Adibvafa Fallahpour

Negin Baghbanzadeh, Pritam Sarkar, Michael Colacci et al.

High-stakes clinical use of large vision-language models (LVLMs) requires reasoning that is grounded in visual evidence and clinical knowledge, not just correct final answers. We introduce OpenMedReason, a large-scale, open multimodal medical reasoning corpus comprising approximately 450K image-question-answer instances whose reasoning traces are primarily derived from curated biomedical, human-authored scientific articles. OpenMedReason provides high-fidelity supervision beyond synthetic chains of thought, covering diverse medical domain vision modalities such as radiological scans, microscopic images, visible light photographs, charts, and others. We complement it with OpenMedReason-Bench, a held-out benchmark that allows fine-grained evaluation of LVLMs along three complementary axes of capability, including perception, medical knowledge, and rationale, enabling diagnostic evaluation beyond final-answer accuracy. OpenMedReason is a rich training resource that exhibits its effectiveness in both supervised fine-tuning (SFT) and reinforcement-based alignment. Training with OpenMedReason yields a 20% average improvement in VQA accuracy over the base model and achieves performance within 4.2% of the strongest comparable-scale medical LVLMs. Fine-grained performance analysis confirms that the gains are not concentrated in any single axis: OpenMedReason improves perception, medical knowledge, and rationale jointly, and its reasoning traces are preferred over those of the base model in 86.1% of pairwise comparisons. We release the code and dataset at huggingface.co/datasets/neginb/OpenMedReason.

Arnav Shah, Junzhe Li, Parsa Idehpour et al.

Genomic foundation models have the potential to decode DNA syntax, yet face a fundamental tradeoff in their input representation. Standard fixed-vocabulary tokenizers fragment biologically meaningful motifs such as codons and regulatory elements, while nucleotide-level models preserve biological coherence but incur prohibitive computational costs for long contexts. We introduce dnaHNet, a state-of-the-art tokenizer-free autoregressive model that segments and models genomic sequences end-to-end. Using a differentiable dynamic chunking mechanism, dnaHNet compresses raw nucleotides into latent tokens adaptively, balancing compression with predictive accuracy. Pretrained on prokaryotic genomes, dnaHNet outperforms leading architectures including StripedHyena2 in scaling and efficiency. This recursive chunking yields quadratic FLOP reductions, enabling $>3 \times$ inference speedup over Transformers. On zero-shot tasks, dnaHNet achieves superior performance in predicting protein variant fitness and gene essentiality, while automatically discovering hierarchical biological structures without supervision. These results establish dnaHNet as a scalable, interpretable framework for next-generation genomic modeling.

Jun Ma, Zongxin Yang, Sumin Kim et al.

Medical image and video segmentation is a critical task for precision medicine, which has witnessed considerable progress in developing task or modality-specific and generalist models for 2D images. However, there have been limited studies on building general-purpose models for 3D images and videos with comprehensive user studies. Here, we present MedSAM2, a promptable segmentation foundation model for 3D image and video segmentation. The model is developed by fine-tuning the Segment Anything Model 2 on a large medical dataset with over 455,000 3D image-mask pairs and 76,000 frames, outperforming previous models across a wide range of organs, lesions, and imaging modalities. Furthermore, we implement a human-in-the-loop pipeline to facilitate the creation of large-scale datasets resulting in, to the best of our knowledge, the most extensive user study to date, involving the annotation of 5,000 CT lesions, 3,984 liver MRI lesions, and 251,550 echocardiogram video frames, demonstrating that MedSAM2 can reduce manual costs by more than 85%. MedSAM2 is also integrated into widely used platforms with user-friendly interfaces for local and cloud deployment, making it a practical tool for supporting efficient, scalable, and high-quality segmentation in both research and healthcare environments.