#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.RO
One Policy for 100 Household Tasks: Our Solution for the 2026 BEHAVIOR Challenge
Ilia Larchenko, Gleb Zarin, Atindra Nair and 4 more
We describe our solution for the 2026 BEHAVIOR Challenge: 100 long-horizon household tasks in the OmniGibson simulator. We placed 9th on the final leaderboard, the only independent team in the top 10. The core of the solution is a single vision-language-action (VLA) model, one checkpoint for all 100 tasks, built on our 1st-place 2025 solution, which is based on $π_{0.5}$. On the 50 tasks shared with 2025, its Q rises from 0.260 to 0.371; across all 100 tasks it scores 0.392. Our main conclusion from 2025 was that the model was undertrained, so most of the 2026 work went into training the model for longer, optimizing some training parameters, making each training step slightly faster and reducing the gradient noise: a migration from 50 to 100 tasks (semantic stages built from the demonstrations' skill annotations, task and stage embeddings of new tasks warm-started from similar old ones, and a 21-dimensional action space matching the teleoperation controls); variance-reduced multi-sample flow matching with a simple noise-vs-compute model that picks the number of action-expert samples per observation without ablations; and a 200k-step training run, about one pass over the 211M frames of the demonstrations. A cloud evaluation infrastructure keeps a shared record with provenance, episode diagnostics and restorable simulator states, and runs six simulators on one GPU together faster than real time. On top of the learned policy, 14 tasks are routed to a GPT-6 Astra coding agent that controls the robot through observation and motion tools, starting every episode from a frozen copy of its own practice session on training instances. Across these 14 tasks, Astra's mean Q is 0.639, against 0.108 for the learned policy. The public submission included only part of the Astra results and scored 0.446 Q with 27.3% full-task success.
#03Nov 10, 2026
cs.LG
TimeSeek: Multi-Task and Multi-Domain Pretraining for Generalized Time Series Analytics
Peng Chen, Yihang Wang, Zhongwen Rao and 6 more
Time series analytics has been widely applied across various domains. While existing time series foundation models (TSFMs) have demonstrated promising results, they still face two major challenges: 1) Most TSFMs mainly rely on stacking Transformer layers to increase parameter size, lacking the ability to adaptively model complex time series patterns from multi-domain data. 2) Current TSFMs are primarily pre-trained for specific tasks, e.g., forecasting or anomaly detection, and a few models support multiple tasks, but they fail to fully leverage task specificity and commonality, resulting in suboptimal performance. To address these challenges, we propose TimeSeek, a novel generalized time series analytics model that adaptively models time series patterns from multi-domain data and unifies multiple tasks in pre-training. Conceptually, TimeSeek is guided by selective information sharing under domain and task heterogeneity. From the perspective of multi-domain data, we propose a Multi-Domain Feature Extractor that adaptively captures temporal dependencies and channel correlations based on domain-specific characteristics, including progressive multi-scale modeling and adaptive slot channel modeling. From the perspective of the diversity of tasks, we propose multi-task collaborative training, which leverages task specificity and task commonality through task customization and cross-task training, effectively unifying multiple tasks in pre-training and better adapting to diverse downstream scenarios. After pre-training on large-scale time series data, TimeSeek achieves state-of-the-art performance in forecasting, anomaly detection, and classification tasks across both few-shot learning and zero-shot situations, together with favorable inference efficiency.
#04Nov 10, 2026
cs.AI
An Energy-Based Perspective on Machine Learning
Bo Dai, Yilun Du
Energy-based models (EBMs) define a distribution through a scalar energy, $p_θ(x)\propto\exp(-E_θ(x))$, and are usually presented as one model family among many. This tutorial has a broader goal: beyond introducing EBMs, it uses them as a single lens that connects the different aspects of machine learning. Any EBM is specified by three choices, the energy, which determines what the model represents; the inference procedure, which samples from or optimizes the energy; and the learning method, which fits the energy to data. We first develop these components, including sampling, variational inference, and learning by maximum likelihood, noise contrastive estimation, pseudolikelihood, score matching, and adversarial training, and show that the learning methods share one contrastive structure. We then show that discriminative models, generative models such as GANs, normalizing flows, diffusion and autoregressive models, representation learning methods such as contrastive learning, word2vec, BERT, denoising auto-encoders, and diffusion representations, reinforcement learning with EBM policies and world models, inverse reinforcement learning, and planning, as well as inference-time computation with verifiers, are all EBMs that differ in these three choices, mostly in how they handle the partition function and sampling. This view explains existing methods, organizes them into a common framework, and suggests new algorithms by replacing one component while keeping the others, with composition of energies as a principled way to combine learned models at inference time.
#05Nov 10, 2026
cs.LG
Discovering Equations for the Thermodynamics of South Asian Monsoon Precipitation
Savannah L. Ferretti, Jane W. Baldwin, Michael S. Pritchard and 1 more
South Asian monsoon precipitation depends on the thermodynamic structure of the lower troposphere, but how its ingredients combine to shape precipitation remains unclear, partly because this dependence is nonlocal in the vertical. We use symbolic distillation, which combines neural networks and symbolic regression, to discover interpretable precipitation equations from 21 years of June-August reanalysis data. Neural networks first learn the vertical thermodynamic structure most relevant to precipitation, condensing each variable into a single interpretable feature not tied to a particular vertical grid. Then, symbolic regression derives closed-form equations from these features and the surface state. Our best equation explains 1.5 times as much precipitation variance as a widely used buoyancy-based diagnostic and recovers about 85% of neural network skill while using about a thousand times fewer parameters. Unlike the buoyancy diagnostic, which adds moisture and instability, the equations treat them as competing controls, with the heaviest precipitation occurring when the lower free troposphere is humid. Over ocean, sensible heating is associated with additional precipitation mainly when near-surface air is warm and moist, improving predicted precipitation and its diurnal cycle. Although the learned features were optimized only for precipitation prediction, the equations largely respond to each feature as expected from convective physics, consistent with the reanalysis. These responses reduce the dependence of monsoon precipitation on the entire vertical column to a few simple, testable constraints that could guide data-driven precipitation models to make them more physically consistent.