#01Nov 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.
#02Nov 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.
#03Nov 5, 2026
cs.AI
RM-VLM: From Natural-Language Task Descriptions to Vision-Grounded Reward Machines
Roko Parac, Christos Ziakas, Leo Ardon and 1 more
Reward machines (RMs) have been proposed as a reward formulation in reinforcement learning (RL) to capture non-Markovian tasks where credit assignment depends on history. By representing reward functions as automata, RMs expose the task's temporal structure and allow such rewards to be handled within a Markovian framework. However, they assume a labelling function, a proposition-grounding oracle for observations, which must be manually engineered for each environment, limiting their wider applicability. In this work, we address this limitation by proposing RM-VLM, a novel approach in which a large language model (LLM) generates an RM from a natural-language task description, and a vision-language model (VLM) acts as the labelling function, grounding the RM's propositions over image-based observations during RM-guided policy learning. A VLM-based value function estimator is used to assess the agent's progress towards each RM transition and derive a dense reward signal. We evaluate RM-VLM on three domains covering non-Markovian grid-world navigation, robotic manipulation, and 3D object collection. Our experimental results show that RM-VLM consistently achieves higher task success rates than existing VLM-based reward methods across all tested domains.
#04Nov 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.
#05Nov 5, 2026
cs.LG
XStack: A Benchmark for ML Repo Migration
Linrong Cai, Taiming Lu, Haozhe Chen and 1 more
ML code should run where researchers choose, not where it was first written. Today, machine learning code mainly lives in two ecosystems, PyTorch on NVIDIA GPUs and JAX on Google TPUs. Migrating repositories between them means building and testing across frameworks and hardware. This migration is (1) a practical need, since it unlocks different hardware for researchers, and (2) a natural benchmark: it involves different frameworks and hardware, covers whole repositories, and is long-horizon and challenging. We introduce XStack, a benchmark that evaluates agents on migrating ML repositories between these two ecosystems. Each agent receives a PyTorch repository and a clean TPU machine and must deliver a JAX repository. Its output passes if it meets our grading criteria, based on the source repository's published result, authenticated and calibrated by us. Migration by agents remains unreliable: Claude Opus 5 passes 75%, GPT-5.6-sol 45%, and every other agent at most 40%. XStack is a step toward freeing ML code from its ecosystem. We release XStack to make progress toward reliable migration across frameworks and hardware measurable.