OneProt: Towards Multi-Modal Protein Foundation Models

Recent AI advances have enabled multi-modal systems to model and translate diverse information spaces. Extending beyond text and vision, we introduce OneProt, a multi-modal AI for proteins that integrates structural, sequence, alignment, and binding site data. Using the ImageBind framework, OneProt aligns the latent spaces of modality encoders along protein sequences. It demonstrates strong performance in retrieval tasks and surpasses state-of-the-art methods in various downstream tasks, including metal ion binding classification, gene-ontology annotation, and enzyme function prediction. This work expands multi-modal capabilities in protein models, paving the way for applications in drug discovery, biocatalytic reaction planning, and protein engineering.

Stein Variational Newton Neural Network Ensembles

Deep neural network ensembles are powerful tools for uncertainty quantification, which have recently been re-interpreted from a Bayesian perspective. However, current methods inadequately leverage second-order information of the loss landscape, despite the recent availability of efficient Hessian approximations. We propose a novel approximate Bayesian inference method that modifies deep ensembles to incorporate Stein Variational Newton updates. Our approach uniquely integrates scalable modern Hessian approximations, achieving faster convergence and more accurate posterior distribution approximations. We validate the effectiveness of our method on diverse regression and classification tasks, demonstrating superior performance with a significantly reduced number of training epochs compared to existing ensemble-based methods, while enhancing uncertainty quantification and robustness against overfitting.

Parameter-efficient Bayesian Neural Networks for Uncertainty-aware Depth Estimation

State-of-the-art computer vision tasks, like monocular depth estimation (MDE), rely heavily on large, modern Transformer-based architectures. However, their application in safety-critical domains demands reliable predictive performance and uncertainty quantification. While Bayesian neural networks provide a conceptually simple approach to serve those requirements, they suffer from the high dimensionality of the parameter space. Parameter-efficient fine-tuning (PEFT) methods, in particular low-rank adaptations (LoRA), have emerged as a popular strategy for adapting large-scale models to down-stream tasks by performing parameter inference on lower-dimensional subspaces. In this work, we investigate the suitability of PEFT methods for subspace Bayesian inference in large-scale Transformer-based vision models. We show that, indeed, combining BitFit, DiffFit, LoRA, and CoLoRA, a novel LoRA-inspired PEFT method, with Bayesian inference enables more robust and reliable predictive performance in MDE.

FSP-Laplace: Function-Space Priors for the Laplace Approximation in Bayesian Deep Learning

Laplace approximations are popular techniques for endowing deep networks with epistemic uncertainty estimates as they can be applied without altering the predictions of the neural network, and they scale to large models and datasets. While the choice of prior strongly affects the resulting posterior distribution, computational tractability and lack of interpretability of weight space typically limit the Laplace approximation to isotropic Gaussian priors, which are known to cause pathological behavior as depth increases. As a remedy, we directly place a prior on function space. More precisely, since Lebesgue densities do not exist on infinite-dimensional function spaces, we have to recast training as finding the so-called weak mode of the posterior measure under a Gaussian process (GP) prior restricted to the space of functions representable by the neural network. Through the GP prior, one can express structured and interpretable inductive biases, such as regularity or periodicity, directly in function space, while still exploiting the implicit inductive biases that allow deep networks to generalize. After model linearization, the training objective induces a negative log-posterior density to which we apply a Laplace approximation, leveraging highly scalable methods from matrix-free linear algebra. Our method provides improved results where prior knowledge is abundant, e.g., in many scientific inference tasks. At the same time, it stays competitive for black-box regression and classification tasks where neural networks typically excel.

Towards Dynamic Feature Acquisition on Medical Time Series by Maximizing Conditional Mutual Information

Knowing which features of a multivariate time series to measure and when is a key task in medicine, wearables, and robotics. Better acquisition policies can reduce costs while maintaining or even improving the performance of downstream predictors. Inspired by the maximization of conditional mutual information, we propose an approach to train acquirers end-to-end using only the downstream loss. We show that our method outperforms random acquisition policy, matches a model with an unrestrained budget, but does not yet overtake a static acquisition strategy. We highlight the assumptions and outline avenues for future work.

How Useful is Intermittent, Asynchronous Expert Feedback for Bayesian Optimization?

Bayesian optimization (BO) is an integral part of automated scientific discovery -- the so-called self-driving lab -- where human inputs are ideally minimal or at least non-blocking. However, scientists often have strong intuition, and thus human feedback is still useful. Nevertheless, prior works in enhancing BO with expert feedback, such as by incorporating it in an offline or online but blocking (arrives at each BO iteration) manner, are incompatible with the spirit of self-driving labs. In this work, we study whether a small amount of randomly arriving expert feedback that is being incorporated in a non-blocking manner can improve a BO campaign. To this end, we run an additional, independent computing thread on top of the BO loop to handle the feedback-gathering process. The gathered feedback is used to learn a Bayesian preference model that can readily be incorporated into the BO thread, to steer its exploration-exploitation process. Experiments on toy and chemistry datasets suggest that even just a few intermittent, asynchronous expert feedback can be useful for improving or constraining BO. This can especially be useful for its implication in improving self-driving labs, e.g. making them more data-efficient and less costly.

Gaussian Stochastic Weight Averaging for Bayesian Low-Rank Adaptation of Large Language Models

Fine-tuned Large Language Models (LLMs) often suffer from overconfidence and poor calibration, particularly when fine-tuned on small datasets. To address these challenges, we propose a simple combination of Low-Rank Adaptation (LoRA) with Gaussian Stochastic Weight Averaging (SWAG), facilitating approximate Bayesian inference in LLMs. Through extensive testing across several Natural Language Processing (NLP) benchmarks, we demonstrate that our straightforward and computationally efficient approach improves model generalization and calibration. We further show that our method exhibits greater robustness against distribution shift, as reflected in its performance on out-of-distribution tasks.

On the Challenges and Opportunities in Generative AI

The field of deep generative modeling has grown rapidly and consistently over the years. With the availability of massive amounts of training data coupled with advances in scalable unsupervised learning paradigms, recent large-scale generative models show tremendous promise in synthesizing high-resolution images and text, as well as structured data such as videos and molecules. However, we argue that current large-scale generative AI models do not sufficiently address several fundamental issues that hinder their widespread adoption across domains. In this work, we aim to identify key unresolved challenges in modern generative AI paradigms that should be tackled to further enhance their capabilities, versatility, and reliability. By identifying these challenges, we aim to provide researchers with valuable insights for exploring fruitful research directions, thereby fostering the development of more robust and accessible generative AI solutions.

Shaving Weights with Occam's Razor: Bayesian Sparsification for Neural Networks Using the Marginal Likelihood

Neural network sparsification is a promising avenue to save computational time and memory costs, especially in an age where many successful AI models are becoming too large to na\"ively deploy on consumer hardware. While much work has focused on different weight pruning criteria, the overall sparsifiability of the network, i.e., its capacity to be pruned without quality loss, has often been overlooked. We present Sparsifiability via the Marginal likelihood (SpaM), a pruning framework that highlights the effectiveness of using the Bayesian marginal likelihood in conjunction with sparsity-inducing priors for making neural networks more sparsifiable. Our approach implements an automatic Occam's razor that selects the most sparsifiable model that still explains the data well, both for structured and unstructured sparsification. In addition, we demonstrate that the pre-computed posterior Hessian approximation used in the Laplace approximation can be re-used to define a cheap pruning criterion, which outperforms many existing (more expensive) approaches. We demonstrate the effectiveness of our framework, especially at high sparsity levels, across a range of different neural network architectures and datasets.

Position Paper: Bayesian Deep Learning in the Age of Large-Scale AI

In the current landscape of deep learning research, there is a predominant emphasis on achieving high predictive accuracy in supervised tasks involving large image and language datasets. However, a broader perspective reveals a multitude of overlooked metrics, tasks, and data types, such as uncertainty, active and continual learning, and scientific data, that demand attention. Bayesian deep learning (BDL) constitutes a promising avenue, offering advantages across these diverse settings. This paper posits that BDL can elevate the capabilities of deep learning. It revisits the strengths of BDL, acknowledges existing challenges, and highlights some exciting research avenues aimed at addressing these obstacles. Looking ahead, the discussion focuses on possible ways to combine large-scale foundation models with BDL to unlock their full potential.