#01Nov 10, 2026
cs.LG
Emergent Biological Capabilities in a Foundation Model for Molecular Interactions
Adi Mashiach
Foundation models trained on large unlabeled corpora develop emergent capabilities, tasks that go beyond the training objective. We extend this paradigm to multimodal biology with Bonbon, a foundation model for molecular interactions trained on approximately 3.2 trillion tokens of paired protein-ligand sequences. From a single representation space, Bonbon exhibits three zero-shot emergent capabilities at hierarchical levels of resolution: functional (mechanism of action), residue (binding site localization, including orthosteric/allosteric discrimination), and bond (covalent versus non-covalent engagement). All three capabilities generalize to out-of-distribution complexes. Bonbon was trained on protein-ligand sequences alone, without any task-specific supervision and without structural coordinates. We conducted controlled scaling experiments across six model scales from 42M to 1.6B parameters; every capability evaluated shows a sharp jump at the largest scale on continuous metrics, even as pretraining loss decreases smoothly. This demonstrates that loss-based scaling laws alone are insufficient to predict when zero-shot emergent capabilities become available. The capabilities reported here emerge after training at a 1:2,000 parameter-to-token ratio to accommodate the sparsity of paired biological interaction data. The same frozen representations achieve state-of-the-art binding and affinity prediction at five orders of magnitude greater speed than co-folding methods. In prospective wet-lab validation across nine disease targets spanning seven protein families, Bonbon achieves a 61.5% dose-response hit rate on de novo compounds, yielding structurally novel molecules not previously reported to inhibit these proteins, including for out-of-distribution targets.
#02Nov 10, 2026
cs.LG
AutoScaffold: AI-Guided Scaffolding for Reinforcement Learning of Language Models
Zijian Zhang, Rizhen Hu, Jiangweizhi Peng and 4 more
Reinforcement learning with verifiable rewards (RLVR) produces rich training experience, yet outcome rewards reduce each attempt to a single number and leave most of this information unused. Training-time scaffolds, such as strategies or hints added to the prompt during training, offer a natural way to turn this information into guidance, but their design and adaptation are largely left to humans and tailored to specific domains. We introduce AutoScaffold, a unified AI-for-AI framework that turns a student's training experience into adaptive scaffolds, with minimal domain-specific information and no human intervention during training. A frozen teacher periodically examines this experience, diagnoses bottlenecks, and designs scaffolds in two forms: (i) strategies shared across a class of tasks and (ii) hints for individual hard tasks, adjusting the content and amount of support as the student learns. The scaffolds are removed at evaluation. We apply the same framework to ALFWorld, search-based QA, mathematical reasoning, and GPU kernel generation. When evaluated without scaffolds, students trained with AutoScaffold outperform those trained with the corresponding RL baselines in all four domains, with gains of 7.2 points in ALFWorld success and 4.0 points in average QA exact match. On GPU kernel generation, AutoScaffold increases the fraction of tasks with a correct kernel that runs faster than the PyTorch reference by up to 5.0 points. On math, our student surpasses QuestA's reported accuracy using approximately one-third as many student training steps. Analyses show that the teacher identifies a different failure in each task class and shifts its scaffolds from step-by-step workflows to targeted fixes as the student improves, and that its revised scaffolds help the student learn more than keeping the previous scaffold or using no scaffold.
#03Nov 10, 2026
cs.CV
UGG: Unified Generative Geometry Model
Amani Kiruga, Zhiyi Li, Ruojin Cai and 4 more
Understanding 4D scenes is a core challenge in visual intelligence, requiring models to jointly capture scene geometry, appearance, and dynamics from partial observations. However, existing approaches are subdivided into feedforward models for direct geometric prediction, and generative models for visual synthesis. We introduce UGG, a unified framework for 4D scene understanding that jointly models RGB video and geometric representations such as depth and camera pose. By assigning different noise levels across modalities and time, UGG formulates visual generation and geometric prediction as conditional completion within a single generative model. This flexible formulation enables the model to learn from diverse, heterogeneous datasets with different subsets of geometric and visual annotations. Furthermore, our generative formulation enables inference-time search over multiple plausible scene hypotheses, using geometric evidence extracted from observed RGB frames to improve geometric prediction without ground truth geometry. We demonstrate UGG's effectiveness over non-unified baselines across camera-controlled video generation, depth estimation, and camera pose prediction, including in challenging sparse observation settings. Code and visualizations are available at https://ugg-model.github.io/
#04Nov 10, 2026
cs.LG
A Theory of Policy Optimization in Post-Training: Coverage Collapse and Reference Resets
Audrey Huang, Nan Jiang, Sham M. Kakade and 3 more
Policy optimization is central to language model post-training, yet principled guidance remains limited. We revisit its theoretical foundations to identify algorithms that learn near-optimal policies using total samples and gradient steps governed by the base model's response coverage, a measure of how readily it generates optimal responses. We call such algorithms coverage-preserving. This guarantee captures the goal of amplifying capabilities accessible through sampling from the base model. (1) Coverage collapse. REINFORCE, the basis for PPO and GRPO, can drive the probability of optimal responses to near zero, even as reward improves. This coverage collapse stalls optimization, and convergence can require exponentially many steps despite good initial coverage. The failure arises even with exact gradients and persists under KL regularization to the base model. (2) Reference resets. We show that repeatedly resetting the KL reference to the most recent policy mitigates coverage collapse. We formalize this intervention in Approximate Policy Mirror Descent (APMD), a meta-algorithm that approximately solves a sequence of KL-regularized RL subproblems. APMD enables stronger regularization, making each subproblem easier to solve, while reference resets allow convergence to global optimality. (3) Coverage-preserving algorithms. For softmax linear policies over pretrained features, we use APMD to establish the first global convergence guarantees showing that widely used families of post-training algorithms are coverage-preserving. These include stylized PPO and GRPO variants with explicit KL regularization and reference resets, and squared-loss algorithms that implement them implicitly, including those used to train the Kimi models. These results clarify how regularization, clipping, and objective choice affect the sampling and optimization costs of post-training.
#05Nov 10, 2026
stat.ML
A Theory of Cross-Validation Variance
Nathaniel S. O'Connell, Jaime L. Speiser
Cross-validation estimates predictive performance by repeatedly splitting the data into training and validation sets, fitting the model on the first and evaluating it on the second. Every observation influences the estimate in two roles, through its own evaluation when it is held out and through the models it helps fit when it trains. The random splits determine its weight in each role. From this representation, we prove an exact finite-sample identity for the variance of the cross-validated estimate. For a given splitting scheme with a common training set size, the variance is a function of these weights, with constants of the model, the metric, and the population. It covers metrics averaged over observations, such as mean squared error, and over case--control pairs, such as the AUC. The identity shows which schemes to use. The variance decomposes into sampling variance, which depends only on the training size, and variance due to the random fold splitting, which arises when the weights change from one draw of the splits to the next. K-fold cross-validation, whose weights are equal across observations by design, is therefore variance optimal at first order; Monte Carlo and bootstrap cross-validation are not. The first-order variance of K-fold does not depend on K, and under reasonable conditions on the model leave-one-out has the smallest variance of any K-fold scheme. For the AUC the same holds for leave-pair-out, which evaluates every case--control pair. Finally, we show the cross-validated estimate is asymptotically normal with the identity's full variance. Together, these results provide a general theoretical foundation for inference on cross-validated performance and establish principles for selecting variance-optimal cross-validation designs.