#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.AI
Learning a patient world model for health system simulation in intensive care
Yingtai Li, Ruoyan Wang, Yu Li and 1 more
Designing healthcare strategies requires anticipating their clinical and operational consequences before implementation, a task that often relies on health system simulation. Such a simulation necessitates modeling how patient states evolve and generate care demands. However, conventional approaches typically tailor compact state transitions to a single policy question and omit history-dependent dynamics, thus requiring the redefinition of states and transitions when there is a new question that entails different clinical information. We propose to learn a patient world model from longitudinal EHRs using a neural network to provide a shared clinical representation of patient trajectories that can serve simulation questions across scenarios. Taking ICU operations as an example, we train the model on MIMIC-IV, freeze it, and couple its time-queryable predictions to shared ICU calendars, resources, and queues via scenario-specific mappings, so that one model renders admission demand, care tasks, and discharge proposals across simulations evaluating ICU bed capacity, care dispatch, and post-ICU transfer capacity. Experiments show that our model matches Markov and semi-Markov comparators in aggregate occupancy and directional responses to capacity and dispatch policies. It also reproduces policy gains from replayed observed trajectories. For patients entering the same support state from different prior trajectories, the learned representation captures a 24-h recovery difference (-6.4 predicted versus -6.7 observed percentage points), a contrast missed by compact state models, which propagates into distinct simulated care demand, queue burden, and bed use. These results indicate that a learned world model of patient dynamics has the potential to replace question-specific state models, allowing new care policies to be evaluated by reconfiguring the scenario without model rebuilding.
#03Nov 5, 2026
cs.RO
Social Humanoid: Socially Responsive Human-Humanoid Interaction
Vongani H. Maluleke, James Ni, Kie Horiuchi and 7 more
Humanoid robots are typically trained as solitary agents, leaving them unable to coordinate physically with human partners who naturally anticipate and adjust to one another. To bridge this gap, we present Social Humanoid, a hierarchical system that generates and executes socially responsive whole-body motion on a 29-DoF Unitree G1 conditioned on a human partner's motion. Its high-level policy performs flexible sequence modeling of human and humanoid motion through a shared tokenized representation, generating reactive humanoid motion and anticipating the partner's motion when they are occluded, while a low-level whole-body tracking controller executes the generated motion on the robot. To train the system, we introduce a two-phase adaptive retargeting procedure that retargets one interaction partner to the robot while morphing the other partner to preserve contact dynamics, reachability, and relative body scale. We apply this procedure across five motion-capture datasets to produce a new Human-Humanoid Interaction (HHI) benchmark of 260 hours of human-humanoid interactions. Our results demonstrate that Social Humanoid produces coordinated, human-aligned behavior across diverse interaction types in simulation and the real world. Project page: https://von31.github.io/social-humanoid/
#04Nov 5, 2026
cs.AI
ReproBridge: Building Reproducibility into ML Research Artifacts
Yubo Wang, Rui Meng, Jaehyun Nam and 2 more
Reproducing machine learning experiments requires reconstructing procedures from information scattered across papers, released code, and supporting artifacts. For coding agents, reproduction success can therefore depend on their ability to fill in missing details, rather than on the released artifacts alone. We ask whether preserving recovered procedures and decisions improves subsequent independent reproduction. We define a standardized artifact design comprising a refined codebase, environment setup, experiment launchers, and a reproduction guide, and introduce ReproBridge, an agent workflow for constructing these refined reproducible artifacts. ReproBridge-Bench provides 1,029 tasks from 387 experiments across 36 papers, anchored by five human-verified reference scores per task. Agents attempt tasks in fresh sessions with raw code or refined artifacts; a separate Auditor checks execution evidence. Across four evaluated models, refined artifacts raise mean reproduction success from 76.4% to 92.6% and reduce downstream API spending by 19.7% on average. The cross-model success-rate spread narrows from 21.6 to 3.9 percentage points, with all four models achieving mean success rates above 90%. Removing any component reduces success in the ablation study, with the largest losses from code and environment removal. These results suggest that preserving execution knowledge helps even models with lower raw-code success reproduce experiments more reliably and at lower API cost.
#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.