59 citations · 211 across the 39 of their papers we have counts for
40 papers
SimpleDesign: A Joint Model for Protein Sequence and Structure Codesign
Jiarui Lu, Yuyang Wang, Yizhe Zhang +4
Proteins are fundamental to biological processes, with their function determined by the complex interplay between the amino acid sequence and the three-dimensional structure. Devel…
MM-ToolSandBox: A Unified Framework for Evaluating Visual Tool-Calling Agents
Kaixin Ma, Di Feng, Alexander Metz +3
We introduce MM-ToolSandBox, a benchmark and evaluation framework for visually grounded tool-calling agents. The framework provides a stateful execution environment spanning 500+ t…
Sparse Evidence Can Suffice: Agentic Evidence Seeking for Multimodal Video Misinformation Detection
Haochen Zhao, Yongxiu Xu, Xinkui Lin +6
Multimodal video misinformation detection is commonly formulated as a holistic video-understanding task, where the entire video and its associated content are processed and judged…
Learning Structure, Energy, and Dynamics: A Survey of Artificial Intelligence for Protein Dynamics
Haocheng Tang, Liang Shi, Ya-Shi Zhang +3
Protein dynamics underlie many biological functions, yet remain difficult to characterize due to the high computational cost of molecular dynamics simulations and the scarcity of d…
Atomic Trajectory Modeling with State Space Models for Biomolecular Dynamics
Liang Shi, Jiarui Lu, Junqi Liu +3
Understanding the dynamic behavior of biomolecules is fundamental to elucidating biological function and facilitating drug discovery. While Molecular Dynamics (MD) simulations prov…
ASTRA-bench: Evaluating Tool-Use Agent Reasoning and Action Planning with Personal User Context
Zidi Xiu, David Q. Sun, Kevin Cheng +9
Next-generation AI must manage vast personal data, diverse tools, and multi-step reasoning, yet most benchmarks remain context-free and single-turn. We present ASTRA-bench (Assista…
Conditionally Site-Independent Neural Evolution of Antibody Sequences
Stephen Zhewen Lu, Aakarsh Vermani, Kohei Sanno +4
Common deep learning approaches for antibody engineering focus on modeling the marginal distribution of sequences. By treating sequences as independent samples, however, these meth…
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…
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…
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…
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…
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…
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…
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…
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…
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…
Reaction-conditioned De Novo Enzyme Design with GENzyme
Chenqing Hua, Jiarui Lu, Yong Liu +7
The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has revolutionized protein structure modeling and interaction prediction, primarily from a binding…
Structure Language Models for Protein Conformation Generation
Jiarui Lu, Xiaoyin Chen, Stephen Zhewen Lu +4
Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Tradi…
MMAU: A Holistic Benchmark of Agent Capabilities Across Diverse Domains
Guoli Yin, Haoping Bai, Shuang Ma +21
Recent advances in large language models (LLMs) have increased the demand for comprehensive benchmarks to evaluate their capabilities as human-like agents. Existing benchmarks, whi…
ToolSandbox: A Stateful, Conversational, Interactive Evaluation Benchmark for LLM Tool Use Capabilities
Jiarui Lu, Thomas Holleis, Yizhe Zhang +9
Recent large language models (LLMs) advancements sparked a growing research interest in tool assisted LLMs solving real-world challenges, which calls for comprehensive evaluation o…
Apple Intelligence Foundation Language Models
Tom Gunter, Zirui Wang, Chong Wang +152
We present foundation language models developed to power Apple Intelligence features, including a ~3 billion parameter model designed to run efficiently on devices and a large serv…
MMIDR: Teaching Large Language Model to Interpret Multimodal Misinformation via Knowledge Distillation
Longzheng Wang, Xiaohan Xu, Lei Zhang +5
Automatic detection of multimodal misinformation has gained a widespread attention recently. However, the potential of powerful Large Language Models (LLMs) for multimodal misinfor…
Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations
Jiarui Lu, Zuobai Zhang, Bozitao Zhong +2
The protein dynamics are common and important for their biological functions and properties, the study of which usually involves time-consuming molecular dynamics (MD) simulations…
ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation
Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan +3
Protein function annotation is an important yet challenging task in biology. Recent deep learning advancements show significant potential for accurate function prediction by learni…