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cs.LG updates on arXiv.org

Memory-Guided Trust-Region Bayesian Optimization (MG-TuRBO) for High Dimensions EngageTriBoost: Predictive Modeling of User Engagement in Digital Mental Health Intervention Using Explainable Machine Learning Reservoir observer enhanced with residual calibration and attention mechanism Efficient RL Training for LLMs with Experience Replay Wireless Communication Enhanced Value Decomposition for Multi-Agent Reinforcement Learning Adversarial Sensor Errors for Safe and Robust Wind Turbine Fleet Control IKKA: Inversion Classification via Critical Anomalies for Robust Visual Servoing Adaptive Simulation Experiment for LLM Policy Optimization EvoLen: Evolution-Guided Tokenization for DNA Language Model Smartwatch-Based Sitting Time Estimation in Real-World Office Settings Structural Evaluation Metrics for SVG Generation via Leave-One-Out Analysis Loom: A Scalable Analytical Neural Computer Architecture Spectral Geometry of LoRA Adapters Encodes Training Objective and Predicts Harmful Compliance Finite-Sample Analysis of Nonlinear Independent Component Analysis:Sample Complexity and Identifiability Bounds How does Chain of Thought decompose complex tasks? Uncertainty-Aware Transformers: Conformal Prediction for Language Models Adaptive Candidate Point Thompson Sampling for High-Dimensional Bayesian Optimization Using Synthetic Data for Machine Learning-based Childhood Vaccination Prediction in Narok, Kenya Delve into the Applicability of Advanced Optimizers for Multi-Task Learning Bridging SFT and RL: Dynamic Policy Optimization for Robust Reasoning Multi-Agent Decision-Focused Learning via Value-Aware Sequential Communication Predictive Entropy Links Calibration and Paraphrase Sensitivity in Medical Vision-Language Models Efficient Hierarchical Implicit Flow Q-learning for Offline Goal-conditioned Reinforcement Learning Modality-Aware Zero-Shot Pruning and Sparse Attention for Efficient Multimodal Edge Inference The nextAI Solution to the NeurIPS 2023 LLM Efficiency Challenge Feature-Label Modal Alignment for Robust Partial Multi-Label Learning Integrated electro-optic attention nonlinearities for transformers Toward World Models for Epidemiology Tracing the Chain: Deep Learning for Stepping-Stone Intrusion Detection Batch Distillation Data for Developing Machine Learning Anomaly Detection Methods
A Simple yet Effective DDG Predictor is An Unsupervised A...
Lirong Wu, Yunfan Liu, Haitao Lin, Yufei Huang, Guojiang Zhao, Z · 2025-02-10 · via cs.LG updates on arXiv.org

The proteins that exist today have been optimized over billions of years of natural evolution, during which nature creates random mutations and selects them. The discovery of functionally promising mutations is challenged by the limited evolutionary accessible regions, i.e., only a small region on the fitness landscape is beneficial. There have been numerous priors used to constrain protein evolution to regions of landscapes with high-fitness variants, among which the change in binding free energy (DDG) of protein complexes upon mutations is one of the most commonly used priors. However, the huge mutation space poses two challenges: (1) how to improve the efficiency of DDG prediction for fast mutation screening; and (2) how to explain mutation preferences and efficiently explore accessible evolutionary regions. To address these challenges, we propose a lightweight DDG predictor (Light-DDG), which adopts a structure-aware Transformer as the backbone and enhances it by knowledge distilled from existing powerful but computationally heavy DDG predictors. Additionally, we augmented, annotated, and released a large-scale dataset containing millions of mutation data for pre-training Light-DDG. We find that such a simple yet effective Light-DDG can serve as a good unsupervised antibody optimizer and explainer. For the target antibody, we propose a novel Mutation Explainer to learn mutation preferences, which accounts for the marginal benefit of each mutation per residue. To further explore accessible evolutionary regions, we conduct preference-guided antibody optimization and evaluate antibody candidates quickly using Light-DDG to identify desirable mutations.