#01Nov 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.
#02Nov 10, 2026
cs.LG
A Margin Perspective on LoRA: Robustness to Catastrophic Forgetting and Adapter Merging (MaLoRA)
Ziqing Xu, Hancheng Min, Lachlan Ewen MacDonald and 4 more
Low-rank adaptation (LoRA) is the de facto method for parameter-efficient fine-tuning of large neural networks, achieving strong task adaptation with minimal trainable parameters and low optimization cost. Beyond this efficiency, practitioners have observed two striking properties: \textit{robustness to catastrophic forgetting} and the ability to \textit{merge independently trained adapters} into a single model that performs competitively across multiple tasks. These properties are central to continual and multi-task learning, yet remain poorly understood. In this work, we provide a theoretical explanation through a unified \textit{margin-based perspective}. We analyze LoRA in multiclass linear classification under a near-orthogonal task regime with $\ell_2$-regularization, and characterize the optimal LoRA adapter across regularization regimes. Our analysis shows that, in an intermediate regime of regularization parameters, the optimal adapter aligns with the \emph{max-margin solution} on the fine-tuning data. Building on this characterization, we derive two key consequences. First, we obtain closed-form expressions for the margins on pre-training and fine-tuning data, revealing a precise margin trade-off: the regularization parameter controls the balance between retention and adaptation. Second, we analyze adapter merging, proving that merged models achieve positive margin on each task and deriving optimal mixing coefficients that balance margins across tasks and maximize the margin over their union. These results lead to a simple, training-free merging rule, which we term \textit{margin-based LoRA merging} (MaLoRA). Experiments on modern architectures and real datasets validate our theoretical predictions, showing that MaLoRA matches or outperforms several adapter-merging baselines across a range of vision and language classification tasks.
#03Nov 10, 2026
cs.LG
Pyrite: Building and Benchmarking Protein-Ligand Pose Ranking Agents
Megha Srivastava, Michael H. Lim, Allison M. Keys and 2 more
Predicting how a ligand binds to its target is central to small-molecule drug discovery. Modern cofolding models can generate diverse candidate poses, but reliably ranking these candidates remains challenging. We introduce Pyrite, a pairwise pose-ranking benchmark comprising 1,500 pose pairs across diverse protein-ligand complexes. Expert chemists equipped with 3D visualization tools and physics-based scores perform near chance, highlighting the difficulty of interpreting available chemical signals. To investigate automated ranking, we introduce PyriteRep, a structured representation of molecular geometry, protein-ligand interactions, and physicochemical scores, and develop two LLM-based agents: PyriteReasoner, which directly compares poses through text-based reasoning, and PyriteFeaturizer, which generates executable code to construct features for logistic regression, optionally incorporating features derived from LLM subcalls. These agents achieve up to 67% and 74% accuracy, respectively, exceeding observed expert performance. LLM-guided feature discovery generally outperforms direct reasoning, while Group Relative Policy Optimization (GRPO) improves open-weight models, enabling them to match or surpass closed-source frontier models in our evaluations. These results establish Pyrite as a challenging test of pose-ranking ability and highlight LLM-guided feature discovery as a promising approach to interpret and combine the outputs of computational chemistry tools.
#04Nov 10, 2026
cs.LG
Forward-Value Discretization: Faster Stochastic Diffusion Sampling Without High-Order Approximation
Yuchen Jiao, Na Li, Changxiao Cai and 2 more
Stochastic diffusion samplers often require substantially more neural function evaluations (NFEs) than deterministic samplers to achieve comparable sample quality. Although higher-order discretization accelerates deterministic sampling, its benefits for stochastic sampling remains unclear. We establish matching upper and worst-case lower bounds showing that stochastic samplers with higher-order approximations remain first-order convergent, even with exact score functions. Thus, increasing the approximation order does not generally improve the convergence order. Motivated by this limitation, we introduce forward-value discretization, a training-free framework that evaluates the data/noise prediction model at a lookahead estimate constructed from previous predictions. For deterministic sampling, the resulting Forward DPMSolver (F-DPMSolver), improves sample quality at low NFE budgets through its DDIM-based variant, despite remaining first-order convergent. For stochastic sampling, we develop Forward DDPM (F-DDPM), which evaluates the model at a cleaner lookahead point adjusted for subsequent noise injection. This estimate reuses both the previous model prediction and the previously injected noise. Both variants admit first-order convergence guarantees with one model evaluation per iteration. Across CIFAR-10, ImageNet, FFHQ, and LSUN, F-DDPM consistently achieves lower FID than the evaluated stochastic baselines at matched NFE budgets. With 1.5 times as many NFEs as deterministic baselines, it achieves competitive sample quality, narrowing the practical efficiency gap between stochastic and deterministic sampling. Code is available at https://github.com/Na-Li66/F-DDPM.
#05Nov 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.