FUSE: Measure-Theoretic Compact Fuzzy Set Representation for Taxonomy Expansion

Taxonomy Expansion, which models complex concepts and their relations, can be formulated as a set representation learning task. The generalization of set, fuzzy set, incorporates uncertainty and measures the information within a semantic concept, making it suitable for concept modeling. Existing works usually model sets as vectors or geometric objects such as boxes, which are not closed under set operations. In this work, we propose a sound and efficient formulation of set representation learning based on its volume approximation as a fuzzy set. The resulting embedding framework, Fuzzy Set Embedding (FUSE), satisfies all set operations and compactly approximates the underlying fuzzy set, hence preserving information while being efficient to learn, relying on minimum neural architecture. We empirically demonstrate the power of FUSE on the task of taxonomy expansion, where FUSE achieves remarkable improvements up to 23% compared with existing baselines. Our work marks the first attempt to understand and efficiently compute the embeddings of fuzzy sets.

FD-Bench: A Modular and Fair Benchmark for Data-driven Fluid Simulation

Data-driven modeling of fluid dynamics has advanced rapidly with neural PDE solvers, yet a fair and strong benchmark remains fragmented due to the absence of unified PDE datasets and standardized evaluation protocols. Although architectural innovations are abundant, fair assessment is further impeded by the lack of clear disentanglement between spatial, temporal and loss modules. In this paper, we introduce FD-Bench, the first fair, modular, comprehensive and reproducible benchmark for data-driven fluid simulation. FD-Bench systematically evaluates 85 baseline models across 10 representative flow scenarios under a unified experimental setup. It provides four key contributions: (1) a modular design enabling fair comparisons across spatial, temporal, and loss function modules; (2) the first systematic framework for direct comparison with traditional numerical solvers; (3) fine-grained generalization analysis across resolutions, initial conditions, and temporal windows; and (4) a user-friendly, extensible codebase to support future research. Through rigorous empirical studies, FD-Bench establishes the most comprehensive leaderboard to date, resolving long-standing issues in reproducibility and comparability, and laying a foundation for robust evaluation of future data-driven fluid models. The code is open-sourced at https://anonymous.4open.science/r/FD-Bench-15BC.

LLM-DSE: Searching Accelerator Parameters with LLM Agents

Even though high-level synthesis (HLS) tools mitigate the challenges of programming domain-specific accelerators (DSAs) by raising the abstraction level, optimizing hardware directive parameters remains a significant hurdle. Existing heuristic and learning-based methods struggle with adaptability and sample efficiency.We present LLM-DSE, a multi-agent framework designed specifically for optimizing HLS directives. Combining LLM with design space exploration (DSE), our explorer coordinates four agents: Router, Specialists, Arbitrator, and Critic. These multi-agent components interact with various tools to accelerate the optimization process. LLM-DSE leverages essential domain knowledge to identify efficient parameter combinations while maintaining adaptability through verbal learning from online interactions. Evaluations on the HLSyn dataset demonstrate that LLM-DSE achieves substantial $2.55\times$ performance gains over state-of-the-art methods, uncovering novel designs while reducing runtime. Ablation studies validate the effectiveness and necessity of the proposed agent interactions. Our code is open-sourced here: https://github.com/Nozidoali/LLM-DSE.

LIFT: LLM-Based Pragma Insertion for HLS via GNN Supervised Fine-Tuning

FPGAs are increasingly adopted in datacenter environments for their reconfigurability and energy efficiency. High-Level Synthesis (HLS) tools have eased FPGA programming by raising the abstraction level from RTL to untimed C/C++, yet attaining high performance still demands expert knowledge and iterative manual insertion of optimization pragmas to modify the microarchitecture. To address this challenge, we propose LIFT, a large language model (LLM)-based coding assistant for HLS that automatically generates performance-critical pragmas given a C/C++ design. We fine-tune the LLM by tightly integrating and supervising the training process with a graph neural network (GNN), combining the sequential modeling capabilities of LLMs with the structural and semantic understanding of GNNs necessary for reasoning over code and its control/data dependencies. On average, LIFT produces designs that improve performance by 3.52x and 2.16x than prior state-of the art AutoDSE and HARP respectively, and 66x than GPT-4o.

Agree to Disagree? A Meta-Evaluation of LLM Misgendering

Numerous methods have been proposed to measure LLM misgendering, including probability-based evaluations (e.g., automatically with templatic sentences) and generation-based evaluations (e.g., with automatic heuristics or human validation). However, it has gone unexamined whether these evaluation methods have convergent validity, that is, whether their results align. Therefore, we conduct a systematic meta-evaluation of these methods across three existing datasets for LLM misgendering. We propose a method to transform each dataset to enable parallel probability- and generation-based evaluation. Then, by automatically evaluating a suite of 6 models from 3 families, we find that these methods can disagree with each other at the instance, dataset, and model levels, conflicting on 20.2% of evaluation instances. Finally, with a human evaluation of 2400 LLM generations, we show that misgendering behaviour is complex and goes far beyond pronouns, which automatic evaluations are not currently designed to capture, suggesting essential disagreement with human evaluations. Based on our findings, we provide recommendations for future evaluations of LLM misgendering. Our results are also more widely relevant, as they call into question broader methodological conventions in LLM evaluation, which often assume that different evaluation methods agree.

A Comprehensive Survey in LLM(-Agent) Full Stack Safety: Data, Training and Deployment

The remarkable success of Large Language Models (LLMs) has illuminated a promising pathway toward achieving Artificial General Intelligence for both academic and industrial communities, owing to their unprecedented performance across various applications. As LLMs continue to gain prominence in both research and commercial domains, their security and safety implications have become a growing concern, not only for researchers and corporations but also for every nation. Currently, existing surveys on LLM safety primarily focus on specific stages of the LLM lifecycle, e.g., deployment phase or fine-tuning phase, lacking a comprehensive understanding of the entire "lifechain" of LLMs. To address this gap, this paper introduces, for the first time, the concept of "full-stack" safety to systematically consider safety issues throughout the entire process of LLM training, deployment, and eventual commercialization. Compared to the off-the-shelf LLM safety surveys, our work demonstrates several distinctive advantages: (I) Comprehensive Perspective. We define the complete LLM lifecycle as encompassing data preparation, pre-training, post-training, deployment and final commercialization. To our knowledge, this represents the first safety survey to encompass the entire lifecycle of LLMs. (II) Extensive Literature Support. Our research is grounded in an exhaustive review of over 800+ papers, ensuring comprehensive coverage and systematic organization of security issues within a more holistic understanding. (III) Unique Insights. Through systematic literature analysis, we have developed reliable roadmaps and perspectives for each chapter. Our work identifies promising research directions, including safety in data generation, alignment techniques, model editing, and LLM-based agent systems. These insights provide valuable guidance for researchers pursuing future work in this field.

Heuristic Methods are Good Teachers to Distill MLPs for Graph Link Prediction

Link prediction is a crucial graph-learning task with applications including citation prediction and product recommendation. Distilling Graph Neural Networks (GNNs) teachers into Multi-Layer Perceptrons (MLPs) students has emerged as an effective approach to achieve strong performance and reducing computational cost by removing graph dependency. However, existing distillation methods only use standard GNNs and overlook alternative teachers such as specialized model for link prediction (GNN4LP) and heuristic methods (e.g., common neighbors). This paper first explores the impact of different teachers in GNN-to-MLP distillation. Surprisingly, we find that stronger teachers do not always produce stronger students: MLPs distilled from GNN4LP can underperform those distilled from simpler GNNs, while weaker heuristic methods can teach MLPs to near-GNN performance with drastically reduced training costs. Building on these insights, we propose Ensemble Heuristic-Distilled MLPs (EHDM), which eliminates graph dependencies while effectively integrating complementary signals via a gating mechanism. Experiments on ten datasets show an average 7.93% improvement over previous GNN-to-MLP approaches with 1.95-3.32 times less training time, indicating EHDM is an efficient and effective link prediction method.

Protein Large Language Models: A Comprehensive Survey

Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surveys focus on specific aspects or applications, this work provides the first comprehensive overview of Protein LLMs, covering their architectures, training datasets, evaluation metrics, and diverse applications. Through a systematic analysis of over 100 articles, we propose a structured taxonomy of state-of-the-art Protein LLMs, analyze how they leverage large-scale protein sequence data for improved accuracy, and explore their potential in advancing protein engineering and biomedical research. Additionally, we discuss key challenges and future directions, positioning Protein LLMs as essential tools for scientific discovery in protein science. Resources are maintained at https://github.com/Yijia-Xiao/Protein-LLM-Survey.

QLASS: Boosting Language Agent Inference via Q-Guided Stepwise Search

Language agents have become a promising solution to complex interactive tasks. One of the key ingredients to the success of language agents is the reward model on the trajectory of the agentic workflow, which provides valuable guidance during training or inference. However, due to the lack of annotations of intermediate interactions, most existing works use an outcome reward model to optimize policies across entire trajectories. This may lead to sub-optimal policies and hinder the overall performance. To address this, we propose QLASS (Q-guided Language Agent Stepwise Search), to automatically generate annotations by estimating Q-values in a stepwise manner for open language agents. By introducing a reasoning tree and performing process reward modeling, QLASS provides effective intermediate guidance for each step. With the stepwise guidance, we propose a Q-guided generation strategy to enable language agents to better adapt to long-term value, resulting in significant performance improvement during model inference on complex interactive agent tasks. Notably, even with almost half the annotated data, QLASS retains strong performance, demonstrating its efficiency in handling limited supervision. We also empirically demonstrate that QLASS can lead to more effective decision making through qualitative analysis. We will release our code and data.

Inferring from Logits: Exploring Best Practices for Decoding-Free Generative Candidate Selection

Generative Language Models rely on autoregressive decoding to produce the output sequence token by token. Many tasks such as preference optimization, require the model to produce task-level output consisting of multiple tokens directly by selecting candidates from a pool as predictions. Determining a task-level prediction from candidates using the ordinary token-level decoding mechanism is constrained by time-consuming decoding and interrupted gradients by discrete token selection. Existing works have been using decoding-free candidate selection methods to obtain candidate probability from initial output logits over vocabulary. Though these estimation methods are widely used, they are not systematically evaluated, especially on end tasks. We introduce an evaluation of a comprehensive collection of decoding-free candidate selection approaches on a comprehensive set of tasks, including five multiple-choice QA tasks with a small candidate pool and four clinical decision tasks with a massive amount of candidates, some with 10k+ options. We evaluate the estimation methods paired with a wide spectrum of foundation LMs covering different architectures, sizes and training paradigms. The results and insights from our analysis inform the future model design.