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Triangle Multiplication Is All You Need For Biomolecular Structure Representations
Ouyang-Zhang, Jeffrey, Murugan, Pranav, Diaz, Daniel J., Scarpellini, Gianluca, Bowen, Richard Strong, Gruver, Nate, Klivans, Adam, Krähenbühl, Philipp, Faust, Aleksandra, Al-Shedivat, Maruan
A major bottleneck lies in the Pairformer backbone of AlphaFold3-style models, which relies on computationally expensive triangular primitives--especially triangle attention--for pairwise reasoning. AlphaFold (Senior et al., 2020; Jumper et al., 2021) has transformed protein structure prediction and At this scale, runtime and memory efficiency are critical bottlenecks: for example, Boltz-1 (Wohlwend et al., 2024) requires over 15 minutes to process a single 2048-token We introduce Pairmixer, a streamlined alternative to the Pairformer backbone of AlphaFold3 (Abram-son et al., 2024). Figure 1: Pairmixer is an efficient architecture for biomolecular structure prediction. By reducing both runtime and memory requirements, Pairmixer expands the scope of feasible downstream applications of structure prediction. Early approaches such as trRosetta (Y ang et al., 2020) and AlphaFold1 (Senior et al., 2020) leveraged convolutional neural networks to extract pairwise residue The Pairformer has since become the de-facto backbone architecture for biomolecular structure prediction (IntFold et al., 2025; Boitreaud et al., 2024; Wohlwend et al., 2024; ByteDance et al., 2025).
EVER: Edge-Assisted Auto-Verification for Mobile MR-Aided Operation
Chen, Jiangong, Zhu, Mingyu, Li, Bin
Mixed Reality (MR)-aided operation overlays digital objects on the physical world to provide a more immersive and intuitive operation process. A primary challenge is the precise and fast auto-verification of whether the user follows MR guidance by comparing frames before and after each operation. The pre-operation frame includes virtual guiding objects, while the post-operation frame contains physical counterparts. Existing approaches fall short of accounting for the discrepancies between physical and virtual objects due to imperfect 3D modeling or lighting estimation. In this paper, we propose EVER: an edge-assisted auto-verification system for mobile MR-aided operations. Unlike traditional frame-based similarity comparisons, EVER leverages the segmentation model and rendering pipeline adapted to the unique attributes of frames with physical pieces and those with their virtual counterparts; it adopts a threshold-based strategy using Intersection over Union (IoU) metrics for accurate auto-verification. To ensure fast auto-verification and low energy consumption, EVER offloads compute-intensive tasks to an edge server. Through comprehensive evaluations of public datasets and custom datasets with practical implementation, EVER achieves over 90% verification accuracy within 100 milliseconds (significantly faster than average human reaction time of approximately 273 milliseconds), while consuming only minimal additional computational resources and energy compared to a system without auto-verification.
HUME: Measuring the Human-Model Performance Gap in Text Embedding Tasks
Assadi, Adnan El, Chung, Isaac, Solomatin, Roman, Muennighoff, Niklas, Enevoldsen, Kenneth
Comparing human and model performance offers a valuable perspective for understanding the strengths and limitations of embedding models, highlighting where they succeed and where they fail to capture meaning and nuance. However, such comparisons are rarely made, as human performance on embedding tasks is difficult to measure. To fill this gap, we introduce HUME: Human Evaluation Framework for Text Embeddings. While frameworks like MTEB provide broad model evaluation, they lack reliable estimates of human performance, limiting the interpretability of model scores. We measure human performance across 16 MTEB datasets spanning reranking, classification, clustering, and semantic textual similarity across linguistically diverse high- and low-resource languages. Humans achieve an average performance of 77.6% compared to 80.1% for the best embedding model, though with substantial variation: models reach high performance on some datasets while struggling on notably low-resource languages. Our human annotations also reveal multiple dataset issues. We additionally benchmark nine LLMs as annotators on reranking, classification, and STS tasks, finding that they fall short of human performance (76.1% vs. 81.2%) despite offering scalability advantages. We provide human performance baselines, insights into task difficulty patterns, and an extensible evaluation framework that enables a more meaningful interpretation of results and informs the development of both models and benchmarks. Our code, dataset, and leaderboard are publicly available at https://github.com/embeddings-benchmark/mteb.
Locality-Sensitive Hashing-Based Efficient Point Transformer for Charged Particle Reconstruction
Govil, Shitij, Rodgers, Jack P., Chou, Yuan-Tang, Miao, Siqi, Saha, Amit, Anand, Advaith, Lieret, Kilian, DeZoort, Gage, Liu, Mia, Duarte, Javier, Li, Pan, Hsu, Shih-Chieh
Charged particle track reconstruction is a foundational task in collider experiments and the main computational bottleneck in particle reconstruction. Graph neural networks (GNNs) have shown strong performance for this problem, but costly graph construction, irregular computations, and random memory access patterns substantially limit their throughput. The recently proposed Hashing-based Efficient Point Transformer (HEPT) offers a theoretically guaranteed near-linear complexity for large point cloud processing via locality-sensitive hashing (LSH) in attention computations; however, its evaluations have largely focused on embedding quality, and the object condensation pipeline on which HEPT relies requires a post-hoc clustering step (e.g., DBScan) that can dominate runtime. In this work, we make two contributions. First, we present a unified, fair evaluation of physics tracking performance for HEPT and a representative GNN-based pipeline under the same dataset and metrics. Second, we introduce HEPTv2 by extending HEPT with a lightweight decoder that eliminates the clustering stage and directly predicts track assignments. This modification preserves HEPT's regular, hardware-friendly computations while enabling ultra-fast end-to-end inference. On the TrackML dataset, optimized HEPTv2 achieves approximately 28 ms per event on an A100 while maintaining competitive tracking efficiency. These results position HEPTv2 as a practical, scalable alternative to GNN-based pipelines for fast tracking.
Random Feature Spiking Neural Networks
Gollwitzer, Maximilian, Dietrich, Felix
Spiking Neural Networks (SNNs) as Machine Learning (ML) models have recently received a lot of attention as a potentially more energy-efficient alternative to conventional Artificial Neural Networks. The non-differentiability and sparsity of the spiking mechanism can make these models very difficult to train with algorithms based on propagating gradients through the spiking non-linearity. We address this problem by adapting the paradigm of Random Feature Methods (RFMs) from Artificial Neural Networks (ANNs) to Spike Response Model (SRM) SNNs. This approach allows training of SNNs without approximation of the spike function gradient. Concretely, we propose a novel data-driven, fast, high-performance, and interpretable algorithm for end-to-end training of SNNs inspired by the SWIM algorithm for RFM-ANNs, which we coin S-SWIM. We provide a thorough theoretical discussion and supplementary numerical experiments showing that S-SWIM can reach high accuracies on time series forecasting as a standalone strategy and serve as an effective initialisation strategy before gradient-based training. Additional ablation studies show that our proposed method performs better than random sampling of network weights.
Justice in Judgment: Unveiling (Hidden) Bias in LLM-assisted Peer Reviews
Vasu, Sai Suresh Macharla, Sheth, Ivaxi, Wang, Hui-Po, Binkyte, Ruta, Fritz, Mario
The adoption of large language models (LLMs) is transforming the peer review process, from assisting reviewers in writing more detailed evaluations to generating entire reviews automatically. While these capabilities offer exciting opportunities, they also raise critical concerns about fairness and reliability. In this paper, we investigate bias in LLM-generated peer reviews by conducting controlled experiments on sensitive metadata, including author affiliation and gender. Our analysis consistently shows affiliation bias favoring institutions highly ranked on common academic rankings. Additionally, we find some gender preferences, which, even though subtle in magnitude, have the potential to compound over time. Notably, we uncover implicit biases that become more evident with token-based soft ratings.
Convolutional Monge Mapping between EEG Datasets to Support Independent Component Labeling
Meek, Austin, Mendoza-Cardenas, Carlos H., Brockmeier, Austin J.
EEG recordings contain rich information about neural activity but are subject to artifacts, noise, and superficial differences due to sensors, amplifiers, and filtering. Independent component analysis and automatic labeling of independent components (ICs) enable artifact removal in EEG pipelines. Convolutional Monge Mapping Normalization (CMMN) is a recent tool used to achieve spectral conformity of EEG signals, which was shown to improve deep neural network approaches for sleep staging. Here we propose a novel extension of the CMMN method with two alternative approaches to computing the source reference spectrum the target signals are mapped to: (1) channel-averaged and $l_1$-normalized barycenter, and (2) a subject-to-subject mapping that finds the source subject with the closest spectrum to the target subject. Notably, our extension yields space-time separable filters that can be used to map between datasets with different numbers of EEG channels. We apply these filters in an IC classification task, and show significant improvement in recognizing brain versus non-brain ICs. Clinical relevance - EEG recordings are used in the diagnosis and monitoring of multiple neuropathologies, including epilepsy and psychosis. While EEG analysis can benefit from automating artifact removal through independent component analysis and labeling, differences in recording equipment and context (the presence of noise from electrical wiring and other devices) may impact the performance of machine learning models, but these differences can be minimized by appropriate spectral normalization through filtering.
SignBind-LLM: Multi-Stage Modality Fusion for Sign Language Translation
Thomas, Marshall, Fish, Edward, Bowden, Richard
Despite progress in gloss-free Sign Language Translation (SLT), traditional single modality end-to-end approaches consistently fail on two critical components of natural signing: the precise recognition of high-speed fingerspelling and the integration of asynchronous non-manual cues from the face. Recent progress in SLT with Large Language Models has side stepped this challenge, forcing a single network to learn these simultaneously resulting in poor performance when tasked with translating crucial information such as names, places, and technical terms. We introduce SignBind-LLM, a modular framework designed to overcome these limitations. Our approach employs separate, specialized predictors for continuous signing, fingerspelling, and lipreading. Each expert network first decodes its specific modality into a sequence of tokens. These parallel streams are then fused by a lightweight transformer that resolves temporal misalignments before passing the combined representation to a Large Language Model (LLM) for final sentence generation. Our method establishes a new state-of-the-art on the How2Sign, ChicagoFSWildPlus, and BOBSL datasets with a BLEU-4 score of 22.1, 73.2% letter accuracy and BLEU-4 score of 6.8 respectively. These results validate our core hypothesis: isolating and solving distinct recognition tasks before fusion provides a more powerful and effective pathway to robust, high-fidelity sign language translation.
OPTIC-ER: A Reinforcement Learning Framework for Real-Time Emergency Response and Equitable Resource Allocation in Underserved African Communities
Public service systems in many African regions suffer from delayed emergency response and spatial inequity, causing avoidable suffering. This paper introduces OPTIC-ER, a reinforcement learning (RL) framework for real-time, adaptive, and equitable emergency response. OPTIC-ER uses an attention-guided actor-critic architecture to manage the complexity of dispatch environments. Its key innovations are a Context-Rich State Vector, encoding action sub-optimality, and a Precision Reward Function, which penalizes inefficiency. Training occurs in a high-fidelity simulation using real data from Rivers State, Nigeria, accelerated by a precomputed Travel Time Atlas. The system is built on the TALS framework (Thin computing, Adaptability, Low-cost, Scalability) for deployment in low-resource settings. In evaluations on 500 unseen incidents, OPTIC-ER achieved a 100.00% optimal action selection rate, confirming its robustness and generalization. Beyond dispatch, the system generates Infrastructure Deficiency Maps and Equity Monitoring Dashboards to guide proactive governance and data-informed development. This work presents a validated blueprint for AI-augmented public services, showing how context-aware RL can bridge the gap between algorithmic decision-making and measurable human impact.
TaoSR1: The Thinking Model for E-commerce Relevance Search
Dong, Chenhe, Yao, Shaowei, Jiao, Pengkun, Yang, Jianhui, Jin, Yiming, Huang, Zerui, Zhou, Xiaojiang, Ou, Dan, Tang, Haihong, Zheng, Bo
Query-product relevance prediction is a core task in e-commerce search. BERT-based models excel at semantic matching but lack complex reasoning capabilities. While Large Language Models (LLMs) are explored, most still use discriminative fine-tuning or distill to smaller models for deployment. We propose a framework to directly deploy LLMs for this task, addressing key challenges: Chain-of-Thought (CoT) error accumulation, discriminative hallucination, and deployment feasibility. Our framework, TaoSR1, involves three stages: (1) Supervised Fine-Tuning (SFT) with CoT to instill reasoning; (2) Offline sampling with a pass@N strategy and Direct Preference Optimization (DPO) to improve generation quality; and (3) Difficulty-based dynamic sampling with Group Relative Policy Optimization (GRPO) to mitigate discriminative hallucination. Additionally, post-CoT processing and a cumulative probability-based partitioning method enable efficient online deployment. TaoSR1 significantly outperforms baselines on offline datasets and achieves substantial gains in online side-by-side human evaluations, introducing a novel paradigm for applying CoT reasoning to relevance classification.