Omar Ibrahim

h-index30
2papers

2 Papers

CLDec 18, 2025Code
Benchmarking and Adapting On-Device Large Language Models for Clinical Decision Support

Alif Munim, Jun Ma, Omar Ibrahim et al.

Large language models (LLMs) have rapidly advanced in clinical decision-making, yet the deployment of proprietary systems is hindered by privacy concerns and reliance on cloud-based infrastructure. Open-source alternatives allow local inference but often require large model sizes that limit their use in resource-constrained clinical settings. Here, we benchmark two on-device LLMs, gpt-oss-20b and gpt-oss-120b, across three representative clinical tasks: general disease diagnosis, specialty-specific (ophthalmology) diagnosis and management, and simulation of human expert grading and evaluation. We compare their performance with state-of-the-art proprietary models (GPT-5 and o4-mini) and a leading open-source model (DeepSeek-R1), and we further evaluate the adaptability of on-device systems by fine-tuning gpt-oss-20b on general diagnostic data. Across tasks, gpt-oss models achieve performance comparable to or exceeding DeepSeek-R1 and o4-mini despite being substantially smaller. In addition, fine-tuning remarkably improves the diagnostic accuracy of gpt-oss-20b, enabling it to approach the performance of GPT-5. These findings highlight the potential of on-device LLMs to deliver accurate, adaptable, and privacy-preserving clinical decision support, offering a practical pathway for broader integration of LLMs into routine clinical practice.

LGMay 29, 2025Code
BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model

Adibvafa Fallahpour, Andrew Magnuson, Purav Gupta et al. · deepmind, utoronto

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