Enzyme function annotation and the identification of candidate enzymes for a given reaction are essential steps in connecting genomic information to biochemical reaction networks. However, existing methods rely on sequence or structural similarity or on training with known enzyme--reaction pairs, making it difficult to integrate biochemical evidence across large candidate spaces; they also struggle with retrieval tasks involving enzyme families whose members are highly similar. Here, we introduce RIVER (Reaction--enzyme Inference via Evidence-guided Retrieval), a multi-agent framework for bidirectional enzyme--reaction retrieval that identifies potentially catalyzed reactions for a given enzyme and ranks candidate enzymes for a given reaction. RIVER coordinates large language models, specialized biochemical computational tools, and external knowledge resources to assemble evidence at multiple levels, including reaction chemistry, protein sequences and domains, catalytic mechanisms, and database annotations. Dedicated validation modules further examine evidence gaps and potential conflicts and rerank candidates using traceable evidence records. On public benchmarks, RIVER achieves the highest success rates in both enzyme retrieval and enzyme annotation. In family-specific enzyme retrieval, RIVER outperforms the evaluated baselines on the selected datasets and metrics. In Escherichia coli enzyme retrieval tasks constructed from recent literature, RIVER achieves the best retrieval results with closed-source and open-source model configurations, substantially outperforming closed-source general-purpose and biology-specialized multi-agent systems, including Claude Code, Codex, and Phylo Max. These results suggest that evidence-guided multi-agent retrieval can prioritize biochemically supported enzyme--reaction relationships, providing a basis for subsequent experimental validation.
Knowledge distillation is widely used to transfer behavior from a large teacher model to a smaller student. It is often assumed to be safe when the teacher is clean, because classic backdoor attacks rely on poisoned labels and triggers in supervised training, whereas distillation trains the student to match a teacher's outputs. We show that this assumption can fail when the distillation dataset itself is poisoned. Our attack injects triggered and manipulated images that a clean teacher already predicts as an attacker chosen target label, which causes the student to learn a backdoor even though the teacher remains unaffected. We evaluate this threat across multiple manipulation strategies, including targeted adversarial perturbations and targeted GAN based class transitions, and study how distillation settings influence both accuracy and attack success. We show that the attack remains effective even at a 10% poisoning rates. The results demonstrate that a clean teacher alone is not a sufficient safeguard: poisoned distillation data can produce a strongly backdoored student while maintaining competitive performance on clean images. These findings show that the integrity and provenance of distillation data are part of the security boundary of data intensive KD pipelines, even when the teacher itself is trusted.
In biodiversity monitoring, a single image raises several questions: which taxon, how many, which trait, and whether the individual has been seen before. Vision-language models (VLMs) could answer all of these from the image, but their ability is largely untested in biology, as existing benchmarks focus mostly on species identification within a few taxonomic groups. We present Bio-VQA, the largest biological visual question answering (VQA) benchmark and the only one to span four aspects of biological visual understanding: hierarchical taxonomic reasoning, fine-grained attribute grounding, quantitative spatial reasoning, and individual re-identification. Bio-VQA contains 1.86M questions over 217K images from 11 public datasets, and extends right-or-wrong scoring to graded scoring, so a near-miss counts for more than a distant one. Evaluating 18 open-weight models from 3.75B to 38.4B parameters, we find that general visual capabilities do not transfer to biological organisms: the best model counts animals exactly on 41.7% of images with 2 to 10 individuals, less than half its accuracy on everyday objects at the same counts. Taxonomic accuracy falls to one sixth, from 0.72 at phylum to 0.12 at scientific name, and scaling helps mostly at coarse ranks. The gap to a domain specialist widens accordingly, from 0.731 against BioCLIP-2's 0.874 at class (1.2x) to 0.269 against 0.544 at scientific name (2x). On trait size measurement, 15 of the 18 models do no better than an image-blind baseline that predicts one fixed number for every specimen, and on re-identification, 17 of the 18 models fall below chance under adversarial conditions. These failures persist across a tenfold range of model size. We hope Bio-VQA becomes a standard test of how well VLM capabilities transfer to the biological domain.
Real-time full-duplex speech models can listen while speaking, enabling natural interaction without rigid turn boundaries. Existing benchmarks evaluate turn-taking, interruption handling and multi-round dialogue, but largely centre on a designated user rather than an assistant participating in a shared conversation among several people. We introduce Duplex-MPE to evaluate when such an assistant should answer, remain silent or stop speaking. The benchmark contains 2,000 scenarios with three or four human speakers and one assistant, each paired across explicit and implicit addressing of the same request. Models receive continuous conversation audio without transcripts or supplied turn boundaries. Four scores measure fresh response initiation, answer accuracy, silence preservation and stopping when a human resolves a request. We evaluate eight open-weight speech systems: MiniCPM-o 4.5, Moshi, FLM-Audio, Voila, Freeze-Omni, Realtime-Venus-Audio, Moshika-RL-Seamless and PersonaPlex. MiniCPM-o 4.5 leads on three scored capabilities, while frequent speech from other systems can coexist with inaccurate answers or failures to remain silent. A transcript-based Gemini 3.1 Pro reference responds 64.3 percentage points more often to explicit than implicit requests; paired tests detect no significant response-presence difference for the speech systems.
We present GPU-accelerated Bregman Douglas--Rachford splitting algorithm (BDRS) for discrete optimal transport problem in three input formats: an explicit cost matrix, a point cloud with a ground cost between them, and a separable cost on a regular grid. For each input format, we propose hardware-aware designs of mathematically equivalent representations for the BDRS iterations to enhance numerical stability and empirical runtime. We benchmark the three proposed implementations against eight GPU baseline solvers from the literature on the same device. We demonstrate that our implementations of BDRS achieve state-of-the-art performance on their respective input formats. To the best of our knowledge, this is the first cross-solver study of GPU DOT solvers with a unified measure of optimality.
Zhuo Chen, Minghao Li, Xiaoqian Ma Xiaohongshu, Siqi Fan University of Electronic Science and Technology of China, Xiusheng Huang, Zhang Liujie Xiaohongshu, Weihang Chen
Singular Value Decomposition (SVD) enables hardware-agnostic LLM compression via low-rank approximation, yet optimal rank allocation remains a bottleneck. Existing methods predominantly derive layer importance from performance-oriented proxies. Yet, these metrics fail to distinguish between representational importance and structural compressibility, consequently obscuring the fine-grained influence of spectral distribution shape. We demonstrate this disconnect through spectral analysis, revealing that layers with similar information capacity can exhibit markedly different singular value decay behaviors, corresponding to varying degrees of redundancy in the spectral tail. This imperfect coupling implies that allocation strategies driven solely by importance leave significant compression opportunities underexploited. To address this gap, we propose HiSVD, a hierarchical rank allocation framework with two stages: (1) Capacity-Anchored Baseline Allocation, which preserves representational stability by aligning rank budgets with information capacity; and (2) Redundancy-Aware Refinement, which modulates this baseline using tail redundancy to penalize structural excess. Experiments on LLMs demonstrate that HiSVD achieves superior compression efficiency, significantly outperforming state-of-the-art baselines by effectively exploiting this spectral heterogeneity.
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Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表