Dynamic neural networks toolkits such as PyTorch, DyNet, and Chainer offer more flexibility for implementing models that cope with data of varying dimensions and structure, relative to toolkits that operate on statically declared computations (e.g., TensorFlow, CNTK, and Theano). However, existing toolkits - both static and dynamic - require that the developer organize the computations into the batches necessary for exploiting high-performance data-parallel algorithms and hardware. This batching task is generally difficult, but it becomes a major hurdle as architectures become complex. In this paper, we present an algorithm, and its implementation in the DyNet toolkit, for automatically batching operations. Developers simply write minibatch computations as aggregations of single instance computations, and the batching algorithm seamlessly executes them, on the fly, in computationally efficient batches. On a variety of tasks, we obtain throughput similar to manual batches, as well as comparable speedups over single-instance learning on architectures that are impractical to batch manually.

Gaussian Process bandit optimization has emerged as a powerful tool for optimizing noisy black box functions. One example in machine learning is hyper-parameter optimization where each evaluation of the target function may require training a model which may involve days or even weeks of computation. Most methods for this so-called "Bayesian optimization" only allow sequential exploration of the parameter space. However, it is often desirable to propose batches or sets of parameter values to explore simultaneously, especially when there are large parallel processing facilities at our disposal. Batch methods require modeling the interaction between the different evaluations in the batch, which can be expensive in complex scenarios. In this paper, we propose a new approach for parallelizing Bayesian optimization by modeling the diversity of a batch via Determinantal point processes (DPPs) whose kernels are learned automatically. This allows us to generalize a previous result as well as prove better regret bounds based on DPP sampling. Our experiments on a variety of synthetic and real-world robotics and hyper-parameter optimization tasks indicate that our DPP-based methods, especially those based on DPP sampling, outperform state-of-the-art methods.

We introduce Dataset Grouper, a library to create large-scale group-structured (e.g., federated) datasets, enabling federated learning simulation at the scale of foundation models. This library facilitates the creation of group-structured versions of existing datasets based on user-specified partitions, and directly leads to a variety of useful heterogeneous datasets that can be plugged into existing software frameworks. Dataset Grouper offers three key advantages. First, it scales to settings where even a single group's dataset is too large to fit in memory. Second, it provides flexibility, both in choosing the base (non-partitioned) dataset and in defining partitions.

The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that generate independent samples from complex molecular distributions, eliminating the cost of sampling rare transition events. However, a sampling problem remains when computing observables that rely on states which are rare in equilibrium, for example folding free energies. Here, we introduce enhanced diffusion sampling, enabling efficient exploration of rare-event regions while preserving unbiased thermodynamic estimators. The key idea is to perform quantitatively accurate steering protocols to generate biased ensembles and subsequently recover equilibrium statistics via exact reweighting. We instantiate our framework in three algorithms: UmbrellaDiff (umbrella sampling with diffusion models), $Δ$G-Diff (free-energy differences via tilted ensembles), and MetaDiff (a batchwise analogue for metadynamics). Across toy systems, protein folding landscapes and folding free energies, our methods achieve fast, accurate, and scalable estimation of equilibrium properties within GPU-minutes to hours per system -- closing the rare-event sampling gap that remained after the advent of diffusion-model equilibrium samplers.

Adapting to dynamic data distributions is a practical yet challenging task.

However, it was recently shown that gradient inversion attacks can reconstruct this data from the shared gradients.