Predicting cancer drug response from transcriptomic profiles is a cornerstone of precision oncology, yet the scientific value of machine learning models hinges not solely on predictive accuracy, but also on their capacity to generate reliable biological insights. Current explainability approaches in this setting are computationally costly, lack robustness, and reduce complex drug response to univariate gene importance scores, overlooking the coordinated gene activity that drives sensitivity and resistance. In this work, we present ILLUME+, a scalable post-hoc explainability framework that moves beyond single-gene assessments to capture multiple, complementary forms of explanation. Integrated into our end-to-end pipeline, ILLUME+ produces more stable gene importance scores than existing baselines, recovers established drug-gene associations and mechanisms of action, and enables AI-assisted hypothesis generation to uncover novel interaction-driven molecular signals in cancer biology.
A central design principle in modern machine learning and artificial intelligence is to align a model's inductive bias with the structure of its input data. For matrix-valued inputs, relevant matrix-level relationships can be characterised through spectral values and spectral sub…
Automating theoretical research is constrained not only by the generation of candidate results, but also by their reliable evaluation. A common approach is to close the research loop with a large language model (LLM) reviewer. However, such reviewers remain empirically unreliable…
Singular value soft-thresholding can be computed via a reduction to the matrix polar decomposition, which allows one to exploit GPU-friendly algorithms for computing the polar decomposition. Empirically, there is a significant speed-up on GPUs compared to the standard approach us…
In this paper, we propose a new solution for addressing the content cold-start problem in industry-scale search and recommender systems. Compared to prior approaches, we have made the following new contributions: 1) our solution spans the entire multi-stage funnel and generalizes…
Dysphagia is a debilitating late effect of head and neck cancer (HNC) treatment, yet timely identification of at-risk patients remains challenging in survivorship care. Definitive assessment relies on videofluoroscopic imaging, as captured by the Dynamic Imaging Grade of Swallowi…
Electroencephalography (EEG) is widely used to diagnose neurological conditions, but its analysis usually relies on either predefined spectral features or deep neural networks. Predefined features carry a strong bias, since they fix in advance what counts as informative, while de…