#01Nov 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.
#02Nov 5, 2026
cs.LG
Same Behavior, Different Mechanism: What Finite Experiments Can Certify About Integrated Information
Linqian Wu, Diaoxuan He
Interpretability, AI auditing and assessments of machine consciousness increasingly rest on mechanism-level quantities: functionals of a system's causal transition law that describe how it computes, not what it outputs. Experiments see that law only through finite, partial and noisy interventions. We ask when such a quantity is identifiable from an experiment's access, continuous in the mechanism and certifiable from finite data, and answer exactly for a deliberately demanding case - the integrated information $\varphi$ of integrated information theory - in stochastic networks of four and five units with known ground truth. Behavior can be silent: a recurrent and a feed-forward network with identical input-output laws at their response delay carry 0.28 and 0 bits, yet internal recordings separate them within 4-53 trials. Partial access can be just as blind: in our examples, units left out of a one-step recording impose precision floors of 0.30-1.02 bits that no sample size lowers, and in all-but-self parity networks, recordings of any length see several hidden units only through the product of their fidelities - a symmetry that one intervention broke in exact checks. The measure has sharp edges: because $\varphi$ selects a partition, and the cause and effect it specifies, by one criterion and reports another, infinitesimal changes of mechanism that cross an edge change it by 25-100% at 99% of the edges we found in random networks, and about 1% of surrogate models that fit interventional data almost perfectly misreport it by more than 20%. One-sided claims survive: the same data certify a lower bound on both sides of an edge, and we prove $\varphi>1.004$ bits throughout a 64-dimensional region of mechanisms and certify it from about $10^7$ controlled transitions with false-certificate probability at most $α$. Measurability is thus a design question with computable answers.
#03Nov 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.
#04Nov 5, 2026
cs.AI
Benchmarks as Software: Terminal-Bench and the Case for Continuous Benchmarks
E. Kelly Buchanan, Crystal Zhou, Scott W. Linderman and 1 more
Coding agents are among the most economically consequential deployments of LLMs to date, making reliable evaluation increasingly important. Yet even benchmarks that are carefully validated at release can become stale. As models improve, they can discover valid solutions that existing verifiers reject, while changes to evaluation infrastructure can invalidate assumptions embedded in tasks and tests. We call the resulting accumulation of defects benchmark maintenance debt: a growing gap between benchmark scores and the capabilities they are intended to measure. We introduce a continuous-validation workflow for agentic benchmarks that combines community reports, task artifacts, agent traces, automated oracle checks, and human-gated repairs. We apply this workflow to Terminal-Bench 2.0, a benchmark that underwent extensive human and LM-assisted review and red-teaming before release. Our audit identifies issues in roughly 30% of the benchmark, and we release the resulting repairs as Terminal-Bench 2.1. These repairs change evaluation results: accuracy increased by over 10 percentage points and leaderboard positions move by up to three ranks, even as the overall ranking remains highly correlated (Spearman rho = 0.958). We evaluate how resource allocation shapes benchmark conclusions. We show that fixed wall-clock can materially change agent performance: For example, extending the time limit closes a 20pp harness gap on GPT 5.4 and shrinks a 30 pp gap on GPT 5.4 mini to 5 pp. Benchmark maintenance is therefore not only about repairing task artifacts: resource budgets are part of the measurement specification and must be validated alongside the tasks themselves. More broadly, benchmark maintenance debt is not just accumulated implementation bugs: our results show that as models improve, both evaluation assumptions and resource settings may need to be revalidated.
#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.