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20212026
most citedPEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding

59 citations · 211 across the 39 of their papers we have counts for

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Showing 2025Show all

9 papers · 1 filter

cs.CL2025

Controlling Performance and Budget of a Centralized Multi-agent LLM System with Reinforcement Learning

Bowen Jin, TJ Collins, Donghan Yu +10

Large language models (LLMs) exhibit complementary strengths across domains and come with varying inference costs, motivating the design of multi-agent LLM systems where specialize…

cs.LG2025

COMPASS: Benchmarking Constrained Optimization in LLM Agents

Tian Qin, Felix Bai, Ting-Yao Hu +8

Human decision-making often involves constrained optimization. As LLM agents are deployed to assist with real-world tasks like travel planning, shopping, and scheduling, they must…

cs.LG2025★ 3 cited

SimpleFold: Folding Proteins is Simpler than You Think

Yuyang Wang, Jiarui Lu, Navdeep Jaitly +2

Protein folding models have achieved groundbreaking results typically via a combination of integrating domain knowledge into the architectural blocks and training pipelines. Noneth…

cs.LG2025

Apple Intelligence Foundation Language Models: Tech Report 2025

Ethan Li, Anders Boesen Lindbo Larsen, Chen Zhang +395

We introduce two multilingual, multimodal foundation language models that power Apple Intelligence features across Apple devices and services: i a 3B-parameter on-device model opti…

cs.AI2025

Measuring Scientific Capabilities of Language Models with a Systems Biology Dry Lab

Haonan Duan, Stephen Zhewen Lu, Caitlin Fiona Harrigan +5

Designing experiments and result interpretations are core scientific competencies, particularly in biology, where researchers perturb complex systems to uncover the underlying syst…

cs.LG2025

AXLearn: Modular, Hardware-Agnostic Large Model Training

Mark Lee, Chang Lan, Tom Gunter +34

AXLearn is a production system which facilitates scalable and high-performance training of large deep learning models. Compared to other state-of-art deep learning systems, AXLearn…

cs.LG2025

Efficient Regression-Based Training of Normalizing Flows for Boltzmann Generators

Danyal Rehman, Oscar Davis, Jiarui Lu +5

Simulation-free training frameworks have been at the forefront of the generative modelling revolution in continuous spaces, leading to large-scale diffusion and flow matching model…

q-bio.BM2025★ 1 cited

Aligning Protein Conformation Ensemble Generation with Physical Feedback

Jiarui Lu, Xiaoyin Chen, Stephen Zhewen Lu +4

Protein dynamics play a crucial role in protein biological functions and properties, and their traditional study typically relies on time-consuming molecular dynamics (MD) simulati…

cs.AI2025

Self-Evolving Curriculum for LLM Reasoning

Xiaoyin Chen, Jiarui Lu, Minsu Kim +6

Reinforcement learning (RL) has proven effective for fine-tuning large language models (LLMs), significantly enhancing their reasoning abilities in domains such as mathematics and…