#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
Unpacking the Compute Efficiency of Strong-to-Weak OPD against GRPO
Zeyu Leo Liu, Yang Li, Bo Pang and 7 more
On-policy distillation (OPD) trains a student on its own rollouts under a frozen teacher's per-token supervision. Does this dense signal reduce the training FLOPs needed to reach a target accuracy compared with reinforcement learning? We systematically compare vanilla reverse-KL OPD with Group Relative Policy Optimization (GRPO) across task difficulty, student and teacher size, domain, and optimization choices, measuring held-out accuracy against training FLOPs. With an external post-trained teacher, OPD generally loses to GRPO in accuracy per training FLOP at matched settings, even when the teacher is further trained with GRPO, and often suffers response-length inflation. Yet a different teacher changes the picture: when the teacher is the student's own GRPO checkpoint, OPD recovers that checkpoint's accuracy on math with $50\times$ fewer distillation FLOPs than GRPO needs to reach the same accuracy. Following the same teacher setting, we consistently observe this high efficiency with a larger student, on code, and in a second model family. On a single domain, however, the GRPO checkpoint is already the desired model, so distilling it adds to total compute. Across domains, separate GRPO checkpoints hold different capabilities, and no single checkpoint serves every domain. Multi-teacher OPD (DeepSeek-AI, 2026) consolidates per-domain GRPO experts into a single student that matches each expert's accuracy, with the distillation stage costing only 5.2% (on 2 domains) and 8.0% (on 4 domains) of the specialist training FLOPs. Counting specialist training and distillation together, this pipeline reaches joint GRPO's performance on the 2-domain mix with 42.0% fewer total FLOPs.
#03Nov 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.
#04Nov 5, 2026
cs.LG
Adversarial Training with Large Step Sizes: Implicit Bias, Optimization, and Sharpness
Yi Feng, Andrea Paudice
Adversarial Training (AT) is an important method for improving model robustness. We study the dynamics of deterministic Gradient Descent (GD) in AT. Most existing works in this direction focus on the small or vanishing step sizes regime, where GD resembles a continuous-time flow. However, such step sizes can make training inefficient and are rarely used in practice. In this paper, we study the AT dynamics of GD with large constant step sizes. We first study GD in adversarial linear logistic regression, focusing on two aspects: where the model parameters converge (implicit bias) and how quickly the losses decrease (optimization). We then turn to neural networks training and study how the sharpness of losses evolve during AT. Our results advance the understanding of the behaviors of GD with large step sizes in AT and highlight three key differences from its behavior in Standard Training (ST): (i) the implicit bias gap between AT and ST, previously established only for small step sizes, persists for arbitrarily large constant step sizes, (ii) different from ST, there is no uniform rate of convergence for the optimization error in AT, and (iii) sharpness can exhibit two-stage dynamics that differ from the Edge-of-Stability behavior observed in ST.
#05Nov 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.