis generators. We construct a dataset of background-hypothesis pairs from biomedical literature, carefully partitioned into training, seen, and unseen test sets based on publication date to mitigate data contamination. Using this dataset, we assess the hypothesis generation capabilities of top-tier instructed models in zero-shot, few-shot, and fine-tuning settings. To enhance the exploration of uncertainty, a crucial aspect of scientific discovery, we incorporate tool use and multi-agent interactions in our evaluation framework. Furthermore, we propose four novel metrics grounded in extensive literature review to evaluate the quality of generated hypotheses, considering both LLM-based and human assessments. Our experiments yield two key findings: 1) LLMs can generate novel and validated hypotheses, even when tested on literature unseen during training, and 2) Increasing uncertainty through multi-agent interactions and tool use can facilitate diverse candidate generation and improve zero-shot hypothesis generation performance. However, we also observe that the integration of additional knowledge through few-shot learning and tool use may not always lead to performance gains, highlighting the need for careful consideration of the type and scope of external knowledge incorporated. These findings underscore the potential of LLMs as powerful aids in biomedical hypothesis generation and provide valuable insights to guide further research in this area.

As language models grow ever larger, the need for large-scale high-quality text datasets has never been more pressing, especially in multilingual settings. The BigScience workshop, a 1-year international and multidisciplinary initiative, was formed with the goal of researching and training large language models as a values-driven undertaking, putting issues of ethics, harm, and governance in the foreground. This paper documents the data creation and curation efforts undertaken by BigScience to assemble the Responsible Open-science Open-collaboration Text Sources (ROOTS) corpus, a 1.6TB dataset spanning 59 languages that was used to train the 176-billion-parameter BigScience Large Open-science Open-access Multilingual (BLOOM) language model. We further release a large initial subset of the corpus and analyses thereof, and hope to empower large-scale monolingual and multilingual modeling projects with both the data and the processing tools, as well as stimulate research around this large multilingual corpus.

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

Large language models (LLMs) have surged in popularity and are extensively used in commercial applications, where the efficiency of model serving is crucial for the user experience. Most current research focuses on optimizing individual sub-procedures, e.g. local inference and communication, however, there is no comprehensive framework that provides a holistic system view for optimizing LLM serving in an end-to-end manner. In this work, we conduct a detailed analysis to identify major bottlenecks that impact end-to-end latency in LLM serving systems. Our analysis reveals that a comprehensive LLM serving endpoint must address a series of efficiency bottlenecks that extend beyond LLM inference. We then propose ScaleLLM, an optimized system for resource-efficient LLM serving. Our extensive experiments reveal that with 64 concurrent requests, ScaleLLM achieves a 4.3x speed up over vLLM and outperforms state-of-the-arts with 1.5x higher throughput.

Large Language Models (LLMs) are increasingly capable of generating complete applications from natural language instructions, creating new opportunities in science and education. In these domains, interactive scientific demonstrations are particularly valuable for explaining concepts, supporting new teaching methods, and presenting research findings. Generating such demonstrations requires models to combine accurate scientific knowledge with the ability to implement interactive front-end code that behaves correctly and responds to user actions. This capability goes beyond the scope of existing benchmarks, which typically evaluate either knowledge question answering without grounding in code or static web code generation without scientific interactivity. To evaluate this integrated ability, we design a hybrid framework that combines programmatic functional testing to rigorously verify interaction logic with visually-grounded qualitative testing to assess rendered outputs against reference snapshots. Building on this framework, we present InteractScience, a benchmark consisting of a substantial set of carefully designed questions across five scientific domains, each paired with unit tests, reference snapshots, and checklists. We evaluate 30 leading open- and closed-source LLMs and report results that highlight ongoing weaknesses in integrating domain knowledge with interactive front-end coding. Our work positions InteractScience as the first benchmark to automatically measure this combined capability with realistic interactive operations, providing a foundation for advancing reliable and educationally useful scientific demonstration code generation. All code and data are publicly available at https://github.com/open-compass/InteractScience.

Large language models are being widely used across industries to generate content that contributes directly to key performance metrics, such as conversion rates. Pretrained models, however, often fall short when it comes to aligning with human preferences or optimizing for business objectives. As a result, fine-tuning with good-quality labeled data is essential to guide models to generate content that achieves better results. Controlled experiments, like A/B tests, can provide such data, but they are often expensive and come with significant engineering and logistical challenges. Meanwhile, companies have access to a vast amount of historical (observational) data that remains underutilized. In this work, we study the challenges and opportunities of fine-tuning LLMs using observational data. We show that while observational outcomes can provide valuable supervision, directly fine-tuning models on such data can lead them to learn spurious correlations. We present empirical evidence of this issue using various real-world datasets and propose DeconfoundLM, a method that explicitly removes the effect of known confounders from reward signals. Using simulation experiments, we demonstrate that DeconfoundLM improves the recovery of causal relationships and mitigates failure modes found in fine-tuning methods that ignore or naively incorporate confounding variables. Our findings highlight that while observational data presents risks, with the right causal corrections, it can be a powerful source of signal for LLM alignment. Please refer to the project page for code and related resources.

Hypothesis ranking is a crucial component of automated scientific discovery, particularly in natural sciences where wet-lab experiments are costly and throughput-limited. Existing approaches focus on pre-experiment ranking, relying solely on large language model's internal reasoning without incorporating empirical outcomes from experiments. We introduce the task of experiment-guided ranking, which aims to prioritize candidate hypotheses based on the results of previously tested ones. However, developing such strategies is challenging due to the impracticality of repeatedly conducting real experiments in natural science domains. To address this, we propose a simulator grounded in three domain-informed assumptions, modeling hypothesis performance as a function of similarity to a known ground truth hypothesis, perturbed by noise. We curate a dataset of 124 chemistry hypotheses with experimentally reported outcomes to validate the simulator. Building on this simulator, we develop a pseudo experiment-guided ranking method that clusters hypotheses by shared functional characteristics and prioritizes candidates based on insights derived from simulated experimental feedback. Experiments show that our method outperforms pre-experiment baselines and strong ablations.

Federated Learning (FL) is a recent model training paradigm in which client devices collaboratively train a model without ever aggregating their data. Crucially, this scheme offers users potential privacy and security benefits by only ever communicating updates to the model weights to a central server as opposed to traditional machine learning (ML) training which directly communicates and aggregates data. However, FL training suffers from statistical heterogeneity as clients may have differing local data distributions. Large language models (LLMs) offer a potential solution to this issue of heterogeneity given that they have consistently been shown to be able to learn on vast amounts of noisy data. While LLMs are a promising development for resolving the consistent issue of non-I.I.D. Clients in federated settings exacerbate two other bottlenecks in FL: limited local computing and expensive communication. This thesis aims to develop efficient training methods for LLMs in FL. To this end, we employ two critical techniques in enabling efficient training. First, we use low-rank adaptation (LoRA) to reduce the computational load of local model training. Second, we communicate sparse updates throughout training to significantly cut down on communication costs. Taken together, our method reduces communication costs by up to 10x over vanilla LoRA and up to 5x over more complex sparse LoRA baselines while achieving greater utility. We emphasize the importance of carefully applying sparsity and picking effective rank and sparsity configurations for federated LLM training.

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

We observe an empirical phenomenon in Large Language Models (LLMs) -- very few activations exhibit significantly larger values than others (e.g., 100,000 times larger). We call them massive activations. First, we demonstrate the widespread existence of massive activations across various LLMs and characterize their locations. Second, we find their values largely stay constant regardless of the input, and they function as indispensable bias terms in LLMs. Third, these massive activations lead to the concentration of attention probabilities to their corresponding tokens, and further, implicit bias terms in the self-attention output. Last, we also study massive activations in Vision Transformers. Code is available at https://github.com/locuslab/massive-activations.

Foundation Models (FMs) serve as a general class for the development of artificial intelligence systems, offering broad potential for generalization across a spectrum of downstream tasks. Despite extensive research into self-supervised learning as the cornerstone of FMs, several outstanding issues persist in Graph Foundation Models that rely on graph self-supervised learning, namely: 1) Homogenization. The extent of generalization capability on downstream tasks remains unclear. 2) Scalability. It is unknown how effectively these models can scale to large datasets. 3) Efficiency. The training time and memory usage of these models require evaluation. 4) Training Stop Criteria. Determining the optimal stopping strategy for pre-training across multiple tasks to maximize performance on downstream tasks. To address these questions, we have constructed a rigorous benchmark that thoroughly analyzes and studies the generalization and scalability of self-supervised Graph Neural Network (GNN) models. Regarding generalization, we have implemented and compared the performance of various self-supervised GNN models, trained to generate node representations, across tasks such as node classification, link prediction, and node clustering. For scalability, we have compared the performance of various models after training using full-batch and mini-batch strategies. Additionally, we have assessed the training efficiency of these models by conducting experiments to test their GPU memory usage and throughput. Through these experiments, we aim to provide insights to motivate future research. The code for this benchmark is publicly available at https://github.com/NYUSHCS/GraphFM.

Large language models (LLMs) have shown impressive performance in code understanding and generation, making coding tasks a key focus for researchers due to their practical applications and value as a testbed for LLM evaluation. Data synthesis and filtering techniques have been widely adopted and shown to be highly effective in this context. In this paper, we present a focused survey and taxonomy of these techniques, emphasizing recent advancements. We highlight key challenges, explore future research directions, and offer practical guidance for new researchers entering the field.

Evaluating large language models' (LLMs) long-context understanding capabilities remains challenging. We present SCALAR (Scientific Citation-based Live Assessment of Long-context Academic Reasoning), a novel benchmark that leverages academic papers and their citation networks. SCALAR features automatic generation of high-quality ground truth labels without human annotation, controllable difficulty levels, and a dynamic updating mechanism that prevents data contamination. Using ICLR 2025 papers, we evaluate 8 state-of-the-art LLMs, revealing key insights about their capabilities and limitations in processing long scientific documents across different context lengths and reasoning types. Our benchmark provides a reliable and sustainable way to track progress in long-context understanding as LLM capabilities evolve.

Visual Language Models (VLMs) demonstrate impressive capabilities in processing multimodal inputs, yet applications such as visual agents, which require handling multiple images and high-resolution videos, demand enhanced long-range modeling. Moreover, existing open-source VLMs lack systematic exploration into extending their context length, and commercial models often provide limited details. To tackle this, we aim to establish an effective solution that enhances long context performance of VLMs while preserving their capacities in short context scenarios. Towards this goal, we make the best design choice through extensive experiment settings from data curation to context window extending and utilizing: (1) we analyze data sources and length distributions to construct ETVLM - a data recipe to balance the performance across scenarios; (2) we examine existing position extending methods, identify their limitations and propose M-RoPE++ as an enhanced approach; we also choose to solely instruction-tune the backbone with mixed-source data; (3) we discuss how to better utilize extended context windows and propose hybrid-resolution training. Built on the Qwen-VL series model, we propose Giraffe, which is effectively extended to 128K lengths. Evaluated on extensive long context VLM benchmarks such as VideoMME and Viusal Haystacks, our Giraffe achieves state-of-the-art performance among similarly sized open-source long VLMs and is competitive with commercial model GPT-4V. We will open-source the code, data, and models.

Large language models have become a potential pathway toward achieving artificial general intelligence. Recent works on multi-modal large language models have demonstrated their effectiveness in handling visual modalities. In this work, we extend the research of MLLMs to point clouds and present the LAMM-Dataset and LAMM-Benchmark for 2D image and 3D point cloud understanding. We also establish an extensible framework to facilitate the extension of MLLMs to additional modalities. Our main contribution is three-fold: 1) We present the LAMM-Dataset and LAMM-Benchmark, which cover almost all high-level vision tasks for 2D and 3D vision. Extensive experiments validate the effectiveness of our dataset and benchmark. 2) We demonstrate the detailed methods of constructing instruction-tuning datasets and benchmarks for MLLMs, which will enable future research on MLLMs to scale up and extend to other domains, tasks, and modalities faster. 3) We provide a primary but potential MLLM training framework optimized for modalities' extension. We also provide baseline models, comprehensive experimental observations, and analysis to accelerate future research. Codes and datasets are now available at https://github.com/OpenLAMM/LAMM.

Current long context large language models (LLMs) can process inputs up to 100,000 tokens, yet struggle to generate outputs exceeding even a modest length of 2,000 words. Through controlled experiments, we find that the model's effective generation length is inherently bounded by the sample it has seen during supervised fine-tuning (SFT). In other words, their output limitation is due to the scarcity of long-output examples in existing SFT datasets. To address this, we introduce AgentWrite, an agent-based pipeline that decomposes ultra-long generation tasks into subtasks, enabling off-the-shelf LLMs to generate coherent outputs exceeding 20,000 words. Leveraging AgentWrite, we construct LongWriter-6k, a dataset containing 6,000 SFT data with output lengths ranging from 2k to 32k words. By incorporating this dataset into model training, we successfully scale the output length of existing models to over 10,000 words while maintaining output quality. We also develop LongBench-Write, a comprehensive benchmark for evaluating ultra-long generation capabilities. Our 9B parameter model, further improved through DPO, achieves state-of-the-art performance on this benchmark, surpassing even much larger proprietary models. In general, our work demonstrates that existing long context LLM already possesses the potential for a larger output window--all you need is data with extended output during model alignment to unlock this capability. Our code & models are at: https://github.com/THUDM/LongWriter.

Foundation models, or large atomistic models (LAMs), aim to universally represent the ground-state potential energy surface (PES) of atomistic systems as defined by density functional theory (DFT). The scaling law is pivotal in the development of large models, suggesting that their generalizability in downstream tasks consistently improves with increased model size, expanded training datasets, and larger computational budgets. In this study, we present DPA3, a multi-layer graph neural network founded on line graph series (LiGS), designed explicitly for the era of LAMs. We demonstrate that the generalization error of the DPA3 model adheres to the scaling law. The scalability in the number of model parameters is attained by stacking additional layers within DPA3. Additionally, the model employs a dataset encoding mechanism that decouples the scaling of training data size from the model size within its multi-task training framework. When trained as problem-oriented potential energy models, the DPA3 model exhibits superior accuracy in the majority of benchmark cases, encompassing systems with diverse features, including molecules, bulk materials, surface and cluster catalysts, two-dimensional materials, and battery materials. When trained as a LAM on the OpenLAM-v1 dataset, the DPA-3.1-3M model exhibits state-of-the-art performance in the LAMBench benchmark suite for LAMs, demonstrating lowest overall zero-shot generalization error across 17 downstream tasks from a broad spectrum of research domains. This performance suggests superior accuracy as an out-of-the-box potential model, requiring minimal fine-tuning data for downstream scientific applications.

Large Language Models (LLMs) have become ubiquitous across various domains, transforming the way we interact with information and conduct research. However, most high-performing LLMs remain confined behind proprietary walls, hindering scientific progress. Most open-source LLMs, on the other hand, are limited in their ability to support longer sequence lengths, which is a key requirement for many tasks that require inference over an input context. To address this, we have trained XGen, a series of 7B parameter models on up to 8K sequence length for up to 1.5T tokens. We have also finetuned the XGen models on public-domain instructional data, creating their instruction-tuned counterparts (XGen-Inst). We open-source our models for both research advancements and commercial applications. Our evaluation on standard benchmarks shows that XGen models achieve comparable or better results when compared with state-of-the-art open-source LLMs. Our targeted evaluation on long sequence modeling tasks shows the benefits of our 8K-sequence models over 2K-sequence open-source LLMs.

Land Use and Land Cover (LULC) mapping is a fundamental task in Earth Observation (EO). However, current LULC models are typically developed for a specific modality and a fixed class taxonomy, limiting their generability and broader applicability. Recent advances in foundation models (FMs) offer promising opportunities for building universal models. Yet, task-agnostic FMs often require fine-tuning for downstream applications, whereas task-specific FMs rely on massive amounts of labeled data for training, which is costly and impractical in the remote sensing (RS) domain. To address these challenges, we propose LandSegmenter, an LULC FM framework that resolves three-stage challenges at the input, model, and output levels. From the input side, to alleviate the heavy demand on labeled data for FM training, we introduce LAnd Segment (LAS), a large-scale, multi-modal, multi-source dataset built primarily with globally sampled weak labels from existing LULC products. LAS provides a scalable, cost-effective alternative to manual annotation, enabling large-scale FM training across diverse LULC domains. For model architecture, LandSegmenter integrates an RS-specific adapter for cross-modal feature extraction and a text encoder for semantic awareness enhancement. At the output stage, we introduce a class-wise confidence-guided fusion strategy to mitigate semantic omissions and further improve LandSegmenter's zero-shot performance. We evaluate LandSegmenter on six precisely annotated LULC datasets spanning diverse modalities and class taxonomies. Extensive transfer learning and zero-shot experiments demonstrate that LandSegmenter achieves competitive or superior performance, particularly in zero-shot settings when transferred to unseen datasets. These results highlight the efficacy of our proposed framework and the utility of weak supervision for building task-specific FMs.

Large Language Models (LLMs) have demonstrated remarkable performance across a wide range of natural language processing tasks. However, their remarkable parameter size and their impressive high requirement of computing resources pose challenges for their practical deployment. Recent research has revealed that specific capabilities of LLMs, such as numerical reasoning, can be transferred to smaller models through distillation. Some studies explore the potential of leveraging LLMs to perform table-based reasoning. Nevertheless, prior to our work, there has been no investigation into the prospect of specialising table reasoning skills in smaller models specifically tailored for table-to-text generation tasks. In this paper, we propose a novel table-based reasoning distillation, with the aim of distilling distilling LLMs into tailored, smaller models specifically designed for table-based reasoning task. Experimental results have shown that a 0.22 billion parameter model (Flan-T5-base) fine-tuned using distilled data, not only achieves a significant improvement compared to traditionally fine-tuned baselines but also surpasses specific LLMs like gpt-3.5-turbo on the scientific table-to-text generation dataset (SciGen). The code and data are released in https://github.com/Bernard-Yang/TableDistill.

In recent years, multimodal large language models (MLLMs) have shown strong potential in real-world applications. They are developing rapidly due to their remarkable ability to comprehend multimodal information and their inherent powerful cognitive and reasoning capabilities. Among MLLMs, vision language models (VLM) stand out for their ability to understand vision information. However, the scaling trend of VLMs under the current mainstream paradigm has not been extensively studied. Whether we can achieve better performance by training even larger models is still unclear. To address this issue, we conducted experiments on the pretraining stage of MLLMs. We conduct our experiment using different encoder sizes and large language model (LLM) sizes. Our findings indicate that merely increasing the size of encoders does not necessarily enhance the performance of VLMs. Moreover, we analyzed the effects of LLM backbone parameter size and data quality on the pretraining outcomes. Additionally, we explored the differences in scaling laws between LLMs and VLMs.

Alignment, endowing a pre-trained Large language model (LLM) with the ability to follow instructions, is crucial for its real-world applications. Conventional supervised fine-tuning (SFT) methods formalize it as causal language modeling typically with a cross-entropy objective, requiring a large amount of high-quality instruction-response pairs. However, the quality of widely used SFT datasets can not be guaranteed due to the high cost and intensive labor for the creation and maintenance in practice. To overcome the limitations associated with the quality of SFT datasets, we introduce a novel preference-oriented supervised fine-tuning approach, namely PoFT. The intuition is to boost SFT by imposing a particular preference: favoring the target model over aligned LLMs on the same SFT data. This preference encourages the target model to predict a higher likelihood than that predicted by the aligned LLMs, incorporating assessment information on data quality (i.e., predicted likelihood by the aligned LLMs) into the training process. Extensive experiments are conducted, and the results validate the effectiveness of the proposed method. PoFT achieves stable and consistent improvements over the SFT baselines across different training datasets and base models. Moreover, we prove that PoFT can be integrated with existing SFT data filtering methods to achieve better performance, and further improved by following preference optimization procedures, such as DPO.

Existing benchmarks for evaluating long-context language models (LCLMs) primarily focus on long-context recall, requiring models to produce short responses based on a few critical snippets while processing thousands of irrelevant tokens. We introduce LongProc (Long Procedural Generation), a new benchmark that requires both the integration of highly dispersed information and long-form generation. LongProc consists of six diverse procedural generation tasks, such as extracting structured information from HTML pages into a TSV format and executing complex search procedures to create travel plans. These tasks challenge LCLMs by testing their ability to follow detailed procedural instructions, synthesize and reason over dispersed information, and generate structured, long-form outputs (up to 8K tokens). Furthermore, as these tasks adhere to deterministic procedures and yield structured outputs, they enable reliable rule-based evaluation. We evaluate 17 LCLMs on LongProc across three difficulty levels, with maximum numbers of output tokens set at 500, 2K, and 8K. Notably, while all tested models claim a context window size above 32K tokens, open-weight models typically falter on 2K-token tasks, and closed-source models like GPT-4o show significant degradation on 8K-token tasks. Further analysis reveals that LCLMs struggle to maintain long-range coherence in long-form generations. These findings highlight critical limitations in current LCLMs and suggest substantial room for improvement. Data and code available at: https://princeton-pli.github.io/LongProc

Large Language Models have recently gained significant attention in scientific discovery for their extensive knowledge and advanced reasoning capabilities. However, they encounter challenges in effectively simulating observational feedback and grounding it with language to propel advancements in physical scientific discovery. Conversely, human scientists undertake scientific discovery by formulating hypotheses, conducting experiments, and revising theories through observational analysis. Inspired by this, we propose to enhance the knowledge-driven, abstract reasoning abilities of LLMs with the computational strength of simulations. We introduce Scientific Generative Agent (SGA), a bilevel optimization framework: LLMs act as knowledgeable and versatile thinkers, proposing scientific hypotheses and reason about discrete components, such as physics equations or molecule structures; meanwhile, simulations function as experimental platforms, providing observational feedback and optimizing via differentiability for continuous parts, such as physical parameters. We conduct extensive experiments to demonstrate our framework's efficacy in constitutive law discovery and molecular design, unveiling novel solutions that differ from conventional human expectations yet remain coherent upon analysis.

We find that, simply via a sampling-and-voting method, the performance of large language models (LLMs) scales with the number of agents instantiated. Also, this method is orthogonal to existing complicated methods to further enhance LLMs, while the degree of enhancement is correlated to the task difficulty. We conduct comprehensive experiments on a wide range of LLM benchmarks to verify the presence of our finding, and to study the properties that can facilitate its occurrence. Our code is publicly available at: https://anonymous.4open.science/r/more_agent_is_all_you_need.

Foundation Models (FMs) are models trained on large corpora of data that, at very large scale, can generalize to new tasks without any task-specific finetuning. As these models continue to grow in size, innovations continue to push the boundaries of what these models can do on language and image tasks. This paper aims to understand an underexplored area of FMs: classical data tasks like cleaning and integration. As a proof-of-concept, we cast five data cleaning and integration tasks as prompting tasks and evaluate the performance of FMs on these tasks. We find that large FMs generalize and achieve SoTA performance on data cleaning and integration tasks, even though they are not trained for these data tasks. We identify specific research challenges and opportunities that these models present, including challenges with private and domain specific data, and opportunities to make data management systems more accessible to non-experts. We make our code and experiments publicly available at: https://github.com/HazyResearch/fm_data_tasks.

Large language model (LLM)-powered agents are increasingly used to plan and execute scientific workflows, yet most research cyberinfrastructure (CI) exposes heterogeneous APIs and implements security models that present barriers for use by agents. We report on our experience using the Model Context Protocol (MCP) as a unifying interface that makes research capabilities discoverable, invokable, and composable. Our approach is pragmatic: we implement thin MCP servers over mature services, including Globus Transfer, Compute, and Search; status APIs exposed by computing facilities; Octopus event fabric; and domain-specific tools such as Garden and Galaxy. We use case studies in computational chemistry, bioinformatics, quantum chemistry, and filesystem monitoring to illustrate how this MCP-oriented architecture can be used in practice. We distill lessons learned and outline open challenges in evaluation and trust for agent-led science.

Recent advancements have positioned AI, and particularly Large Language Models (LLMs), as transformative tools for scientific research, capable of addressing complex tasks that require reasoning, problem-solving, and decision-making. Their exceptional capabilities suggest their potential as scientific research assistants but also highlight the need for holistic, rigorous, and domain-specific evaluation to assess effectiveness in real-world scientific applications. This paper describes a multifaceted methodology for Evaluating AI models as scientific Research Assistants (EAIRA) developed at Argonne National Laboratory. This methodology incorporates four primary classes of evaluations. 1) Multiple Choice Questions to assess factual recall; 2) Open Response to evaluate advanced reasoning and problem-solving skills; 3) Lab-Style Experiments involving detailed analysis of capabilities as research assistants in controlled environments; and 4) Field-Style Experiments to capture researcher-LLM interactions at scale in a wide range of scientific domains and applications. These complementary methods enable a comprehensive analysis of LLM strengths and weaknesses with respect to their scientific knowledge, reasoning abilities, and adaptability. Recognizing the rapid pace of LLM advancements, we designed the methodology to evolve and adapt so as to ensure its continued relevance and applicability. This paper describes the methodology state at the end of February 2025. Although developed within a subset of scientific domains, the methodology is designed to be generalizable to a wide range of scientific domains.

Inference scaling empowers LLMs with unprecedented reasoning ability, with reinforcement learning as the core technique to elicit complex reasoning. However, key technical details of state-of-the-art reasoning LLMs are concealed (such as in OpenAI o1 blog and DeepSeek R1 technical report), thus the community still struggles to reproduce their RL training results. We propose the Decoupled Clip and Dynamic sAmpling Policy Optimization (DAPO) algorithm, and fully open-source a state-of-the-art large-scale RL system that achieves 50 points on AIME 2024 using Qwen2.5-32B base model. Unlike previous works that withhold training details, we introduce four key techniques of our algorithm that make large-scale LLM RL a success. In addition, we open-source our training code, which is built on the verl framework, along with a carefully curated and processed dataset. These components of our open-source system enhance reproducibility and support future research in large-scale LLM RL.

Large foundation models, including large language models (LLMs), vision transformers (ViTs), diffusion, and LLM-based multimodal models, are revolutionizing the entire machine learning lifecycle, from training to deployment. However, the substantial advancements in versatility and performance these models offer come at a significant cost in terms of hardware resources. To support the growth of these large models in a scalable and environmentally sustainable way, there has been a considerable focus on developing resource-efficient strategies. This survey delves into the critical importance of such research, examining both algorithmic and systemic aspects. It offers a comprehensive analysis and valuable insights gleaned from existing literature, encompassing a broad array of topics from cutting-edge model architectures and training/serving algorithms to practical system designs and implementations. The goal of this survey is to provide an overarching understanding of how current approaches are tackling the resource challenges posed by large foundation models and to potentially inspire future breakthroughs in this field.

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.

In real-world NLP applications, Large Language Models (LLMs) offer promising solutions due to their extensive training on vast datasets. However, the large size and high computation demands of LLMs limit their practicality in many applications, especially when further fine-tuning is required. To address these limitations, smaller models are typically preferred for deployment. However, their training is hindered by the scarcity of labeled data. In contrast, unlabeled data is often readily which can be leveraged by using LLMs to generate pseudo-labels for training smaller models. This enables the smaller models (student) to acquire knowledge from LLMs(teacher) while reducing computational costs. This process introduces challenges, such as potential noisy pseudo-labels. Selecting high-quality and informative data is therefore critical to enhance model performance while improving the efficiency of data utilization. To address this, we propose LLKD that enables Learning with Less computational resources and less data for Knowledge Distillation from LLMs. LLKD is an adaptive sample selection method that incorporates signals from both the teacher and student. Specifically, it prioritizes samples where the teacher demonstrates high confidence in its labeling, indicating reliable labels, and where the student exhibits a high information need, identifying challenging samples that require further learning. Our comprehensive experiments show that LLKD achieves superior performance across various datasets with higher data efficiency.

In many scientific fields, large language models (LLMs) have revolutionized the way text and other modalities of data (e.g., molecules and proteins) are handled, achieving superior performance in various applications and augmenting the scientific discovery process. Nevertheless, previous surveys on scientific LLMs often concentrate on one or two fields or a single modality. In this paper, we aim to provide a more holistic view of the research landscape by unveiling cross-field and cross-modal connections between scientific LLMs regarding their architectures and pre-training techniques. To this end, we comprehensively survey over 260 scientific LLMs, discuss their commonalities and differences, as well as summarize pre-training datasets and evaluation tasks for each field and modality. Moreover, we investigate how LLMs have been deployed to benefit scientific discovery. Resources related to this survey are available at https://github.com/yuzhimanhua/Awesome-Scientific-Language-Models.

In recent years, the rapid advancement of Large Language Models (LLMs) has transformed the landscape of scientific research, offering unprecedented support across various stages of the research cycle. This paper presents the first systematic survey dedicated to exploring how LLMs are revolutionizing the scientific research process. We analyze the unique roles LLMs play across four critical stages of research: hypothesis discovery, experiment planning and implementation, scientific writing, and peer reviewing. Our review comprehensively showcases the task-specific methodologies and evaluation benchmarks. By identifying current challenges and proposing future research directions, this survey not only highlights the transformative potential of LLMs, but also aims to inspire and guide researchers and practitioners in leveraging LLMs to advance scientific inquiry. Resources are available at the following repository: https://github.com/du-nlp-lab/LLM4SR

Large Language Models (LLMs) and LLM-based agents show great promise in accelerating scientific research. Existing benchmarks for measuring this potential and guiding future development continue to evolve from pure recall and rote knowledge tasks, towards more practical work such as literature review and experimental planning. Bioinformatics is a domain where fully autonomous AI-driven discovery may be near, but no extensive benchmarks for measuring progress have been introduced to date. We therefore present the Bioinformatics Benchmark (BixBench), a dataset comprising over 50 real-world scenarios of practical biological data analysis with nearly 300 associated open-answer questions designed to measure the ability of LLM-based agents to explore biological datasets, perform long, multi-step analytical trajectories, and interpret the nuanced results of those analyses. We evaluate the performance of two frontier LLMs (GPT-4o and Claude 3.5 Sonnet) using a custom agent framework we open source. We find that even the latest frontier models only achieve 17% accuracy in the open-answer regime, and no better than random in a multiple-choice setting. By exposing the current limitations of frontier models, we hope BixBench can spur the development of agents capable of conducting rigorous bioinformatic analysis and accelerate scientific discovery.

This work introduces LAB (Large-scale Alignment for chatBots), a novel methodology designed to overcome the scalability challenges in the instruction-tuning phase of large language model (LLM) training. Leveraging a taxonomy-guided synthetic data generation process and a multi-phase tuning framework, LAB significantly reduces reliance on expensive human annotations and proprietary models like GPT-4. We demonstrate that LAB-trained models can achieve competitive performance across several benchmarks compared to models trained with traditional human-annotated or GPT-4 generated synthetic data. Thus offering a scalable, cost-effective solution for enhancing LLM capabilities and instruction-following behaviors without the drawbacks of catastrophic forgetting, marking a step forward in the efficient training of LLMs for a wide range of applications.

The success of Large Language Models (LLM) has led researchers to explore Multimodal Large Language Models (MLLM) for unified visual and linguistic understanding. However, the increasing model size and computational complexity of MLLM limit their use in resource-constrained environments. Small-scale MLLM (s-MLLM) aims to retain the capabilities of the large-scale model (l-MLLM) while reducing computational demands, but resulting in a significant decline in performance. To address the aforementioned issues, we propose a novel LLaVA-KD framework to transfer knowledge from l-MLLM to s-MLLM. Specifically, we introduce Multimodal Distillation (MDist) to minimize the divergence between the visual-textual output distributions of l-MLLM and s-MLLM, and Relation Distillation (RDist) to transfer l-MLLM's ability to model correlations between visual features. Additionally, we propose a three-stage training scheme to fully exploit the potential of s-MLLM: 1) Distilled Pre-Training to align visual-textual representations, 2) Supervised Fine-Tuning to equip the model with multimodal understanding, and 3) Distilled Fine-Tuning to further transfer l-MLLM capabilities. Our approach significantly improves performance without altering the small model's architecture. Extensive experiments and ablation studies validate the effectiveness of each proposed component. Code will be available at https://github.com/caiyuxuan1120/LLaVA-KD.

World foundation models, which simulate the physical world by predicting future states from current observations and inputs, have become central to many applications in physical intelligence, including autonomous driving and robotics. However, these models require substantial computational resources for pretraining and are further constrained by available data during post-training. As such, scaling computation at test time emerges as both a critical and practical alternative to traditional model enlargement or re-training. In this work, we introduce SWIFT, a test-time scaling framework tailored for WFMs. SWIFT integrates our extensible WFM evaluation toolkit with process-level inference strategies, including fast tokenization, probability-based Top-K pruning, and efficient beam search. Empirical results on the COSMOS model demonstrate that test-time scaling exists even in a compute-optimal way. Our findings reveal that test-time scaling laws hold for WFMs and that SWIFT provides a scalable and effective pathway for improving WFM inference without retraining or increasing model size. The code is available at https://github.com/Mia-Cong/SWIFT.git.

Large language models (LLMs) have shown significant potential in scientific disciplines such as biomedicine, particularly in hypothesis generation, where they can analyze vast literature, identify patterns, and suggest research directions. However, a key challenge lies in evaluating the truthfulness of generated hypotheses, as verifying their accuracy often requires substantial time and resources. Additionally, the hallucination problem in LLMs can lead to the generation of hypotheses that appear plausible but are ultimately incorrect, undermining their reliability. To facilitate the systematic study of these challenges, we introduce TruthHypo, a benchmark for assessing the capabilities of LLMs in generating truthful biomedical hypotheses, and KnowHD, a knowledge-based hallucination detector to evaluate how well hypotheses are grounded in existing knowledge. Our results show that LLMs struggle to generate truthful hypotheses. By analyzing hallucinations in reasoning steps, we demonstrate that the groundedness scores provided by KnowHD serve as an effective metric for filtering truthful hypotheses from the diverse outputs of LLMs. Human evaluations further validate the utility of KnowHD in identifying truthful hypotheses and accelerating scientific discovery. Our data and source code are available at https://github.com/Teddy-XiongGZ/TruthHypo.

We present the design, implementation and engineering experience in building and deploying MegaScale, a production system for training large language models (LLMs) at the scale of more than 10,000 GPUs. Training LLMs at this scale brings unprecedented challenges to training efficiency and stability. We take a full-stack approach that co-designs the algorithmic and system components across model block and optimizer design, computation and communication overlapping, operator optimization, data pipeline, and network performance tuning. Maintaining high efficiency throughout the training process (i.e., stability) is an important consideration in production given the long extent of LLM training jobs. Many hard stability issues only emerge at large scale, and in-depth observability is the key to address them. We develop a set of diagnosis tools to monitor system components and events deep in the stack, identify root causes, and derive effective techniques to achieve fault tolerance and mitigate stragglers. MegaScale achieves 55.2% Model FLOPs Utilization (MFU) when training a 175B LLM model on 12,288 GPUs, improving the MFU by 1.34x compared to Megatron-LM. We share our operational experience in identifying and fixing failures and stragglers. We hope by articulating the problems and sharing our experience from a systems perspective, this work can inspire future LLM systems research.

Large language models (LLMs) excel in many tasks in NLP and beyond, but most open models have very limited coverage of smaller languages and LLM work tends to focus on languages where nearly unlimited data is available for pretraining. In this work, we study the challenges of creating LLMs for Finnish, a language spoken by less than 0.1% of the world population. We compile an extensive dataset of Finnish combining web crawls, news, social media and eBooks. We pursue two approaches to pretrain models: 1) we train seven monolingual models from scratch (186M to 13B parameters) dubbed FinGPT, 2) we continue the pretraining of the multilingual BLOOM model on a mix of its original training data and Finnish, resulting in a 176 billion parameter model we call BLUUMI. For model evaluation, we introduce FIN-bench, a version of BIG-bench with Finnish tasks. We also assess other model qualities such as toxicity and bias. Our models and tools are openly available at https://turkunlp.org/gpt3-finnish.

Large Language Models (LLMs), such as ChatGPT, LLaMA, GLM, and PaLM, have exhibited remarkable performances across various tasks in recent years. However, LLMs face two main challenges in real-world applications. One challenge is that training LLMs consumes vast computing resources, preventing LLMs from being adopted by small and medium-sized enterprises with limited computing resources. Another is that training LLM requires a large amount of high-quality data, which are often scattered among enterprises. To address these challenges, we propose FATE-LLM, an industrial-grade federated learning framework for large language models. FATE-LLM (1) facilitates federated learning for large language models (coined FedLLM); (2) promotes efficient training of FedLLM using parameter-efficient fine-tuning methods; (3) protects the intellectual property of LLMs; (4) preserves data privacy during training and inference through privacy-preserving mechanisms. We release the code of FATE-LLM at https://github.com/FederatedAI/FATE-LLM to facilitate the research of FedLLM and enable a broad range of industrial applications.

Large language models (LLMs) have emerged as powerful tools in chemistry, significantly impacting molecule design, property prediction, and synthesis optimization. This review highlights LLM capabilities in these domains and their potential to accelerate scientific discovery through automation. We also review LLM-based autonomous agents: LLMs with a broader set of tools to interact with their surrounding environment. These agents perform diverse tasks such as paper scraping, interfacing with automated laboratories, and synthesis planning. As agents are an emerging topic, we extend the scope of our review of agents beyond chemistry and discuss across any scientific domains. This review covers the recent history, current capabilities, and design of LLMs and autonomous agents, addressing specific challenges, opportunities, and future directions in chemistry. Key challenges include data quality and integration, model interpretability, and the need for standard benchmarks, while future directions point towards more sophisticated multi-modal agents and enhanced collaboration between agents and experimental methods. Due to the quick pace of this field, a repository has been built to keep track of the latest studies: https://github.com/ur-whitelab/LLMs-in-science.

Large Language Models (LLMs) have substantially driven scientific progress in various domains, and many papers have demonstrated their ability to tackle complex problems with creative solutions. Our paper introduces a new foundation model, nach0, capable of solving various chemical and biological tasks: biomedical question answering, named entity recognition, molecular generation, molecular synthesis, attributes prediction, and others. nach0 is a multi-domain and multi-task encoder-decoder LLM pre-trained on unlabeled text from scientific literature, patents, and molecule strings to incorporate a range of chemical and linguistic knowledge. We employed instruction tuning, where specific task-related instructions are utilized to fine-tune nach0 for the final set of tasks. To train nach0 effectively, we leverage the NeMo framework, enabling efficient parallel optimization of both base and large model versions. Extensive experiments demonstrate that our model outperforms state-of-the-art baselines on single-domain and cross-domain tasks. Furthermore, it can generate high-quality outputs in molecular and textual formats, showcasing its effectiveness in multi-domain setups.

Large language models (LLMs) have demonstrated remarkable success as foundational models, benefiting various downstream applications through fine-tuning. Recent studies on loss scaling have demonstrated the superior performance of larger LLMs compared to their smaller counterparts. Nevertheless, training LLMs with billions of parameters poses significant challenges and requires considerable computational resources. For example, training a one trillion parameter GPT-style model on 20 trillion tokens requires a staggering 120 million exaflops of computation. This research explores efficient distributed training strategies to extract this computation from Frontier, the world's first exascale supercomputer dedicated to open science. We enable and investigate various model and data parallel training techniques, such as tensor parallelism, pipeline parallelism, and sharded data parallelism, to facilitate training a trillion-parameter model on Frontier. We empirically assess these techniques and their associated parameters to determine their impact on memory footprint, communication latency, and GPU's computational efficiency. We analyze the complex interplay among these techniques and find a strategy to combine them to achieve high throughput through hyperparameter tuning. We have identified efficient strategies for training large LLMs of varying sizes through empirical analysis and hyperparameter tuning. For 22 Billion, 175 Billion, and 1 Trillion parameters, we achieved GPU throughputs of 38.38%, 36.14%, and 31.96%, respectively. For the training of the 175 Billion parameter model and the 1 Trillion parameter model, we achieved 100% weak scaling efficiency on 1024 and 3072 MI250X GPUs, respectively. We also achieved strong scaling efficiencies of 89% and 87% for these two models.

Scientific research faces high costs and inefficiencies with traditional methods, but the rise of deep learning and large language models (LLMs) offers innovative solutions. This survey reviews LLM applications across scientific fields such as biology, medicine, chemistry, and meteorology, underscoring their role in advancing research. However, the continuous expansion of model size has led to significant memory demands, hindering further development and application of LLMs for science. To address this, we review memory-efficient training techniques for LLMs based on the transformer architecture, including distributed training, mixed precision training, and gradient checkpointing. Using AlphaFold 2 as an example, we demonstrate how tailored memory optimization methods can reduce storage needs while preserving prediction accuracy. We also discuss the challenges of memory optimization in practice and potential future directions, hoping to provide valuable insights for researchers and engineers.

Is natural-language-driven earth observation data analysis now feasible with the assistance of Large Language Models (LLMs)? For open science in service of public interest, feasibility requires reliably high accuracy, interactive latencies, low (sustainable) costs, open LLMs, and openly maintainable software -- hence, the challenge. What are the techniques and programming system requirements necessary for satisfying these constraints, and what is the corresponding development and maintenance burden in practice? This study lays the groundwork for exploring these questions, introducing an impactful earth science use-case, and providing a software framework with evaluation data and metrics, along with initial results from employing model scaling, prompt-optimization, and inference-time scaling optimization techniques. While we attain high accuracy (near 100%) across 10 of 11 metrics, the analysis further considers cost (token-spend), latency, and maintainability across this space of techniques. Finally, we enumerate opportunities for further research, general programming and evaluation framework development, and ongoing work for a comprehensive, deployable solution. This is a call for collaboration and contribution.

Efficient molecular modeling and design are crucial for the discovery and exploration of novel molecules, and the incorporation of deep learning methods has revolutionized this field. In particular, large language models (LLMs) offer a fresh approach to tackle scientific problems from a natural language processing (NLP) perspective, introducing a research paradigm called scientific language modeling (SLM). However, two key issues remain: how to quantify the match between model and data modalities and how to identify the knowledge-learning preferences of models. To address these challenges, we propose a multi-modal benchmark, named ChEBI-20-MM, and perform 1263 experiments to assess the model's compatibility with data modalities and knowledge acquisition. Through the modal transition probability matrix, we provide insights into the most suitable modalities for tasks. Furthermore, we introduce a statistically interpretable approach to discover context-specific knowledge mapping by localized feature filtering. Our pioneering analysis offers an exploration of the learning mechanism and paves the way for advancing SLM in molecular science.

Large Language Models (LLMs) have demonstrated strong performance across general NLP tasks, but their utility in automating numerical experiments of complex physical system -- a critical and labor-intensive component -- remains underexplored. As the major workhorse of computational science over the past decades, Computational Fluid Dynamics (CFD) offers a uniquely challenging testbed for evaluating the scientific capabilities of LLMs. We introduce CFDLLMBench, a benchmark suite comprising three complementary components -- CFDQuery, CFDCodeBench, and FoamBench -- designed to holistically evaluate LLM performance across three key competencies: graduate-level CFD knowledge, numerical and physical reasoning of CFD, and context-dependent implementation of CFD workflows. Grounded in real-world CFD practices, our benchmark combines a detailed task taxonomy with a rigorous evaluation framework to deliver reproducible results and quantify LLM performance across code executability, solution accuracy, and numerical convergence behavior. CFDLLMBench establishes a solid foundation for the development and evaluation of LLM-driven automation of numerical experiments for complex physical systems. Code and data are available at https://github.com/NREL-Theseus/cfdllmbench/.

Large language models (LLMs) are increasingly being used for complex research tasks such as literature review, idea generation, and scientific paper analysis, yet their ability to truly understand and process the intricate relationships within complex research papers, such as the logical links between claims and supporting evidence remains largely unexplored. In this study, we present CLAIM-BENCH, a comprehensive benchmark for evaluating LLMs' capabilities in scientific claim-evidence extraction and validation, a task that reflects deeper comprehension of scientific argumentation. We systematically compare three approaches which are inspired by divide and conquer approaches, across six diverse LLMs, highlighting model-specific strengths and weaknesses in scientific comprehension. Through evaluation involving over 300 claim-evidence pairs across multiple research domains, we reveal significant limitations in LLMs' ability to process complex scientific content. Our results demonstrate that closed-source models like GPT-4 and Claude consistently outperform open-source counterparts in precision and recall across claim-evidence identification tasks. Furthermore, strategically designed three-pass and one-by-one prompting approaches significantly improve LLMs' abilities to accurately link dispersed evidence with claims, although this comes at increased computational cost. CLAIM-BENCH sets a new standard for evaluating scientific comprehension in LLMs, offering both a diagnostic tool and a path forward for building systems capable of deeper, more reliable reasoning across full-length papers.

Large language models (LLMs) have achieved remarkable success in NLP and multimodal tasks. Despite these successes, their development faces two main challenges: (i) high computational cost; and (ii) difficulty in conducting fair and objective evaluations. LLMs are prohibitively expensive, making it feasible for only a few major players to undertake their training, thereby constraining both research and application opportunities. This underscores the importance of cost-effective LLM training. In this paper, we utilize a growth strategy to significantly reduce LLM training cost. We demonstrate that an LLM with 101B parameters and 0.31TB tokens can be trained on a 100K budget. We also adopt a systematic evaluation paradigm for the IQ evaluation of LLMs, in complement to existing evaluations that focus more on knowledge-oriented abilities. We introduce our benchmark including evaluations on important aspects of intelligence including symbolic mapping, itrule understanding, pattern mining, and anti-interference. Such evaluations minimize the potential impact of memorization. Experimental results show that our model FLM-101B, trained with a budget of 100K, achieves comparable performance to powerful and well-known models, eg GPT-3 and GLM-130B, especially in the IQ benchmark evaluations with contexts unseen in training data. The checkpoint of FLM-101B will be open-sourced at https://huggingface.co/CofeAI/FLM-101B.

Large language models are emerging as powerful tools for scientific law discovery, a foundational challenge in AI-driven science. However, existing benchmarks for this task suffer from a fundamental methodological trilemma, forcing a trade-off between scientific relevance, scalability, and resistance to memorization. Furthermore, they oversimplify discovery as static function fitting, failing to capture the authentic scientific process of uncovering embedded laws through the interactive exploration of complex model systems. To address these critical gaps, we introduce NewtonBench, a benchmark comprising 324 scientific law discovery tasks across 12 physics domains. Our design mitigates the evaluation trilemma by using metaphysical shifts - systematic alterations of canonical laws - to generate a vast suite of problems that are scalable, scientifically relevant, and memorization-resistant. Moreover, we elevate the evaluation from static function fitting to interactive model discovery, requiring agents to experimentally probe simulated complex systems to uncover hidden principles. Our extensive experiment reveals a clear but fragile capability for discovery in frontier LLMs: this ability degrades precipitously with increasing system complexity and exhibits extreme sensitivity to observational noise. Notably, we uncover a paradoxical effect of tool assistance: providing a code interpreter can hinder more capable models by inducing a premature shift from exploration to exploitation, causing them to satisfice on suboptimal solutions. These results demonstrate that robust, generalizable discovery in complex, interactive environments remains the core challenge. By providing a scalable, robust, and scientifically authentic testbed, NewtonBench offers a crucial tool for measuring true progress and guiding the development of next-generation AI agents capable of genuine scientific discovery.

The exponential growth of large language models (LLMs) has opened up numerous possibilities for multi-modal AGI systems. However, the progress in vision and vision-language foundation models, which are also critical elements of multi-modal AGI, has not kept pace with LLMs. In this work, we design a large-scale vision-language foundation model (InternVL), which scales up the vision foundation model to 6 billion parameters and progressively aligns it with the large language model, using web-scale image-text data from various sources. This model can be broadly applied to and achieve state-of-the-art performance on visual perception tasks such as image-level or pixel-level recognition, vision-language tasks such as zero-shot image/video classification, zero-shot image/video-text retrieval, and link with LLMs to create multi-modal dialogue systems. We hope that our research could contribute to the development of multi-modal large models. Code and models are available at https://github.com/OpenGVLab/InternVL.

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

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.

Collaborative filtering models, particularly graph-based approaches, have demonstrated strong performance in capturing user-item interactions for recommendation systems. However, they continue to struggle in cold-start and data-sparse scenarios. The emergence of large language models (LLMs) like GPT and LLaMA presents new possibilities for enhancing recommendation performance, especially in cold-start settings. Despite their promise, LLMs pose challenges related to scalability and efficiency due to their high computational demands and limited ability to model complex user-item relationships effectively. In this work, we introduce a novel perspective on leveraging LLMs for CF model initialization. Through experiments, we uncover an embedding collapse issue when scaling CF models to larger embedding dimensions. To effectively harness large-scale LLM embeddings, we propose innovative selective initialization strategies utilizing random, uniform, and variance-based index sampling. Our comprehensive evaluation on multiple real-world datasets demonstrates significant performance gains across various CF models while maintaining a lower computational cost compared to existing LLM-based recommendation approaches.

Large Language Models (LLMs) demand significant computational resources, making it essential to enhance their capabilities without retraining from scratch. A key challenge in this domain is catastrophic forgetting (CF), which hampers performance during Continuous Pre-training (CPT) and Continuous Supervised Fine-Tuning (CSFT). We propose Control LLM, a novel approach that leverages parallel pre-trained and expanded transformer blocks, aligning their hidden-states through interpolation strategies This method effectively preserves performance on existing tasks while seamlessly integrating new knowledge. Extensive experiments demonstrate the effectiveness of Control LLM in both CPT and CSFT. On Llama3.1-8B-Instruct, it achieves significant improvements in mathematical reasoning (+14.4% on Math-Hard) and coding performance (+10% on MBPP-PLUS). On Llama3.1-8B, it enhances multilingual capabilities (+10.6% on C-Eval, +6.8% on CMMLU, and +30.2% on CMMLU-0shot-CoT). It surpasses existing methods and achieves SOTA among open-source models tuned from the same base model, using substantially less data and compute. Crucially, these gains are realized while preserving strong original capabilities, with minimal degradation (<4.3% on MMLU) compared to >35% in open-source Math and Coding models. This approach has been successfully deployed in LinkedIn's GenAI-powered job seeker and Ads unit products. To support further research, we release the training and evaluation code (https://github.com/linkedin/ControlLLM) along with models trained on public datasets ( https://huggingface.co/ControlLLM) to the community.

Materials discovery and design are essential for advancing technology across various industries by enabling the development of application-specific materials. Recent research has leveraged Large Language Models (LLMs) to accelerate this process. We explore the potential of LLMs to generate viable hypotheses that, once validated, can expedite materials discovery. Collaborating with materials science experts, we curated a novel dataset from recent journal publications, featuring real-world goals, constraints, and methods for designing real-world applications. Using this dataset, we test LLM-based agents that generate hypotheses for achieving given goals under specific constraints. To assess the relevance and quality of these hypotheses, we propose a novel scalable evaluation metric that emulates the process a materials scientist would use to evaluate a hypothesis critically. Our curated dataset, proposed method, and evaluation framework aim to advance future research in accelerating materials discovery and design with LLMs.

Large language models (LLMs) excel in most NLP tasks but also require expensive cloud servers for deployment due to their size, while smaller models that can be deployed on lower cost (e.g., edge) devices, tend to lag behind in terms of response quality. Therefore in this work we propose a hybrid inference approach which combines their respective strengths to save cost and maintain quality. Our approach uses a router that assigns queries to the small or large model based on the predicted query difficulty and the desired quality level. The desired quality level can be tuned dynamically at test time to seamlessly trade quality for cost as per the scenario requirements. In experiments our approach allows us to make up to 40% fewer calls to the large model, with no drop in response quality.

We introduce F2LLM - Foundation to Feature Large Language Models, a suite of state-of-the-art embedding models in three sizes: 0.6B, 1.7B, and 4B. Unlike previous top-ranking embedding models that require massive contrastive pretraining, sophisticated training pipelines, and costly synthetic training data, F2LLM is directly finetuned from foundation models on 6 million query-document-negative tuples curated from open-source, non-synthetic datasets, striking a strong balance between training cost, model size, and embedding performance. On the MTEB English leaderboard, F2LLM-4B ranks 2nd among models with approximately 4B parameters and 7th overall, while F2LLM-1.7B ranks 1st among models in the 1B-2B size range. To facilitate future research in the field, we release the models, training dataset, and code, positioning F2LLM as a strong, reproducible, and budget-friendly baseline for future works.

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

Large Language Models (LLMs) have become indispensable in numerous real-world applications. Unfortunately, fine-tuning these models at scale, especially in federated settings where data privacy and communication efficiency are critical, presents significant challenges. Existing methods often resort to parameter-efficient fine-tuning (PEFT) to mitigate communication overhead, but this typically comes at the cost of model accuracy. To address these limitations, we propose federated full-parameter tuning at scale for LLMs (Ferret), the first first-order method with shared randomness to enable scalable full-parameter tuning of LLMs across decentralized data sources while maintaining competitive model accuracy. Ferret accomplishes this through three aspects: (1) it employs widely applied first-order methods for efficient local updates; (2) it projects these updates into a low-dimensional space to considerably reduce communication overhead; and (3) it reconstructs local updates from this low-dimensional space with shared randomness to facilitate effective full-parameter global aggregation, ensuring fast convergence and competitive final performance. Our rigorous theoretical analyses and insights along with extensive experiments, show that Ferret significantly enhances the scalability of existing federated full-parameter tuning approaches by achieving high computational efficiency, reduced communication overhead, and fast convergence, all while maintaining competitive model accuracy. Our implementation is available at https://github.com/allen4747/Ferret.

Large Language Models (LLMs) are undergoing a period of rapid updates and changes, with state-of-the-art (SOTA) model frequently being replaced. When applying LLMs to a specific scientific field, it's challenging to acquire unique domain knowledge while keeping the model itself advanced. To address this challenge, a sophisticated large language model system named as Xiwu has been developed, allowing you switch between the most advanced foundation models and quickly teach the model domain knowledge. In this work, we will report on the best practices for applying LLMs in the field of high-energy physics (HEP), including: a seed fission technology is proposed and some data collection and cleaning tools are developed to quickly obtain domain AI-Ready dataset; a just-in-time learning system is implemented based on the vector store technology; an on-the-fly fine-tuning system has been developed to facilitate rapid training under a specified foundation model. The results show that Xiwu can smoothly switch between foundation models such as LLaMA, Vicuna, ChatGLM and Grok-1. The trained Xiwu model is significantly outperformed the benchmark model on the HEP knowledge question-and-answering and code generation. This strategy significantly enhances the potential for growth of our model's performance, with the hope of surpassing GPT-4 as it evolves with the development of open-source models. This work provides a customized LLM for the field of HEP, while also offering references for applying LLM to other fields, the corresponding codes are available on Github.

Foundation Models are neural networks that are capable of simultaneously solving many problems. Large Language Foundation Models like ChatGPT have revolutionized many aspects of daily life, but their impact for science is not yet clear. In this paper, we use a new Foundation Model for hadronic jets to solve three key challenges in collider physics. In particular, we show how experiments can (1) save significant computing power when developing reconstruction algorithms, (2) perform a complete uncertainty quantification for high-dimensional measurements, and (3) search for new physics with model agnostic methods using low-level inputs. In each case, there are significant computational or methodological challenges with current methods that limit the science potential of deep learning algorithms. By solving each problem, we take jet Foundation Models beyond proof-of-principle studies and into the toolkit of practitioners.

To facilitate the research on large language models (LLMs), this paper presents a comprehensive and unified library, LLMBox, to ease the development, use, and evaluation of LLMs. This library is featured with three main merits: (1) a unified data interface that supports the flexible implementation of various training strategies, (2) a comprehensive evaluation that covers extensive tasks, datasets, and models, and (3) more practical consideration, especially on user-friendliness and efficiency. With our library, users can easily reproduce existing methods, train new models, and conduct comprehensive performance comparisons. To rigorously test LLMBox, we conduct extensive experiments in a diverse coverage of evaluation settings, and experimental results demonstrate the effectiveness and efficiency of our library in supporting various implementations related to LLMs. The detailed introduction and usage guidance can be found at https://github.com/RUCAIBox/LLMBox.

Many NLP tasks benefit from using large language models (LLMs) that often have more than 100 billion parameters. With the release of BLOOM-176B and OPT-175B, everyone can download pretrained models of this scale. Still, using these models requires high-end hardware unavailable to many researchers. In some cases, LLMs can be used more affordably via RAM offloading or hosted APIs. However, these techniques have innate limitations: offloading is too slow for interactive inference, while APIs are not flexible enough for research that requires access to weights, attention or logits. In this work, we propose Petals - a system for inference and fine-tuning of large models collaboratively by joining the resources of multiple parties. We demonstrate that this strategy outperforms offloading for very large models, running inference of BLOOM-176B on consumer GPUs with approx 1 step per second, which is enough for many interactive LLM applications. Unlike most inference APIs, Petals also natively exposes hidden states of served models, allowing to train and share custom model extensions based on efficient fine-tuning methods.

Large language models (LLMs) have demonstrated significant potential to accelerate scientific discovery as valuable tools for analyzing data, generating hypotheses, and supporting innovative approaches in various scientific fields. In this work, we investigate how LLMs can handle the transition from conceptual research ideas to well-structured research plans. Effective research planning not only supports scientists in advancing their research but also represents a crucial capability for the development of autonomous research agents. Despite its importance, the field lacks a systematic understanding of LLMs' research planning capability. To rigorously measure this capability, we introduce the Idea2Plan task and Idea2Plan Bench, a benchmark built from 200 ICML 2025 Spotlight and Oral papers released after major LLM training cutoffs. Each benchmark instance includes a research idea and a grading rubric capturing the key components of valid plans. We further propose Idea2Plan JudgeEval, a complementary benchmark to assess the reliability of LLM-based judges against expert annotations. Experimental results show that GPT-5 and GPT-5-mini achieve the strongest performance on the benchmark, though substantial headroom remains for future improvement. Our study provides new insights into LLMs' capability for research planning and lay the groundwork for future progress.

We present a system using Multimodal LLMs (MLLMs) to analyze a large database with tens of millions of images captured at different times, with the aim of discovering patterns in temporal changes. Specifically, we aim to capture frequent co-occurring changes ("trends") across a city over a certain period. Unlike previous visual analyses, our analysis answers open-ended queries (e.g., "what are the frequent types of changes in the city?") without any predetermined target subjects or training labels. These properties cast prior learning-based or unsupervised visual analysis tools unsuitable. We identify MLLMs as a novel tool for their open-ended semantic understanding capabilities. Yet, our datasets are four orders of magnitude too large for an MLLM to ingest as context. So we introduce a bottom-up procedure that decomposes the massive visual analysis problem into more tractable sub-problems. We carefully design MLLM-based solutions to each sub-problem. During experiments and ablation studies with our system, we find it significantly outperforms baselines and is able to discover interesting trends from images captured in large cities (e.g., "addition of outdoor dining,", "overpass was painted blue," etc.). See more results and interactive demos at https://boyangdeng.com/visual-chronicles.

Large foundation models have demonstrated a great ability to achieve general human-level intelligence far beyond traditional approaches. As the technique keeps attracting attention from the AI community, more and more large foundation models have become publically available. However, most of those models exhibit a major deficiency in specialized-task applications, where the step of finetuning is still required for obtaining satisfactory performance. As the number of available models and specialized tasks keeps growing, the job of general finetuning becomes highly nontrivial. In this paper, we take the first step to address this issue. We introduce an extensible and lightweight toolkit, LMFlow, which aims to simplify the finetuning and inference of general large foundation models. LMFlow offers a complete finetuning workflow for a large foundation model to support personalized training with limited computing resources. Furthermore, it supports continuous pretraining, instruction tuning, parameter-efficient finetuning, alignment tuning, and large model inference, along with carefully designed and extensible APIs. This toolkit has been thoroughly tested and is available at https://github.com/OptimalScale/LMFlow.

Despite recent progress, it has been difficult to prevent semantic hallucinations in generative Large Language Models. One common solution to this is augmenting LLMs with a retrieval system and making sure that the generated output is attributable to the retrieved information. Given this new added constraint, it is plausible to expect that the overall quality of the output will be affected, for example, in terms of fluency. Can scaling language models help? Here we examine the relationship between fluency and attribution in LLMs prompted with retrieved evidence in knowledge-heavy dialog settings. Our experiments were implemented with a set of auto-metrics that are aligned with human preferences. They were used to evaluate a large set of generations, produced under varying parameters of LLMs and supplied context. We show that larger models tend to do much better in both fluency and attribution, and that (naively) using top-k retrieval versus top-1 retrieval improves attribution but hurts fluency. We next propose a recipe that could allow smaller models to both close the gap with larger models and preserve the benefits of top-k retrieval while avoiding its drawbacks.

Large language models (LLMs) have achieved substantial progress in processing long contexts but still struggle with long-context reasoning. Existing approaches typically involve fine-tuning LLMs with synthetic data, which depends on annotations from human experts or advanced models like GPT-4, thus restricting further advancements. To address this issue, we investigate the potential for LLMs to self-improve in long-context reasoning and propose \ours, an approach specifically designed for this purpose. This approach is straightforward: we sample multiple outputs for each question, score them with Minimum Bayes Risk, and then apply supervised fine-tuning or preference optimization based on these outputs. Extensive experiments on several leading LLMs demonstrate the effectiveness of \ours, with an absolute improvement of 4.2 points for Llama-3.1-8B-Instruct. Furthermore, \ours achieves superior performance compared to prior approaches that depend on data produced by human experts or advanced models. We anticipate that this work will open new avenues for self-improvement techniques in long-context scenarios, which are essential for the continual advancement of LLMs.

Long-context large language models (LC LLMs) promise to increase reliability of LLMs in real-world tasks requiring processing and understanding of long input documents. However, this ability of LC LLMs to reliably utilize their growing context windows remains under investigation. In this work, we evaluate the performance of state-of-the-art GPT-4 suite of LC LLMs in solving a series of progressively challenging tasks, as a function of factors such as context length, task difficulty, and position of key information by creating a real world financial news dataset. Our findings indicate that LC LLMs exhibit brittleness at longer context lengths even for simple tasks, with performance deteriorating sharply as task complexity increases. At longer context lengths, these state-of-the-art models experience catastrophic failures in instruction following resulting in degenerate outputs. Our prompt ablations also reveal unfortunate continued sensitivity to both the placement of the task instruction in the context window as well as minor markdown formatting. Finally, we advocate for more rigorous evaluation of LC LLMs by employing holistic metrics such as F1 (rather than recall) and reporting confidence intervals, thereby ensuring robust and conclusive findings.

The crystallization of modeling methods around the Transformer architecture has been a boon for practitioners. Simple, well-motivated architectural variations can transfer across tasks and scale, increasing the impact of modeling research. However, with the emergence of state-of-the-art 100B+ parameters models, large language models are increasingly expensive to accurately design and train. Notably, it can be difficult to evaluate how modeling decisions may impact emergent capabilities, given that these capabilities arise mainly from sheer scale alone. In the process of building BLOOM--the Big Science Large Open-science Open-access Multilingual language model--our goal is to identify an architecture and training setup that makes the best use of our 1,000,000 A100-GPU-hours budget. Specifically, we perform an ablation study at the billion-parameter scale comparing different modeling practices and their impact on zero-shot generalization. In addition, we study the impact of various popular pre-training corpora on zero-shot generalization. We also study the performance of a multilingual model and how it compares to the English-only one. Finally, we consider the scaling behaviour of Transformers to choose the target model size, shape, and training setup. All our models and code are open-sourced at https://huggingface.co/bigscience .

Large Language Models (LLMs) are catalyzing a paradigm shift in scientific discovery, evolving from task-specific automation tools into increasingly autonomous agents and fundamentally redefining research processes and human-AI collaboration. This survey systematically charts this burgeoning field, placing a central focus on the changing roles and escalating capabilities of LLMs in science. Through the lens of the scientific method, we introduce a foundational three-level taxonomy-Tool, Analyst, and Scientist-to delineate their escalating autonomy and evolving responsibilities within the research lifecycle. We further identify pivotal challenges and future research trajectories such as robotic automation, self-improvement, and ethical governance. Overall, this survey provides a conceptual architecture and strategic foresight to navigate and shape the future of AI-driven scientific discovery, fostering both rapid innovation and responsible advancement. Github Repository: https://github.com/HKUST-KnowComp/Awesome-LLM-Scientific-Discovery.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

The rapid development of Large Language Models (LLMs) has been pivotal in advancing AI, with pre-trained LLMs being adaptable to diverse downstream tasks through fine-tuning. Federated learning (FL) further enhances fine-tuning in a privacy-aware manner by utilizing clients' local data through in-situ computation, eliminating the need for data movement. However, fine-tuning LLMs, given their massive scale of parameters, poses challenges for clients with constrained and heterogeneous resources in FL. Previous methods employed low-rank adaptation (LoRA) for efficient federated fine-tuning but utilized traditional FL aggregation strategies on LoRA adapters. These approaches led to mathematically inaccurate aggregation noise, reducing fine-tuning effectiveness and failing to address heterogeneous LoRAs. In this work, we first highlight the mathematical incorrectness of LoRA aggregation in existing federated fine-tuning methods. We introduce a new approach called FLORA that enables federated fine-tuning on heterogeneous LoRA adapters across clients through a novel stacking-based aggregation method. Our approach is noise-free and seamlessly supports heterogeneous LoRA adapters. Extensive experiments demonstrate FLORA' s superior performance in both homogeneous and heterogeneous settings, surpassing state-of-the-art methods. We envision this work as a milestone for efficient, privacy-preserving, and accurate federated fine-tuning of LLMs. Our code is available at https://github.com/ATP-1010/FederatedLLM.

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.

Recent work has demonstrated that controlled pretraining experiments are a powerful tool for understanding learning, reasoning, and memorization in large language models (LLMs). However, the computational cost of pretraining presents a significant constraint. To overcome this constraint, we propose to conduct multiple pretraining experiments simultaneously during a single training run. We demonstrate the feasibility of this approach by conducting ten experiments during the training of a 1.5B parameter model on 210B tokens. Although we only train a single model, we can replicate the results from multiple previous works on data contamination, poisoning, and memorization. We also conduct novel investigations into knowledge acquisition, mathematical reasoning, and watermarking. For example, we dynamically update the training data until the model acquires a particular piece of knowledge. Remarkably, the influence of the ten experiments on the model's training dynamics and overall performance is minimal. However, interactions between different experiments may act as a potential confounder in our approach. We propose to test for interactions with continual pretraining experiments, finding them to be negligible in our setup. Overall, our findings suggest that performing multiple pretraining experiments in a single training run can enable rigorous scientific experimentation with large models on a compute budget.

Large language models (LLMs) can produce erroneous responses that sound fluent and convincing, raising the risk that users will rely on these responses as if they were correct. Mitigating such overreliance is a key challenge. Through a think-aloud study in which participants use an LLM-infused application to answer objective questions, we identify several features of LLM responses that shape users' reliance: explanations (supporting details for answers), inconsistencies in explanations, and sources. Through a large-scale, pre-registered, controlled experiment (N=308), we isolate and study the effects of these features on users' reliance, accuracy, and other measures. We find that the presence of explanations increases reliance on both correct and incorrect responses. However, we observe less reliance on incorrect responses when sources are provided or when explanations exhibit inconsistencies. We discuss the implications of these findings for fostering appropriate reliance on LLMs.

Large language models (LLMs) have had a transformative impact on a variety of scientific tasks across disciplines such as biology, chemistry, medicine, and physics. However, ensuring the safety alignment of these models in scientific research remains an underexplored area, with existing benchmarks primarily focus on textual content and overlooking key scientific representations such as molecular, protein, and genomic languages. Moreover, the safety mechanisms of LLMs in scientific tasks are insufficiently studied. To address these limitations, we introduce SciSafeEval, a comprehensive benchmark designed to evaluate the safety alignment of LLMs across a range of scientific tasks. SciSafeEval spans multiple scientific languages - including textual, molecular, protein, and genomic - and covers a wide range of scientific domains. We evaluate LLMs in zero-shot, few-shot and chain-of-thought settings, and introduce a 'jailbreak' enhancement feature that challenges LLMs equipped with safety guardrails, rigorously testing their defenses against malicious intention. Our benchmark surpasses existing safety datasets in both scale and scope, providing a robust platform for assessing the safety and performance of LLMs in scientific contexts. This work aims to facilitate the responsible development and deployment of LLMs, promoting alignment with safety and ethical standards in scientific research.

Following its success for vision and text, the "foundation model" (FM) paradigm -- pretraining large models on massive data, then fine-tuning on target tasks -- has rapidly expanded to domains in the sciences, engineering, healthcare, and beyond. Has this achieved what the original FMs accomplished, i.e. the supplanting of traditional supervised learning in their domains? To answer we look at three modalities -- genomics, satellite imaging, and time series -- with multiple recent FMs and compare them to a standard supervised learning workflow: model development, hyperparameter tuning, and training, all using only data from the target task. Across these three specialized domains, we find that it is consistently possible to train simple supervised models -- no more complicated than a lightly modified wide ResNet or UNet -- that match or even outperform the latest foundation models. Our work demonstrates that the benefits of large-scale pretraining have yet to be realized in many specialized areas, reinforces the need to compare new FMs to strong, well-tuned baselines, and introduces two new, easy-to-use, open-source, and automated workflows for doing so.

Foundation models (FMs), such as GPT-4 and AlphaFold, are reshaping the landscape of scientific research. Beyond accelerating tasks such as hypothesis generation, experimental design, and result interpretation, they prompt a more fundamental question: Are FMs merely enhancing existing scientific methodologies, or are they redefining the way science is conducted? In this paper, we argue that FMs are catalyzing a transition toward a new scientific paradigm. We introduce a three-stage framework to describe this evolution: (1) Meta-Scientific Integration, where FMs enhance workflows within traditional paradigms; (2) Hybrid Human-AI Co-Creation, where FMs become active collaborators in problem formulation, reasoning, and discovery; and (3) Autonomous Scientific Discovery, where FMs operate as independent agents capable of generating new scientific knowledge with minimal human intervention. Through this lens, we review current applications and emerging capabilities of FMs across existing scientific paradigms. We further identify risks and future directions for FM-enabled scientific discovery. This position paper aims to support the scientific community in understanding the transformative role of FMs and to foster reflection on the future of scientific discovery. Our project is available at https://github.com/usail-hkust/Awesome-Foundation-Models-for-Scientific-Discovery.