Retrieval-Augmented Generation (RAG) grounds large language models in external evidence, yet it still falters when answers must be pieced together across semantically distant documents. We close this gap with the Hierarchical Lexical Graph (HLG), a three-tier index that (i) traces every atomic proposition to its source, (ii) clusters propositions into latent topics, and (iii) links entities and relations to expose cross-document paths. On top of HLG we build two complementary, plug-and-play retrievers: StatementGraphRAG, which performs fine-grained entity-aware beam search over propositions for high-precision factoid questions, and TopicGraphRAG, which selects coarse topics before expanding along entity links to supply broad yet relevant context for exploratory queries. Additionally, existing benchmarks lack the complexity required to rigorously evaluate multi-hop summarization systems, often focusing on single-document queries or limited datasets. To address this, we introduce a synthetic dataset generation pipeline that curates realistic, multi-document question-answer pairs, enabling robust evaluation of multi-hop retrieval systems. Extensive experiments across five datasets demonstrate that our methods outperform naive chunk-based RAG achieving an average relative improvement of 23.1% in retrieval recall and correctness. Open-source Python library is available at https://github.com/awslabs/graphrag-toolkit.

Large language models have transformed natural language processing, yet supervised fine-tuning (SFT) remains computationally intensive. This paper formally proves that capabilities acquired through SFT can be approximated by a base transformer model using inference-time techniques, specifically in-context learning (ICL), without altering model parameters, under idealized assumptions including unbounded computational resources and access to the fine-tuning dataset. We extend these results to practical scenarios with finite context lengths and partial dataset access. For text generation tasks with fixed output length $l$, datasets of size $\mathrm{O}\left( \frac{m V}{\varepsilon^2} \log \frac{m}δ \right)$ or, with bounded context, $\mathrm{O}\left( \frac{l \log V}{\varepsilon^2} \log \frac{1}δ \right)$ suffice to approximate fine-tuned behavior across $m$ contexts within error $\varepsilon$, where $V$ is the vocabulary size and $δ$ is the failure probability. For linear classification, datasets of size $\mathrm{O}\left( \frac{d}{\varepsilon} \right)$ or, with fixed context, $\mathrm{O}\left( \frac{1}{\varepsilon^2} \log \frac{1}δ \right)$ are sufficient, where $d$ is the input dimension. Grounded in the Turing completeness of transformers, these results provide a theoretical foundation for resource-efficient deployment of large language models, with practical techniques like retrieval-augmented generation bridging theory to real-world applications.

This paper aims to retrieve proteins with similar structures and semantics from large-scale protein dataset, facilitating the functional interpretation of protein structures derived by structural determination methods like cryo-Electron Microscopy (cryo-EM). Motivated by the recent progress of vision-language models (VLMs), we propose a CLIP-style framework for aligning 3D protein structures with functional annotations using contrastive learning. F or model training, we propose a large-scale dataset of approximately 200,000 protein-caption pairs with rich functional descriptors. W e evaluate our model in both in-domain and more challenging cross-database retrieval on Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) dataset, respectively. In both cases, our approach demonstrates promising zero-shot retrieval performance, highlighting the potential of multimodal foundation models for structure-function understanding in protein biology.

Human reasoning is flexible, adaptive, and grounded in prior experience-qualities that large language models (LLMs) still struggle to emulate. Existing methods either explore diverse reasoning paths at inference time or search for optimal workflows through expensive operations, but both fall short in leveraging multiple reusable strategies in a structured, efficient manner. We propose Guideline Forest, a framework that enhances LLMs reasoning by inducing structured reasoning strategies-called guidelines-from verified examples and executing them via step-wise aggregation. Unlike test-time search or single-path distillation, our method draws on verified reasoning experiences by inducing reusable guidelines and expanding each into diverse variants. Much like human reasoning, these variants reflect alternative thought patterns, are executed in parallel, refined via self-correction, and aggregated step by step-enabling the model to adaptively resolve uncertainty and synthesize robust solutions.We evaluate Guideline Forest on four benchmarks-GSM8K, MATH-500, MBPP, and HumanEval-spanning mathematical and programmatic reasoning. Guideline Forest consistently outperforms strong baselines, including CoT, ReAct, ToT, FoT, and AFlow. Ablation studies further highlight the effectiveness of multi-path reasoning and stepwise aggregation, underscoring the Guideline Forest's adaptability and generalization potential.

To meet the demands of content moderation, online platforms have resorted to automated systems. Newer forms of real-time engagement($\textit{e.g.}$, users commenting on live streams) on platforms like Twitch exert additional pressures on the latency expected of such moderation systems. Despite their prevalence, relatively little is known about the effectiveness of these systems. In this paper, we conduct an audit of Twitch's automated moderation tool ($\texttt{AutoMod}$) to investigate its effectiveness in flagging hateful content. For our audit, we create streaming accounts to act as siloed test beds, and interface with the live chat using Twitch's APIs to send over $107,000$ comments collated from $4$ datasets. We measure $\texttt{AutoMod}$'s accuracy in flagging blatantly hateful content containing misogyny, racism, ableism and homophobia. Our experiments reveal that a large fraction of hateful messages, up to $94\%$ on some datasets, $\textit{bypass moderation}$. Contextual addition of slurs to these messages results in $100\%$ removal, revealing $\texttt{AutoMod}$'s reliance on slurs as a moderation signal. We also find that contrary to Twitch's community guidelines, $\texttt{AutoMod}$ blocks up to $89.5\%$ of benign examples that use sensitive words in pedagogical or empowering contexts. Overall, our audit points to large gaps in $\texttt{AutoMod}$'s capabilities and underscores the importance for such systems to understand context effectively.

Video Diffusion Models (VDMs) have emerged as powerful generative tools, capable of synthesizing high-quality spatiotemporal content. Yet, their potential goes far beyond mere video generation. We argue that the training dynamics of VDMs, driven by the need to model coherent sequences, naturally pushes them to internalize structured representations and an implicit understanding of the visual world. To probe the extent of this internal knowledge, we introduce a few-shot fine-tuning framework that repurposes VDMs for new tasks using only a handful of examples. Our method transforms each task into a visual transition, enabling the training of LoRA weights on short input-output sequences without altering the generative interface of a frozen VDM. Despite minimal supervision, the model exhibits strong generalization across diverse tasks, from low-level vision (for example, segmentation and pose estimation) to high-level reasoning (for example, on ARC-AGI). These results reframe VDMs as more than generative engines. They are adaptable visual learners with the potential to serve as the backbone for future foundation models in vision.

Atomistic simulations are essential tools in chemistry and materials science, accelerating the discovery of novel catalysts, energy storage materials, and pharmaceuticals. However, running these simulations remains challenging due to the wide range of computational methods, diverse software ecosystems, and the need for expert knowledge and manual effort for the setup, execution, and validation stages. In this work, we present ChemGraph, an agentic framework powered by artificial intelligence and state-of-the-art simulation tools to streamline and automate computational chemistry and materials science workflows. ChemGraph leverages graph neural network-based foundation models for accurate yet computationally efficient calculations and large language models (LLMs) for natural language understanding, task planning, and scientific reasoning to provide an intuitive and interactive interface. Users can perform tasks such as molecular structure generation, single-point energy, geometry optimization, vibrational analysis, and thermochemistry calculations with methods ranging from tight-binding and machine learning interatomic potentials to density functional theory or wave function theory-based methods. We evaluate ChemGraph across 13 benchmark tasks and demonstrate that smaller LLMs (GPT-4o-mini, Claude-3.5-haiku, Qwen2.5-14B) perform well on simple workflows, while more complex tasks benefit from using larger models like GPT-4o. Importantly, we show that decomposing complex tasks into smaller subtasks through a multi-agent framework enables smaller LLM models to match or exceed GPT-4o's performance in specific scenarios.

Abstract--The growing convergence between Large Language Models (LLMs) and electroencephalography (EEG) research is enabling new directions in neural decoding, brain-computer interfaces (BCIs), and affective computing. This survey offers a systematic review and structured taxonomy of recent advancements that utilize LLMs for EEG-based analysis and applications. We organize the recent studies into four categories: (1) LLM-inspired foundation models for EEG analysis, (2) EEG-to-language decoding, (3) cross-modal generation including image and 3D object synthesis, and (4) clinical applications and dataset management tools. The survey highlights how transformer-based architectures adapted through fine-tuning, few-shot, and zero-shot learning have enabled EEG-based models to perform complex tasks such as natural language generation, semantic interpretation, and diagnostic assistance. By presenting a structured overview of the employed models and application domains, this survey establishes a comprehensive framework to advance neural signal analysis through the application of language models. The growing use of language models is shaping new developments in both neuroscience and artificial intelligence. Language models such as GPT, BERT [1], [2], [3], and their multi-modal variants have shown remarkable success across tasks involving natural language processing and understanding, generation, and even vision-language fusion. The transformer-based architecture enables these models to effectively process sequential data, contributing to their success across a range of domains beyond natural language processing.

During the preference optimization of large language models (LLMs), distribution shifts may arise between newly generated model samples and the data used to train the reward model (RM). This shift reduces the efficacy of the RM, which in turn negatively impacts the performance of the policy model (PM). To address this challenge, we propose Mutual-Taught, a self-training method that iteratively improves both the PM and RM without requiring additional human annotation. Our approach mirrors the expectation-maximization (EM) algorithm. In the E-step, the PM is updated using feedback from the current RM, guiding the PM toward a better approximation of the latent optimal preference distribution. In the M-step, we update the RM by constructing training data from the outputs of the PM before and after the E-step update. This process ensures that the RM adapts to the evolving policy distribution. Experimental results demonstrate that this iterative approach leads to consistent improvements in both models. Specifically, our 8B policy model, LLaMA-3-8B-Instruct-MT, achieves a length-controlled win rate of 54.1\% on AlpacaEval-2, while our 8B reward model, FsfairX-LLaMA3-RM-MT, performs on par with GPT-4o-2024-08-06 on RewardBench.

Modeling urban crime is an important yet challenging task that requires understanding the subtle visual, social, and cultural cues embedded in urban environments. Previous work has mainly focused on rule-based agent-based modeling (ABM) and deep learning methods. ABMs offer interpretability of internal mechanisms but exhibit limited predictive accuracy. In contrast, deep learning methods are often effective in prediction but are less interpretable and require extensive training data. Moreover, both lines of work lack the cognitive flexibility to adapt to changing environments. Leveraging the capabilities of large language models (LLMs), we propose CrimeMind, a novel LLM-driven ABM framework for simulating urban crime within a multi-modal urban context. A key innovation of our design is the integration of the Routine Activity Theory (RAT) into the agentic workflow of CrimeMind, enabling it to process rich multi-modal urban features and reason about criminal behavior. However, RAT requires LLM agents to infer subtle cues in evaluating environmental safety as part of assessing guardianship, which can be challenging for LLMs. To address this, we collect a small-scale human-annotated dataset and align CrimeMind's perception with human judgment via a training-free textual gradient method. Experiments across four major U.S. cities demonstrate that CrimeMind outperforms both traditional ABMs and deep learning baselines in crime hotspot prediction and spatial distribution accuracy, achieving up to a 24% improvement over the strongest baseline. Furthermore, we conduct counterfactual simulations of external incidents and policy interventions and it successfully captures the expected changes in crime patterns, demonstrating its ability to reflect counterfactual scenarios. Overall, CrimeMind enables fine-grained modeling of individual behaviors and facilitates evaluation of real-world interventions.