The integration of contextual information has significantly enhanced the performance of large language models (LLMs) on knowledge-intensive tasks. However, existing methods often overlook a critical challenge: the credibility of context documents can vary widely, potentially leading to the propagation of unreliable information. In this paper, we introduce CrEst, a novel weakly supervised framework for assessing the credibility of context documents during LLM inference--without requiring manual annotations. Our approach is grounded in the insight that credible documents tend to exhibit higher semantic coherence with other credible documents, enabling automated credibility estimation through inter-document agreement. To incorporate credibility into LLM inference, we propose two integration strategies: a black-box approach for models without access to internal weights or activations, and a white-box method that directly modifies attention mechanisms. Extensive experiments across three model architectures and five datasets demonstrate that CrEst consistently outperforms strong baselines, achieving up to a 26.86% improvement in accuracy and a 3.49% increase in F1 score. Further analysis shows that CrEst maintains robust performance even under high-noise conditions.

We introduce DisProtEdit, a controllable protein editing framework that leverages dual-channel natural language supervision to learn disentangled representations of structural and functional properties. Unlike prior approaches that rely on joint holistic embeddings, DisProtEdit explicitly separates semantic factors, enabling modular and interpretable control. To support this, we construct SwissProtDis, a large-scale multimodal dataset where each protein sequence is paired with two textual descriptions, one for structure and one for function, automatically decomposed using a large language model. DisProtEdit aligns protein and text embeddings using alignment and uniformity objectives, while a disentanglement loss promotes independence between structural and functional semantics. At inference time, protein editing is performed by modifying one or both text inputs and decoding from the updated latent representation. Experiments on protein editing and representation learning benchmarks demonstrate that DisProtEdit performs competitively with existing methods while providing improved interpretability and controllability. On a newly constructed multi-attribute editing benchmark, the model achieves a both-hit success rate of up to 61.7%, highlighting its effectiveness in coordinating simultaneous structural and functional edits.

Applications based on Large Language Models (LLMs) contains a series of tasks to address real-world problems with boosted capability, which have dynamic demand volumes on diverse backends. Existing serving systems treat the resource demands of LLM applications as a blackbox, compromising end-to-end efficiency due to improper queuing order and backend warm up latency. We find that the resource demands of LLM applications can be modeled in a general and accurate manner with Probabilistic Demand Graph (PDGraph). We then propose Hermes, which leverages PDGraph for efficient serving of LLM applications. Confronting probabilistic demand description, Hermes applies the Gittins policy to determine the scheduling order that can minimize the average application completion time. It also uses the PDGraph model to help prewarm cold backends at proper moments. Experiments with diverse LLM applications confirm that Hermes can effectively improve the application serving efficiency, reducing the average completion time by over 70% and the P95 completion time by over 80%.

Recently, multimodal large language models (MLLMs) have attracted increasing research attention due to their powerful visual understanding capabilities. While they have achieved impressive results on various vision tasks, their performance on chart-to-code generation remains suboptimal. This task requires MLLMs to generate executable code that can reproduce a given chart, demanding not only precise visual understanding but also accurate translation of visual elements into structured code. Directly prompting MLLMs to perform this complex task often yields unsatisfactory results. To address this challenge, we propose {ChartIR}, an iterative refinement method based on structured instruction. First, we distinguish two tasks: visual understanding and code translation. To accomplish the visual understanding component, we design two types of structured instructions: description and difference. The description instruction captures the visual elements of the reference chart, while the difference instruction characterizes the discrepancies between the reference chart and the generated chart. These instructions effectively transform visual features into language representations, thereby facilitating the subsequent code translation process. Second, we decompose the overall chart generation pipeline into two stages: initial code generation and iterative refinement, enabling progressive enhancement of the final output. Experimental results show that, compared to other method, our method achieves superior performance on both the open-source model Qwen2-VL and the closed-source model GPT-4o.

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.

Training deep learning (DL) models is a complex process, making it prone to silent errors that are challenging to detect and diagnose. This paper presents TRAINCHECK, a framework that takes a proactive checking approach to address silent training errors. TRAINCHECK automatically infers invariants tailored for DL training. It uses these invariants to proactively detect silent errors during the training process while providing debugging help. To evaluate TRAINCHECK, we reproduce 20 real-world silent training errors with diverse root causes. TRAINCHECK successfully detects 18 errors within a single training iteration. It also uncovers 6 unknown bugs in popular training libraries that lead to silent errors.

Surveys are a cornerstone of Information Systems (IS) research, yet creating high-quality surveys remains labor-intensive, requiring both domain expertise and methodological rigor. With the evolution of large language models (LLMs), new opportunities emerge to automate survey generation. This paper presents the real-world deployment of an LLM-powered system designed to accelerate data collection while maintaining survey quality. Deploying such systems in production introduces real-world complexity, including diverse user needs and quality control. We evaluate the system using the DeLone and McLean IS Success Model to understand how generative AI can reshape a core IS method. This study makes three key contributions. To our knowledge, this is the first application of the IS Success Model to a generative AI system for survey creation. In addition, we propose a hybrid evaluation framework combining automated and human assessments. Finally, we implement safeguards that mitigate post-deployment risks and support responsible integration into IS workflows.

Vision language models (VLMs) respond to user-crafted text prompts and visual inputs, and are applied to numerous real-world problems. VLMs integrate visual modalities with large language models (LLMs), which are well known to be prompt-sensitive. Hence, it is crucial to determine whether VLMs inherit this instability to varying prompts. We therefore investigate which prompt variations VLMs are most sensitive to and which VLMs are most agnostic to prompt variations. To this end, we introduce PARC (Prompt Analysis via Reliability and Calibration), a VLM prompt sensitivity analysis framework built on three pillars: (1) plausible prompt variations in both the language and vision domain, (2) a novel model reliability score with built-in guarantees, and (3) a calibration step that enables dataset- and prompt-spanning prompt variation analysis. Regarding prompt variations, PARC's evaluation shows that VLMs mirror LLM language prompt sensitivity in the vision domain, and most destructive variations change the expected answer. Regarding models, outstandingly robust VLMs among 22 evaluated models come from the InternVL2 family. We further find indications that prompt sensitivity is linked to training data. The code will be at https://github.com/NVlabs/PARC.

This study investigates the current landscape and future directions of protein foundation model research. While recent advancements have transformed protein science and engineering, the field lacks a comprehensive benchmark for fair evaluation and in-depth understanding. Since ESM-1B, numerous protein foundation models have emerged, each with unique datasets and methodologies. However, evaluations often focus on limited tasks tailored to specific models, hindering insights into broader generalization and limitations. Specifically, researchers struggle to understand the relationships between tasks, assess how well current models perform across them, and determine the criteria in developing new foundation models. To fill this gap, we present PFMBench, a comprehensive benchmark evaluating protein foundation models across 38 tasks spanning 8 key areas of protein science. Through hundreds of experiments on 17 state-of-the-art models across 38 tasks, PFMBench reveals the inherent correlations between tasks, identifies top-performing models, and provides a streamlined evaluation protocol. Code is available at \href{https://github.com/biomap-research/PFMBench}{\textcolor{blue}{GitHub}}.

Requiring $10^{13}$-$10^{15}$ FLOPs to calculate one 8 bit weight in an LLM during pretraining is extremely expensive and seems inefficient. To better leverage the huge investments made into pretrained models, we develop the new "Assembly-of-Experts" (AoE) construction method to create capable child variants of existing Mixture-of-Experts parent models in linear time. Model weight tensors get interpolated individually, allowing to enhance or suppress semantic features of the parents. Varying the proportion of weights taken from the parent models, we observe some properties of the AoE child model changing gradually, while other behavioral traits emerge with a sharp transition. Surprisingly, nearly every generated model is functional and capable, which makes searching the model space straightforward. We construct the DeepSeek R1T "Chimera", a 671B open-weights hybrid model combining DeepSeek's V3-0324 and R1 model variants. The child inherits only the routed expert tensors of R1, but still achieves about R1-level intelligence. At the same time, it uses about 40\% fewer output tokens, close to V3 speed. Constructed without any fine-tuning or distillation, the Chimera exhibits surprisingly compact, orderly reasoning compared to its parent models.