We show that deep ensembles become equivariant for all inputs and at all training times by simply using data augmentation. Crucially, equivariance holds off-manifold and for any architecture in the infinite width limit. The equivariance is emergent in the sense that predictions of individual ensemble members are not equivariant but their collective prediction is. Neural tangent kernel theory is used to derive this result and we verify our theoretical insights using detailed numerical experiments.

Self-supervised learning (SSL) has gained increasing attention in the graph learning community, owing to its capability of enabling powerful models pre-trained on large unlabeled graphs for general purposes, facilitating quick adaptation to specific domains. Though promising, existing graph SSL frameworks often struggle to capture both high-level abstract features and fine-grained features simultaneously, leading to sub-optimal generalization abilities across different downstream tasks. To bridge this gap, we present Multi-granularity Graph Semantic Ensemble via Knowledge Distillation, namely MGSE, a plug-and-play graph knowledge distillation framework that can be applied to any existing graph SSL framework to enhance its performance by incorporating the concept of multi-granularity. Specifically, MGSE captures multi-granular knowledge by employing multiple student models to learn from a single teacher model, conditioned by probability distributions with different granularities. We apply it to six state-of-the-art graph SSL frameworks and evaluate their performances over multiple graph datasets across different domains, the experimental results show that MGSE can consistently boost the performance of these existing graph SSL frameworks with up to 9.2% improvement.

Uncertainty decomposition refers to the task of decomposing the total uncertainty of a predictive model into aleatoric (data) uncertainty, resulting from inherent randomness in the data-generating process, and epistemic (model) uncertainty, resulting from missing information in the model's training data. In large language models (LLMs) specifically, identifying sources of uncertainty is an important step toward improving reliability, trustworthiness, and interpretability, but remains an important open research question. In this paper, we introduce an uncertainty decomposition framework for LLMs, called input clarification ensembling, which can be applied to any pre-trained LLM. Our approach generates a set of clarifications for the input, feeds them into an LLM, and ensembles the corresponding predictions. We show that, when aleatoric uncertainty arises from ambiguity or under-specification in LLM inputs, this approach makes it possible to factor an (un-clarified) LLM's predictions into separate aleatoric and epistemic terms, using a decomposition similar to the one employed by Bayesian neural networks. Empirical evaluations demonstrate that input clarification ensembling provides accurate and reliable uncertainty quantification on several language processing tasks. Code and data are available at https://github.com/UCSB-NLP-Chang/llm_uncertainty.

The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly accurate single-state predictors such as AlphaFold and ESMFold and fine-tune them under a custom flow matching framework to obtain sequence-conditioned generative models of protein structure called AlphaFlow and ESMFlow. When trained and evaluated on the PDB, our method provides a superior combination of precision and diversity compared to AlphaFold with MSA subsampling. When further trained on ensembles from all-atom MD, our method accurately captures conformational flexibility, positional distributions, and higher-order ensemble observables for unseen proteins. Moreover, our method can diversify a static PDB structure with faster wall-clock convergence to certain equilibrium properties than replicate MD trajectories, demonstrating its potential as a proxy for expensive physics-based simulations. Code is available at https://github.com/bjing2016/alphaflow.