Jack Naimer | Searcharxiv

arXiv2025

BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model

Unlocking deep and interpretable biological reasoning from complex genomic data remains a major AI challenge limiting scientific progress. While current DNA foundation models excel at representing sequences, they struggle with multi-step reasoning and lack transparent, biologically meaningful explanations. BioReason addresses this by tightly integrating a DNA foundation model with a large language model (LLM), enabling the LLM to directly interpret and reason over genomic information. Through supervised fine-tuning and reinforcement learning, BioReason learns to produce logical, biologically coherent deductions. It achieves major performance gains, boosting KEGG-based disease pathway prediction accuracy from 86% to 98% and improving variant effect prediction by an average of 15% over strong baselines. BioReason can reason over unseen biological entities and explain its decisions step by step, offering a transformative framework for interpretable, mechanistic AI in biology. All data, code, and checkpoints are available at https://github.com/bowang-lab/BioReason

cs.LG↗

arXiv2024

Semantically Safe Robot Manipulation: From Semantic Scene Understanding to Motion Safeguards

Ensuring safe interactions in human-centric environments requires robots to understand and adhere to constraints recognized by humans as "common sense" (e.g., "moving a cup of water above a laptop is unsafe as the water may spill" or "rotating a cup of water is unsafe as it can lead to pouring its content"). Recent advances in computer vision and machine learning have enabled robots to acquire a semantic understanding of and reason about their operating environments. While extensive literature on safe robot decision-making exists, semantic understanding is rarely integrated into these formulations. In this work, we propose a semantic safety filter framework to certify robot inputs with respect to semantically defined constraints (e.g., unsafe spatial relationships, behaviors, and poses) and geometrically defined constraints (e.g., environment-collision and self-collision constraints). In our proposed approach, given perception inputs, we build a semantic map of the 3D environment and leverage the contextual reasoning capabilities of large language models to infer semantically unsafe conditions. These semantically unsafe conditions are then mapped to safe actions through a control barrier certification formulation. We demonstrate the proposed semantic safety filter in teleoperated manipulation tasks and with learned diffusion policies applied in a real-world kitchen environment that further showcases its effectiveness in addressing practical semantic safety constraints. Together, these experiments highlight our approach's capability to integrate semantics into safety certification, enabling safe robot operation beyond traditional collision avoidance.

cs.RO↗