#01Nov 5, 2026
cs.LG
Synthesis of Ovarian Cancer Multi-Omics Datasets: A Biology-Informed Evaluation Framework
Déborah Boyenval, Alina Malyutina, Jaana Oikkonen and 2 more
Paired multi-omic cancer cohorts are costly to assemble and difficult to share, motivating synthetic cohorts as a complementary resource. As generative model development accelerates, we shift the focus from proposing yet another architecture to defining evaluation criteria that determine whether synthetic data preserve biologically relevant structure. We introduce a biology-informed and patient-disjoint framework for evaluating the generation of paired RNA expression and copy-number variation (CNV) profiles, and apply it to the longitudinal DECIDER high-grade serous ovarian cancer cohort. The framework assesses modality-specific fidelity and coherence between RNA and CNV pairs using agreement between real training and held-out data as a reference, alongside complementary training-data proximity diagnostics. We adapt three multi-omic integration architectures based on variational autoencoders to generate paired profiles. The model leading several fidelity and coherence measures also shows the strongest training-data proximity. The protocol and case study offer the community a reference for comparing future multi-omic generators.
#02Nov 5, 2026
stat.ML
Unifying Central Flow, Rod Flow, and the Edge Coupling
Eric Regis, Sinho Chewi
At the edge of stability, the iterates of gradient descent oscillate along the sharp directions of the Hessian. This poses a significant challenge for continuous-time models as the usual continuous-time approximation -- the gradient flow -- admits no oscillations. Several continuous-time models have been proposed to capture the behavior at the edge of stability, among them central flow and rod flow. Although both models can be interpreted as performing a coarse-graining in time, the connection between them remains poorly understood. Here we show that both flows can be derived from a third object, the edge coupling: a functional on consecutive iterates whose critical points are the fixed points and period-two orbits of gradient descent. It is revealed that the two flows correspond to coarse-grainings at different time scales. Rod flow coarse-grains over only the fastest time scale, while central flow coarse-grains over both the fast and intermediate time scales. Furthermore, using the edge coupling, we derive rod flows and central flows for momentum methods such as heavy ball and Adam. We verify the derived flows experimentally on representative neural network architectures, where they track the discrete iterates throughout all phases of training -- including the transition from the stable regime to the edge of stability.
#03Nov 5, 2026
cs.LG
On the limitations of molecular representations
Acer Blake, Fergus Imrie, Charlotte M. Deane
Molecular representations such as fingerprints and learned embeddings play a central role in cheminformatics and small-molecule machine learning. They serve as the primary input for a diverse array of tasks, including clustering, dataset splitting, and virtual screening, yet their evaluation is often limited to downstream model performance on narrow benchmark tasks. We carried out a systematic investigation of the quality of molecular representations, finding that none of the state-of-the-art molecular embedding models capture graph structure, 3D shape, or ADMET endpoint similarity better than fingerprints or physicochemical descriptors. However, classical fingerprints also revealed their own material limitations. For example, we show that depending on the representation, between 225M and $\sim$4B molecules have non-unique representations in the 10.8B Enamine REAL database, with implications for virtual screening. Our findings provide an insight into the current limitations of molecular representations, outlining future research directions for the development of more robust encodings of small molecules.
#04Nov 5, 2026
cs.RO
SHORE: Stability-Hybrid On-Policy Reinforcement Learning for Online Bin Packing
Chang Shi, Ann Majewicz Fey
Online 3D bin packing with a processing buffer requires choosing which box to pack, its orientation, and its placement while keeping the stack stable under unknown future arrivals. A collapse ends the episode and forfeits the remaining volume. Existing methods use geometric rules or hard stability masks, limiting how risk can influence the joint choice of box, orientation, and placement. We propose Stability-Hybrid On-Policy Reinforcement Learning (SHORE), which combines a learned stability probability of a placement with an on-policy estimate of its return conditional on stability. A 3D U-Net learns stability from executed outcomes and simulated alternatives, revealing outcomes of actions underrepresented in early rollouts. A discrete on-policy actor--critic uses stability predictions in both its action values and policy prior, with gates that limit the effect of an untrained or changing model. In deployment, SHORE does not require additional search or simulation overhead. In Isaac Gym, SHORE reaches 73\% space utilization by 0.4M environment steps, while the same learner without stability modeling reaches that level at about 1M. On the expanded 60-box set, SHORE achieves 0.734 space utilization versus 0.588 for the GOPT state-of-the-art baseline, with a higher placement-failure frequency (1.03\% vs. 0.63\%), trading more risk for greater packed volume. The results show faster learning and higher utilization on the more demanding realistic box arrival set. Ablations suggest that simulated alternatives provide useful early supervision, while executed outcomes alone sustain later performance. We also demonstrate the method on a real robot to verify the simplicity of integrating the method to real bin packing pipelines.
#05Nov 5, 2026
cs.LG
User Embeddings are Superpositions of Interpretable Behavioral Modes
Jonathan Kozaczuk, Zheng Dong, Noyan Evirgen and 7 more
User embeddings are central components of modern recommendation, personalization, and behavioral modeling systems. Though these embeddings can compactly encode rich behavioral information, they are inherently dense and opaque, limiting interpretability. To address this gap, we argue that user embeddings can be understood as sparse superpositions of interpretable behavioral modes. This structure is directly predicted by generative models of user behavior for linear embeddings and extends approximately to deep-learning representations by the superposition hypothesis. Superimposed modes can naturally be recovered by sparse dictionary learning methods, such as sparse autoencoders (SAEs), and recovered modes can be automatically named and queried in natural language. We validate mode recovery against known ground truth on synthetic data, where SAEs recover modes better than classical sparse baselines, including on transformer-encoded embeddings. We then apply the method to classical and transformer-based user embeddings from two real-world datasets. We also show how the corresponding natural-language labels enable zero-shot audience retrieval and characterization over embeddings never trained on text. The framework is post-hoc and model-agnostic, requiring no modification to the upstream embedding system.