#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
math.ST
Nonparametric Maximum Likelihood Estimation for Mixtures of Logistic Regressions
Muheng Li, Peize Zhang, Xin Bing
Mixtures of logistic regressions provide a flexible framework for modeling binary responses, extending standard logistic regression to accommodate unobserved heterogeneity while retaining an interpretable regression structure. In this paper, we study such models with an unspecified mixing distribution. We analyze a sieve nonparametric maximum likelihood estimator (NPMLE) and derive nonasymptotic bounds on the estimation error of the resulting mixture regression function under both fixed and random designs. Our results reveal an explicit tradeoff between statistical estimation error and the approximation error induced by the sieve radius, from which we derive convergence rates under several tail conditions on the mixing distribution. For computation, we propose a finite-particle algorithm that approximates the sieve NPMLE by optimizing the locations and weights of a finitely supported mixing distribution. The method offers numerical advantages over existing algorithms and comes with rigorous convergence guarantees. For any fixed dataset, we establish global convergence of the likelihood to the restricted NPMLE value when the number of particles exceeds a finite threshold. When the true mixing distribution is finitely supported, we further establish uniform global convergence guarantees and derive error bounds that separate algorithmic and statistical errors. Our analysis also yields a denoising bound for the mixing distribution and an identifiability result that complements existing results in the literature.
#03Nov 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.
#04Nov 10, 2026
cs.CL
Pterodactyl: Pushing the Limits of Efficient Automated Translation Evaluation
Evelyn Y. Garland, Carola F. Berger
In this paper, we present 1020 Group's submission to the WMT26 shared task on automated quality evaluation. Our system, Pterodactyl, was engineered specifically for subtasks 2 and 3, that is, segment-level quality score prediction and the detection of error-free segments. Pterodactyl is a highly customizable, ultra-low cost system optimized for binary classification in translation triage and data curation. It is based on an LLM-as-a-judge approach, with prompt engineering and model selection guided by ROC analysis. We also developed several variants of Pterodactyl that were specifically adapted for subtasks 3.
#05Nov 10, 2026
cs.LG
TorchCurves: Differentiable Parametric Curves
Alex Shtoff
We present TorchCurves, a PyTorch library that treats vector-valued parametric curves as learnable primitives. Its central operation maps batches of scalar inputs to points on curves represented in B-spline or Legendre polynomial bases, with differentiation through both inputs and coefficients. Curve coefficients can be optimized jointly with the surrounding model or produced by another network. The library provides trainable modules, reusable basis modules, and a functional interface, supporting applications ranging from continuous feature embeddings to Kolmogorov-Arnold networks and functional regression. Its implementation combines classical evaluation algorithms with vectorized PyTorch operations, emphasizing readability and maintainability without custom hardware kernels. Timing experiments compare curve evaluation against NumPy and SciPy and KAN training against EfficientKAN across a range of problem sizes. The results illustrate where this generality remains computationally practical and where overhead is substantial. Library is available on GitHub at https://github.com/alexshtf/torchcurves.