Kaveri A. Thakoor

Iddo Drori, Isht Dwivedi, Pranav Shrestha et al.

We tackle the problem of protein secondary structure prediction using a common task framework. This lead to the introduction of multiple ideas for neural architectures based on state of the art building blocks, used in this task for the first time. We take a principled machine learning approach, which provides genuine, unbiased performance measures, correcting longstanding errors in the application domain. We focus on the Q8 resolution of secondary structure, an active area for continuously improving methods. We use an ensemble of strong predictors to achieve accuracy of 70.7% (on the CB513 test set using the CB6133filtered training set). These results are statistically indistinguishable from those of the top existing predictors. In the spirit of reproducible research we make our data, models and code available, aiming to set a gold standard for purity of training and testing sets. Such good practices lower entry barriers to this domain and facilitate reproducible, extendable research.

Emily Alsentzer, Marie-Laure Charpignon, Bill Chen et al.

The 6th Annual Conference on Health, Inference, and Learning (CHIL 2025), hosted by the Association for Health Learning and Inference (AHLI), was held in person on June 25-27, 2025, at the University of California, Berkeley, in Berkeley, California, USA. As part of this year's program, we hosted Research Roundtables to catalyze collaborative, small-group dialogue around critical, timely topics at the intersection of machine learning and healthcare. Each roundtable was moderated by a team of senior and junior chairs who fostered open exchange, intellectual curiosity, and inclusive engagement. The sessions emphasized rigorous discussion of key challenges, exploration of emerging opportunities, and collective ideation toward actionable directions in the field. In total, eight roundtables were held by 19 roundtable chairs on topics of "Explainability, Interpretability, and Transparency," "Uncertainty, Bias, and Fairness," "Causality," "Domain Adaptation," "Foundation Models," "Learning from Small Medical Data," "Multimodal Methods," and "Scalable, Translational Healthcare Solutions."

Roshan Kenia, Anfei Li, Rishabh Srivastava et al.

Glaucoma is a progressive eye disease that leads to optic nerve damage, causing irreversible vision loss if left untreated. Optical coherence tomography (OCT) has become a crucial tool for glaucoma diagnosis, offering high-resolution 3D scans of the retina and optic nerve. However, the conventional practice of condensing information from 3D OCT volumes into 2D reports often results in the loss of key structural details. To address this, we propose a novel hybrid deep learning model that integrates cross-attention mechanisms into a 3D convolutional neural network (CNN), enabling the extraction of critical features from the superior and inferior hemiretinas, as well as from the optic nerve head (ONH) and macula, within OCT volumes. We introduce Channel Attention REpresentations (CAREs) to visualize cross-attention outputs and leverage them for consistency-based multi-task fine-tuning, aligning them with Gradient-Weighted Class Activation Maps (Grad-CAMs) from the CNN's final convolutional layer to enhance performance, interpretability, and anatomical coherence. We have named this model AI-CNet3D (AI-`See'-Net3D) to reflect its design as an Anatomically-Informed Cross-attention Network operating on 3D data. By dividing the volume along two axes and applying cross-attention, our model enhances glaucoma classification by capturing asymmetries between the hemiretinal regions while integrating information from the optic nerve head and macula. We validate our approach on two large datasets, showing that it outperforms state-of-the-art attention and convolutional models across all key metrics. Finally, our model is computationally efficient, reducing the parameter count by one-hundred--fold compared to other attention mechanisms while maintaining high diagnostic performance and comparable GFLOPS.