#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
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.
#03Nov 5, 2026
cs.RO
Failure Prediction and Classification in Vision-Language-Action Models Via Calibrated Latent Probing
Michal P. Podolinsky, Yunhao Yang, Daniel Little and 6 more
Vision-Language-Action models (VLAs) enable general-purpose embodied intelligence, but their performance is brittle under distribution shift, where unanticipated failures can damage equipment or endanger people. Deploying VLAs in real-world systems therefore requires a runtime monitor that is timely, calibrated, and informative while being efficient enough to run on the edge. Existing methods fail to fulfill these requirements. We present VLA-Tug, a lightweight probe over the latent layers of a VLA backbone that improves early failure detection and bounds the missed-detection and false-alarm rates, with minimal inference overhead. We show that supervising on the pre-failure segment of a trajectory increases early failure detection at matched false-positive rates by up to 30% over the strongest learned baseline. Under shift to unseen tasks, the bounds on missed-detection and false-alarm rates remain valid in up to 86% of runs, versus at most 21% for baselines. Unlike existing methods, VLA-Tug predicts the failure mode to enable corrective actions, raising top-3 accuracy on unseen tasks by up to 44% over a majority baseline. VLA-Tug enables real-time monitoring where the well-timed and informative probe supports lightweight steering that improves task success. We release a dataset of 3,180 annotated manipulation episodes to support future work on latent failure detection in VLAs at https://vla-tug.github.io.
#04Nov 5, 2026
cs.LG
Hybrid Machine Learning for Imbalanced Landing-Phase Safety Event Prediction from Flight Data
Taha Asghar, Bilal Mufti, Syed Qasim Zaheer and 1 more
Landing-phase safety-event prediction requires the detection of rare abnormal approaches within strongly imbalanced multivariate flight data. Capturing coupled temporal behavior while distinguishing event-specific signatures across airport operating contexts remains a central modeling challenge. This study proposes an interpretable hybrid feature-fusion framework for multiclass landing-phase safety-event prediction. A long short-term memory (LSTM) autoencoder trained on nominal flight windows characterizes deviations from routine approach behavior. Its continuous reconstruction-error descriptor is fused with parameter-specific statistical flight-history features and supplied to a class-weighted XGBoost classifier to distinguish Normal, Speed High, Path High, and Flaps Late windows. The framework is evaluated using 53,750 NASA DASHlink approach windows from three arrival airports. Pooled and airport-specific learning strategies are compared alongside component-level benchmarks, repeated pipeline retraining, and feature-attribution analysis. The results demonstrate strong class-balanced detection, with mean macro recall above 0.90 across all airports under repeated partitioning and retraining. Component comparisons establish the importance of class weighting and show that continuous feature fusion outperforms reconstruction-error-only and hard-gate alternatives. Airport-level comparisons reveal benefits from local specialization at the two airports with larger datasets and from pooled training at the airport with the smallest dataset. Feature attributions associate predictions with operationally relevant vertical-path, configuration, speed, and approach-context variables. The framework provides an interpretable approach to rare-event detection and practical guidance for adapting flight-data monitoring models to airport-level data availability.
#05Nov 5, 2026
cs.LG
Towards interpreting any residual stream direction by scaling activation inversion
Celeste De Schamphelaere, Juan J. Vazquez, Ari Spiesberger and 4 more
To interpret a direction in a language model's residual stream, we can look for text that strongly activates it. But when such text is found by scanning a corpus, it is limited to what that corpus contains. We develop Maximally-Activating Example Metamodels (MAEMs), language models which map residual stream directions from a subject model to text exemplars that strongly activate those directions. Our objective is to maximise the cosine similarity of a supplied residual stream direction with the activations of the text generated by the MAEM. This label-free RL objective helps to scale MAEMs on diverse sources of residual stream directions. Empirically, we find the resultant metamodel produces informative exemplars: a Qwen3.6-27B MAEM inverts held-out activations better than corpus search or a natural-language autoencoder (NLA), beats corpus search (at 10M tokens) on a majority of held-out languages/domains, and activates 89% of held-out SAE features. It also identifies concepts behind steering vectors about as well as NLAs, recovers the payloads of LoRA backdoors more often than corpus search, and can even verbalise some model workspace inner monologue. Unlike explanations produced by other metamodels (e.g. NLAs), MAEM exemplars can be verified with a forward pass on the subject model, making the MAEM objective a grounded alternative for scaling the training of metamodels.