#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
cs.LG
Spectral and Subspace Dynamics of LoRA in Supervised Fine-Tuning and Reinforcement Learning
Chenruo Liu, Zihan Wang, Yijun Dong and 1 more
Low-rank adaptation (LoRA) is commonly used in both supervised fine-tuning (SFT) and reinforcement learning (RL), often under similar optimizer settings. Yet, how the different dynamics of the two stages manifest in the low-rank increment that LoRA optimizes remains unclear. Tracking the singular spectrum and subspaces of LoRA updates on mathematical reasoning tasks, we find that RL concentrates the spectrum at every learning rate, while SFT expands it at moderate learning rates; moreover, RL rotates the singular subspaces much faster than SFT at small learning rates. Interpolating between SFT and RL one ingredient at a time, we pinpoint group-mean baseline subtraction as the source of both contrasts. A quadratic multi-index model updated via LoRA unveils the underlying mechanism: group-mean baseline subtraction tilts the balance between two competing forces, coherent fitting and gradient noise, toward spectral concentration and faster subspace rotation, while forcing the risk-favorable learning rate to be low. Guided by these dynamics, we tailor LoRA updates to each stage: in SFT, we flatten the spectrum of the full update to spread adaptation across singular directions, whereas in RL, we flatten the part of the update outside the current LoRA increment span to promote subspace rotation. Experiments on mathematical reasoning tasks across multiple models show that the respective configurations for SFT and RL yield the best performance among the compared methods in most evaluated settings.
#03Nov 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.
#04Nov 5, 2026
cs.CL
Label-Wording Augmentation in a Typed-Decision Encoder: Gains on Unfamiliar Words, Not on Abbreviations or Codes
Vladimir Beskorovainyi
Typed-decision models score options that the caller supplies at request time, so their accuracy depends on label wording that the model's developer does not control. We compare two releases of a 307M-parameter multilingual cross-encoder, Ru-Jev, trained on thirteen Russian-language tasks; the later release adds an augmentation that presents labels in several surface forms. Holding questions fixed and varying only how eighteen routing labels are worded, we evaluate ten label vocabularies, produced by three separate processes and checked for overlap with the training data, with five candidates per question and, for eight of them, also with eighteen. On held-out vocabularies made of ordinary or borrowed words (English-derived jargon, office slang, department names), the augmented release is more accurate in every setting, by up to 0.24. Eleven of these fourteen gains survive a Holm correction (slang with eighteen candidates and descriptive sentences with five do not), and for jargon on all labels the label-level interval excludes zero in both settings. On abbreviations and opaque codes it gives no usable gain: on abbreviations it is not better, and worse on the clean slice, and on opaque codes both releases stay at or below chance once labels related to training options are removed. In most cells where accuracy rises, the risk-coverage area falls, but with eighteen candidates confident errors rise on jargon and slang. On two datasets neither release saw, accuracy moves by -8.4 and +5.6 points. We also report four evaluation hazards from comparing the two releases.
#05Nov 5, 2026
cs.LG
Conformal Prediction for Time-Dependent PDEs
Joshua Stiller, Annika Schneider, Eyke Hüllermeier
Uncertainty quantification is crucial in scientific machine learning, where models inform safety-critical tasks such as flood forecasting, financial risk management, and thermal control in machines. Conformal prediction provides distribution-free coverage guarantees, but in time-dependent settings common to physics and engineering, these guarantees can break down, leading to systematic undercoverage. We study this problem in the context of surrogate models for time-dependent physical systems described by partial differential equations. We prove that in a function space setting, distributions at arbitrarily close times can be mutually singular, making exact coverage guarantees impossible. We further show that in discretized settings, the total variation distance between distributions often saturates exponentially fast with the grid resolution, mandating restrictions on the spatial discretization to ensure coverage. Finally, for certain settings, we show how to use principled weighted conformal prediction to obtain finite-sample coverage guarantees over growing time horizons.