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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
HybriDNA: A Hybrid Transformer-Mamba2 Long-Range DNA Lang...
Mingqian Ma, Guoqing Liu, Chuan Cao, Pan Deng, Tri Dao, Albert G · 2025-02-15 · via cs.LG updates on arXiv.org

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".