José Miguel Hernández-Lobato

Jiajun He, Gergely Flamich, Zongyu Guo et al. · cambridge

COMpression with Bayesian Implicit NEural Representations (COMBINER) is a recent data compression method that addresses a key inefficiency of previous Implicit Neural Representation (INR)-based approaches: it avoids quantization and enables direct optimization of the rate-distortion performance. However, COMBINER still has significant limitations: 1) it uses factorized priors and posterior approximations that lack flexibility; 2) it cannot effectively adapt to local deviations from global patterns in the data; and 3) its performance can be susceptible to modeling choices and the variational parameters' initializations. Our proposed method, Robust and Enhanced COMBINER (RECOMBINER), addresses these issues by 1) enriching the variational approximation while retaining a low computational cost via a linear reparameterization of the INR weights, 2) augmenting our INRs with learnable positional encodings that enable them to adapt to local details and 3) splitting high-resolution data into patches to increase robustness and utilizing expressive hierarchical priors to capture dependency across patches. We conduct extensive experiments across several data modalities, showcasing that RECOMBINER achieves competitive results with the best INR-based methods and even outperforms autoencoder-based codecs on low-resolution images at low bitrates. Our PyTorch implementation is available at https://github.com/cambridge-mlg/RECOMBINER/.

Laurence Illing Midgley, Vincent Stimper, Gregor N. C. Simm et al. · cambridge

Normalizing flows are tractable density models that can approximate complicated target distributions, e.g. Boltzmann distributions of physical systems. However, current methods for training flows either suffer from mode-seeking behavior, use samples from the target generated beforehand by expensive MCMC methods, or use stochastic losses that have high variance. To avoid these problems, we augment flows with annealed importance sampling (AIS) and minimize the mass-covering $α$-divergence with $α=2$, which minimizes importance weight variance. Our method, Flow AIS Bootstrap (FAB), uses AIS to generate samples in regions where the flow is a poor approximation of the target, facilitating the discovery of new modes. We apply FAB to multimodal targets and show that we can approximate them very accurately where previous methods fail. To the best of our knowledge, we are the first to learn the Boltzmann distribution of the alanine dipeptide molecule using only the unnormalized target density, without access to samples generated via Molecular Dynamics (MD) simulations: FAB produces better results than training via maximum likelihood on MD samples while using 100 times fewer target evaluations. After reweighting the samples, we obtain unbiased histograms of dihedral angles that are almost identical to the ground truth.

Vincent Stimper, David Liu, Andrew Campbell et al. · cambridge

Normalizing flows model probability distributions through an expressive tractable density. They transform a simple base distribution, such as a Gaussian, through a sequence of invertible functions, which are referred to as layers. These layers typically use neural networks to become very expressive. Flows are ubiquitous in machine learning and have been applied to image generation, text modeling, variational inference, approximating Boltzmann distributions, and many other problems. Here, we present normflows, a Python package for normalizing flows. It allows to build normalizing flow models from a suite of base distributions, flow layers, and neural networks. The package is implemented in the popular deep learning framework PyTorch, which simplifies the integration of flows in larger machine learning models or pipelines. It supports most of the common normalizing flow architectures, such as Real NVP, Glow, Masked Autoregressive Flows, Neural Spline Flows, Residual Flows, and many more. The package can be easily installed via pip and the code is publicly available on GitHub.

Laurence I. Midgley, Vincent Stimper, Javier Antorán et al. · cambridge, oxford

Coupling normalizing flows allow for fast sampling and density evaluation, making them the tool of choice for probabilistic modeling of physical systems. However, the standard coupling architecture precludes endowing flows that operate on the Cartesian coordinates of atoms with the SE(3) and permutation invariances of physical systems. This work proposes a coupling flow that preserves SE(3) and permutation equivariance by performing coordinate splits along additional augmented dimensions. At each layer, the flow maps atoms' positions into learned SE(3) invariant bases, where we apply standard flow transformations, such as monotonic rational-quadratic splines, before returning to the original basis. Crucially, our flow preserves fast sampling and density evaluation, and may be used to produce unbiased estimates of expectations with respect to the target distribution via importance sampling. When trained on the DW4, LJ13, and QM9-positional datasets, our flow is competitive with equivariant continuous normalizing flows and diffusion models, while allowing sampling more than an order of magnitude faster. Moreover, to the best of our knowledge, we are the first to learn the full Boltzmann distribution of alanine dipeptide by only modeling the Cartesian positions of its atoms. Lastly, we demonstrate that our flow can be trained to approximately sample from the Boltzmann distribution of the DW4 and LJ13 particle systems using only their energy functions.

Jihao Andreas Lin, Javier Antorán, Shreyas Padhy et al. · cambridge

Gaussian processes are a powerful framework for quantifying uncertainty and for sequential decision-making but are limited by the requirement of solving linear systems. In general, this has a cubic cost in dataset size and is sensitive to conditioning. We explore stochastic gradient algorithms as a computationally efficient method of approximately solving these linear systems: we develop low-variance optimization objectives for sampling from the posterior and extend these to inducing points. Counterintuitively, stochastic gradient descent often produces accurate predictions, even in cases where it does not converge quickly to the optimum. We explain this through a spectral characterization of the implicit bias from non-convergence. We show that stochastic gradient descent produces predictive distributions close to the true posterior both in regions with sufficient data coverage, and in regions sufficiently far away from the data. Experimentally, stochastic gradient descent achieves state-of-the-art performance on sufficiently large-scale or ill-conditioned regression tasks. Its uncertainty estimates match the performance of significantly more expensive baselines on a large-scale Bayesian optimization task.

Wenlin Chen, Austin Tripp, José Miguel Hernández-Lobato · cambridge

We propose Adaptive Deep Kernel Fitting with Implicit Function Theorem (ADKF-IFT), a novel framework for learning deep kernel Gaussian processes (GPs) by interpolating between meta-learning and conventional deep kernel learning. Our approach employs a bilevel optimization objective where we meta-learn generally useful feature representations across tasks, in the sense that task-specific GP models estimated on top of such features achieve the lowest possible predictive loss on average. We solve the resulting nested optimization problem using the implicit function theorem (IFT). We show that our ADKF-IFT framework contains previously proposed Deep Kernel Learning (DKL) and Deep Kernel Transfer (DKT) as special cases. Although ADKF-IFT is a completely general method, we argue that it is especially well-suited for drug discovery problems and demonstrate that it significantly outperforms previous state-of-the-art methods on a variety of real-world few-shot molecular property prediction tasks and out-of-domain molecular property prediction and optimization tasks.

Austin Tripp, Sergio Bacallado, Sukriti Singh et al. · cambridge

The Tanimoto coefficient is commonly used to measure the similarity between molecules represented as discrete fingerprints, either as a distance metric or a positive definite kernel. While many kernel methods can be accelerated using random feature approximations, at present there is a lack of such approximations for the Tanimoto kernel. In this paper we propose two kinds of novel random features to allow this kernel to scale to large datasets, and in the process discover a novel extension of the kernel to real-valued vectors. We theoretically characterize these random features, and provide error bounds on the spectral norm of the Gram matrix. Experimentally, we show that these random features are effective at approximating the Tanimoto coefficient of real-world datasets and are useful for molecular property prediction and optimization tasks.

Jihao Andreas Lin, Javier Antorán, José Miguel Hernández-Lobato · cambridge

The Laplace approximation provides a closed-form model selection objective for neural networks (NN). Online variants, which optimise NN parameters jointly with hyperparameters, like weight decay strength, have seen renewed interest in the Bayesian deep learning community. However, these methods violate Laplace's method's critical assumption that the approximation is performed around a mode of the loss, calling into question their soundness. This work re-derives online Laplace methods, showing them to target a variational bound on a mode-corrected variant of the Laplace evidence which does not make stationarity assumptions. Online Laplace and its mode-corrected counterpart share stationary points where 1. the NN parameters are a maximum a posteriori, satisfying the Laplace method's assumption, and 2. the hyperparameters maximise the Laplace evidence, motivating online methods. We demonstrate that these optima are roughly attained in practise by online algorithms using full-batch gradient descent on UCI regression datasets. The optimised hyperparameters prevent overfitting and outperform validation-based early stopping.

Riccardo Barbano, Javier Antorán, Johannes Leuschner et al. · cambridge

Deep learning has been widely used for solving image reconstruction tasks but its deployability has been held back due to the shortage of high-quality training data. Unsupervised learning methods, such as the deep image prior (DIP), naturally fill this gap, but bring a host of new issues: the susceptibility to overfitting due to a lack of robust early stopping strategies and unstable convergence. We present a novel approach to tackle these issues by restricting DIP optimisation to a sparse linear subspace of its parameters, employing a synergy of dimensionality reduction techniques and second order optimisation methods. The low-dimensionality of the subspace reduces DIP's tendency to fit noise and allows the use of stable second order optimisation methods, e.g., natural gradient descent or L-BFGS. Experiments across both image restoration and tomographic tasks of different geometry and ill-posedness show that second order optimisation within a low-dimensional subspace is favourable in terms of optimisation stability to reconstruction fidelity trade-off.

Wenlin Chen, Julien Horwood, Juyeon Heo et al. · cambridge

This work extends the theory of identifiability in supervised learning by considering the consequences of having access to a distribution of tasks. In such cases, we show that linear identifiability is achievable in the general multi-task regression setting. Furthermore, we show that the existence of a task distribution which defines a conditional prior over latent factors reduces the equivalence class for identifiability to permutations and scaling of the true latent factors, a stronger and more useful result than linear identifiability. Crucially, when we further assume a causal structure over these tasks, our approach enables simple maximum marginal likelihood optimization, and suggests potential downstream applications to causal representation learning. Empirically, we find that this straightforward optimization procedure enables our model to outperform more general unsupervised models in recovering canonical representations for both synthetic data and real-world molecular data.

Jihao Andreas Lin, Gergely Flamich, José Miguel Hernández-Lobato · cambridge

This paper studies the qualitative behavior and robustness of two variants of Minimal Random Code Learning (MIRACLE) used to compress variational Bayesian neural networks. MIRACLE implements a powerful, conditionally Gaussian variational approximation for the weight posterior $Q_{\mathbf{w}}$ and uses relative entropy coding to compress a weight sample from the posterior using a Gaussian coding distribution $P_{\mathbf{w}}$. To achieve the desired compression rate, $D_{\mathrm{KL}}[Q_{\mathbf{w}} \Vert P_{\mathbf{w}}]$ must be constrained, which requires a computationally expensive annealing procedure under the conventional mean-variance (Mean-Var) parameterization for $Q_{\mathbf{w}}$. Instead, we parameterize $Q_{\mathbf{w}}$ by its mean and KL divergence from $P_{\mathbf{w}}$ to constrain the compression cost to the desired value by construction. We demonstrate that variational training with Mean-KL parameterization converges twice as fast and maintains predictive performance after compression. Furthermore, we show that Mean-KL leads to more meaningful variational distributions with heavier tails and compressed weight samples which are more robust to pruning.

Jiajun He, José Miguel Hernández-Lobato, Yuanqi Du et al. · cambridge

Diffusion models generate data by removing noise gradually, which corresponds to the time-reversal of a noising process. However, access to only the denoising kernels is often insufficient. In many applications, we need the knowledge of the marginal densities along the generation trajectory, which enables tasks such as inference-time control. To address this gap, in this paper, we introduce the Radon-Nikodym Estimator (RNE). Based on the concept of the \textit{density ratio} between path distributions, it reveals a fundamental connection between marginal densities and transition kernels, providing a flexible plug-and-play framework that unifies (1) diffusion density estimation, (2) inference-time control, and (3) energy-based diffusion training under a single perspective. Experiments demonstrate that RNE delivers strong results in inference-time control applications, such as annealing and model composition, with promising inference-time scaling performance, and achieves a simple yet efficient regularisation for training energy-based diffusion models. Additionally, our proposed RNE is modality-agnostic and applicable not only to continuous diffusion models but also to their discrete diffusion counterparts.

Riccardo Barbano, Johannes Leuschner, Javier Antorán et al.

We investigate adaptive design based on a single sparse pilot scan for generating effective scanning strategies for computed tomography reconstruction. We propose a novel approach using the linearised deep image prior. It allows incorporating information from the pilot measurements into the angle selection criteria, while maintaining the tractability of a conjugate Gaussian-linear model. On a synthetically generated dataset with preferential directions, linearised DIP design allows reducing the number of scans by up to 30% relative to an equidistant angle baseline.

Jiajun He, Zijing Ou, Francisco Vargas et al.

Free energy estimation is a fundamental yet challenging problem, from physics to statistics. Classical approaches rely on thermodynamic transformations, ranging from direct estimation, quasistatic integration, to finite-time averaging. Recent work [He and Du et al., 2025] learns neural transports to significantly accelerate the efficiency in the finite-time regime. In this paper, we generalize this framework to arbitrary state spaces. Building on this view, we develop a generalized neural transport learning approach for efficient estimation. Experiments validate the effectiveness and efficiency of the proposed method beyond continuous settings, extending to discrete and multimodal spaces as well as autoregressive settings. Beyond free energy estimation, we establish algebraic identities and reveal a group-theoretic structure linking infinitesimal time reversal and generalized Doob's $h$-transforms, showing that their compositions form a generalized dihedral group.

Austin Tripp, Krzysztof Maziarz, Sarah Lewis et al.

Retrosynthesis is the task of planning a series of chemical reactions to create a desired molecule from simpler, buyable molecules. While previous works have proposed algorithms to find optimal solutions for a range of metrics (e.g. shortest, lowest-cost), these works generally overlook the fact that we have imperfect knowledge of the space of possible reactions, meaning plans created by algorithms may not work in a laboratory. In this paper we propose a novel formulation of retrosynthesis in terms of stochastic processes to account for this uncertainty. We then propose a novel greedy algorithm called retro-fallback which maximizes the probability that at least one synthesis plan can be executed in the lab. Using in-silico benchmarks we demonstrate that retro-fallback generally produces better sets of synthesis plans than the popular MCTS and retro* algorithms.

Javier Antorán, David Janz, James Urquhart Allingham et al.

The linearised Laplace method for estimating model uncertainty has received renewed attention in the Bayesian deep learning community. The method provides reliable error bars and admits a closed-form expression for the model evidence, allowing for scalable selection of model hyperparameters. In this work, we examine the assumptions behind this method, particularly in conjunction with model selection. We show that these interact poorly with some now-standard tools of deep learning--stochastic approximation methods and normalisation layers--and make recommendations for how to better adapt this classic method to the modern setting. We provide theoretical support for our recommendations and validate them empirically on MLPs, classic CNNs, residual networks with and without normalisation layers, generative autoencoders and transformers.

Austin Tripp, José Miguel Hernández-Lobato

Generating molecules, both in a directed and undirected fashion, is a huge part of the drug discovery pipeline. Genetic algorithms (GAs) generate molecules by randomly modifying known molecules. In this paper we show that GAs are very strong algorithms for such tasks, outperforming many complicated machine learning methods: a result which many researchers may find surprising. We therefore propose insisting during peer review that new algorithms must have some clear advantage over GAs, which we call the GA criterion. Ultimately our work suggests that a lot of research in molecule generation should be re-assessed.

Jihao Andreas Lin, Shreyas Padhy, Javier Antorán et al.

As is well known, both sampling from the posterior and computing the mean of the posterior in Gaussian process regression reduces to solving a large linear system of equations. We study the use of stochastic gradient descent for solving this linear system, and show that when \emph{done right} -- by which we mean using specific insights from the optimisation and kernel communities -- stochastic gradient descent is highly effective. To that end, we introduce a particularly simple \emph{stochastic dual descent} algorithm, explain its design in an intuitive manner and illustrate the design choices through a series of ablation studies. Further experiments demonstrate that our new method is highly competitive. In particular, our evaluations on the UCI regression tasks and on Bayesian optimisation set our approach apart from preconditioned conjugate gradients and variational Gaussian process approximations. Moreover, our method places Gaussian process regression on par with state-of-the-art graph neural networks for molecular binding affinity prediction.

Javier Antorán, Shreyas Padhy, Riccardo Barbano et al.

Large-scale linear models are ubiquitous throughout machine learning, with contemporary application as surrogate models for neural network uncertainty quantification; that is, the linearised Laplace method. Alas, the computational cost associated with Bayesian linear models constrains this method's application to small networks, small output spaces and small datasets. We address this limitation by introducing a scalable sample-based Bayesian inference method for conjugate Gaussian multi-output linear models, together with a matching method for hyperparameter (regularisation) selection. Furthermore, we use a classic feature normalisation method (the g-prior) to resolve a previously highlighted pathology of the linearised Laplace method. Together, these contributions allow us to perform linearised neural network inference with ResNet-18 on CIFAR100 (11M parameters, 100 outputs x 50k datapoints), with ResNet-50 on Imagenet (50M parameters, 1000 outputs x 1.2M datapoints) and with a U-Net on a high-resolution tomographic reconstruction task (2M parameters, 251k output~dimensions).

Pablo Morales-Álvarez, Arne Schmidt, José Miguel Hernández-Lobato et al.

In the last years, the weakly supervised paradigm of multiple instance learning (MIL) has become very popular in many different areas. A paradigmatic example is computational pathology, where the lack of patch-level labels for whole-slide images prevents the application of supervised models. Probabilistic MIL methods based on Gaussian Processes (GPs) have obtained promising results due to their excellent uncertainty estimation capabilities. However, these are general-purpose MIL methods that do not take into account one important fact: in (histopathological) images, the labels of neighboring patches are expected to be correlated. In this work, we extend a state-of-the-art GP-based MIL method, which is called VGPMIL-PR, to exploit such correlation. To do so, we develop a novel coupling term inspired by the statistical physics Ising model. We use variational inference to estimate all the model parameters. Interestingly, the VGPMIL-PR formulation is recovered when the weight that regulates the strength of the Ising term vanishes. The performance of the proposed method is assessed in two real-world problems of prostate cancer detection. We show that our model achieves better results than other state-of-the-art probabilistic MIL methods. We also provide different visualizations and analysis to gain insights into the influence of the novel Ising term. These insights are expected to facilitate the application of the proposed model to other research areas.

RuiKang OuYang, Bo Qiang, José Miguel Hernández-Lobato

Developing an efficient sampler capable of generating independent and identically distributed (IID) samples from a Boltzmann distribution is a crucial challenge in scientific research, e.g. molecular dynamics. In this work, we intend to learn neural samplers given energy functions instead of data sampled from the Boltzmann distribution. By learning the energies of the noised data, we propose a diffusion-based sampler, Noised Energy Matching, which theoretically has lower variance and more complexity compared to related works. Furthermore, a novel bootstrapping technique is applied to NEM to balance between bias and variance. We evaluate NEM and BNEM on a 2-dimensional 40 Gaussian Mixture Model (GMM) and a 4-particle double-well potential (DW-4). The experimental results demonstrate that BNEM can achieve state-of-the-art performance while being more robust.

Fengzhe Zhang, Jiajun He, Laurence I. Midgley et al.

Diffusion models have shown promising potential for advancing Boltzmann Generators. However, two critical challenges persist: (1) inherent errors in samples due to model imperfections, and (2) the requirement of hundreds of functional evaluations (NFEs) to achieve high-quality samples. While existing solutions like importance sampling and distillation address these issues separately, they are often incompatible, as most distillation models lack the necessary density information for importance sampling. This paper introduces a novel sampling method that effectively combines Consistency Models (CMs) with importance sampling. We evaluate our approach on both synthetic energy functions and equivariant n-body particle systems. Our method produces unbiased samples using only 6-25 NFEs while achieving a comparable Effective Sample Size (ESS) to Denoising Diffusion Probabilistic Models (DDPMs) that require approximately 100 NFEs.

Ross M. Clarke, José Miguel Hernández-Lobato

Research into optimisation for deep learning is characterised by a tension between the computational efficiency of first-order, gradient-based methods (such as SGD and Adam) and the theoretical efficiency of second-order, curvature-based methods (such as quasi-Newton methods and K-FAC). Noting that second-order methods often only function effectively with the addition of stabilising heuristics (such as Levenberg-Marquardt damping), we ask how much these (as opposed to the second-order curvature model) contribute to second-order algorithms' performance. We thus study AdamQLR: an optimiser combining damping and learning rate selection techniques from K-FAC (Martens & Grosse, 2015) with the update directions proposed by Adam, inspired by considering Adam through a second-order lens. We evaluate AdamQLR on a range of regression and classification tasks at various scales and hyperparameter tuning methodologies, concluding K-FAC's adaptive heuristics are of variable standalone general effectiveness, and finding an untuned AdamQLR setting can achieve comparable performance vs runtime to tuned benchmarks.

Jiajun He, Yuanqi Du, Francisco Vargas et al. · cambridge

We present Free energy Estimators with Adaptive Transport (FEAT), a novel framework for free energy estimation -- a critical challenge across scientific domains. FEAT leverages learned transports implemented via stochastic interpolants and provides consistent, minimum-variance estimators based on escorted Jarzynski equality and controlled Crooks theorem, alongside variational upper and lower bounds on free energy differences. Unifying equilibrium and non-equilibrium methods under a single theoretical framework, FEAT establishes a principled foundation for neural free energy calculations. Experimental validation on toy examples, molecular simulations, and quantum field theory demonstrates improvements over existing learning-based methods. Our PyTorch implementation is available at https://github.com/jiajunhe98/FEAT.

Elre T. Oldewage, Ross M. Clarke, José Miguel Hernández-Lobato

Despite their popularity in the field of continuous optimisation, second-order quasi-Newton methods are challenging to apply in machine learning, as the Hessian matrix is intractably large. This computational burden is exacerbated by the need to address non-convexity, for instance by modifying the Hessian's eigenvalues as in Saddle-Free Newton methods. We propose an optimisation algorithm which addresses both of these concerns - to our knowledge, the first efficiently-scalable optimisation algorithm to asymptotically use the exact inverse Hessian with absolute-value eigenvalues. Our method frames the problem as a series which principally square-roots and inverts the squared Hessian, then uses it to precondition a gradient vector, all without explicitly computing or eigendecomposing the Hessian. A truncation of this infinite series provides a new optimisation algorithm which is scalable and comparable to other first- and second-order optimisation methods in both runtime and optimisation performance. We demonstrate this in a variety of settings, including a ResNet-18 trained on CIFAR-10.

James Boran Yu, RuiKang OuYang, Julien Horwood et al.

Although diffusion models have successfully extended to function-valued data, stochastic interpolants -- which offer a flexible way to bridge arbitrary distributions -- remain limited to finite-dimensional settings. This work bridges this gap by establishing a rigorous framework for stochastic interpolants in infinite-dimensional Hilbert spaces. We provide comprehensive theoretical foundations, including proofs of well-posedness and explicit error bounds. We demonstrate the effectiveness of the proposed framework for conditional generation, focusing particularly on complex PDE-based benchmarks. By enabling generative bridges between arbitrary functional distributions, our approach achieves state-of-the-art results, offering a powerful, general-purpose tool for scientific discovery.

Javier Antorán, Riccardo Barbano, Johannes Leuschner et al.

Existing deep-learning based tomographic image reconstruction methods do not provide accurate estimates of reconstruction uncertainty, hindering their real-world deployment. This paper develops a method, termed as the linearised deep image prior (DIP), to estimate the uncertainty associated with reconstructions produced by the DIP with total variation regularisation (TV). Specifically, we endow the DIP with conjugate Gaussian-linear model type error-bars computed from a local linearisation of the neural network around its optimised parameters. To preserve conjugacy, we approximate the TV regulariser with a Gaussian surrogate. This approach provides pixel-wise uncertainty estimates and a marginal likelihood objective for hyperparameter optimisation. We demonstrate the method on synthetic data and real-measured high-resolution 2D $μ$CT data, and show that it provides superior calibration of uncertainty estimates relative to previous probabilistic formulations of the DIP. Our code is available at https://github.com/educating-dip/bayes_dip.

Miguel García-Ortegón, Gregor N. C. Simm, Austin J. Tripp et al.

The field of machine learning for drug discovery is witnessing an explosion of novel methods. These methods are often benchmarked on simple physicochemical properties such as solubility or general druglikeness, which can be readily computed. However, these properties are poor representatives of objective functions in drug design, mainly because they do not depend on the candidate's interaction with the target. By contrast, molecular docking is a widely successful method in drug discovery to estimate binding affinities. However, docking simulations require a significant amount of domain knowledge to set up correctly which hampers adoption. To this end, we present DOCKSTRING, a bundle for meaningful and robust comparison of ML models consisting of three components: (1) an open-source Python package for straightforward computation of docking scores; (2) an extensive dataset of docking scores and poses of more than 260K ligands for 58 medically-relevant targets; and (3) a set of pharmaceutically-relevant benchmark tasks including regression, virtual screening, and de novo design. The Python package implements a robust ligand and target preparation protocol that allows non-experts to obtain meaningful docking scores. Our dataset is the first to include docking poses, as well as the first of its size that is a full matrix, thus facilitating experiments in multiobjective optimization and transfer learning. Overall, our results indicate that docking scores are a more appropriate evaluation objective than simple physicochemical properties, yielding more realistic benchmark tasks and molecular candidates.

Erik Daxberger, Eric Nalisnick, James Urquhart Allingham et al.

The Bayesian paradigm has the potential to solve core issues of deep neural networks such as poor calibration and data inefficiency. Alas, scaling Bayesian inference to large weight spaces often requires restrictive approximations. In this work, we show that it suffices to perform inference over a small subset of model weights in order to obtain accurate predictive posteriors. The other weights are kept as point estimates. This subnetwork inference framework enables us to use expressive, otherwise intractable, posterior approximations over such subsets. In particular, we implement subnetwork linearized Laplace as a simple, scalable Bayesian deep learning method: We first obtain a MAP estimate of all weights and then infer a full-covariance Gaussian posterior over a subnetwork using the linearized Laplace approximation. We propose a subnetwork selection strategy that aims to maximally preserve the model's predictive uncertainty. Empirically, our approach compares favorably to ensembles and less expressive posterior approximations over full networks. Our proposed subnetwork (linearized) Laplace method is implemented within the laplace PyTorch library at https://github.com/AlexImmer/Laplace.

Chaochao Lu, Bernhard Schölkopf, José Miguel Hernández-Lobato

We propose a general formulation for addressing reinforcement learning (RL) problems in settings with observational data. That is, we consider the problem of learning good policies solely from historical data in which unobserved factors (confounders) affect both observed actions and rewards. Our formulation allows us to extend a representative RL algorithm, the Actor-Critic method, to its deconfounding variant, with the methodology for this extension being easily applied to other RL algorithms. In addition to this, we develop a new benchmark for evaluating deconfounding RL algorithms by modifying the OpenAI Gym environments and the MNIST dataset. Using this benchmark, we demonstrate that the proposed algorithms are superior to traditional RL methods in confounded environments with observational data. To the best of our knowledge, this is the first time that confounders are taken into consideration for addressing full RL problems with observational data. Code is available at https://github.com/CausalRL/DRL.

Richard Bergna, Stefan Depeweg, José Miguel Hernández-Lobato

Prior-Fitted Networks (PFNs) amortize Bayesian prediction by meta-learning over a synthetic task prior, but their standard output is a posterior predictive distribution over noisy observations. For sequential decision-making, such as active learning and Bayesian optimization, acquisition should prioritize epistemic uncertainty about the latent signal rather than irreducible aleatoric observation noise. We show that this epistemic--aleatoric split is not identifiable in general from the posterior predictive distribution alone, even when that distribution is known exactly. We then exploit a distinctive advantage of PFNs: because the synthetic data-generating process is under our control, each task can contain an explicit latent signal and noise function, and the generator can provide query-level labels for both the noiseless target and the observation-noise variance. We use these labels to train a decoupled PFN with separate latent-signal and aleatoric heads. The observation-level predictive is induced by convolving the latent signal distribution with the learned noise model. Empirically, epistemic-only acquisition mitigates the failure mode of total-variance exploration in noisy and heteroscedastic settings. In matched comparisons, decoupled models usually improve over tuned observation-level baselines, with the clearest gains in HPO; in broader sweeps, a decoupled model obtains the best average rank in both HPO and synthetic BO.

Theodore Papamarkou, Maria Skoularidou, Konstantina Palla et al.

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.

Francisco M. Castro-Macías, Pablo Morales-Álvarez, Saifuddin Syed et al.

Sampling from unnormalized multimodal distributions with limited density evaluations remains a fundamental challenge in machine learning and natural sciences. Successful approaches construct a bridge between a tractable reference and the target distribution. Parallel Tempering (PT) serves as the gold standard, while recent diffusion-based approaches offer a continuous alternative at the cost of neural training. In this work, we introduce Conditional Diffusion Sampling (CDS), a framework that combines these two paradigms. To this end, we derive Conditional Interpolants, a class of stochastic processes whose transport dynamics are governed by an exact, closed-form stochastic differential equation (SDE), requiring no neural approximation. Although these dynamics require sampling from a non-trivial initialization distribution, we show both theoretically and empirically that the cost of this initialization diminishes for sufficiently short diffusion times. CDS leverages this by a two-stage procedure: (1) PT is used to efficiently sample the initial distribution, and then (2) samples are transported via the transport SDE. This combination couples the robust global exploration of PT with efficient local transport. Experiments suggest that CDS has the potential to achieve a superior trade-off between sample quality and density evaluation cost compared to state-of-the-art samplers.

Aliaksandra Shysheya, Cristiana Diaconu, Federico Bergamin et al.

Modelling partial differential equations (PDEs) is of crucial importance in science and engineering, and it includes tasks ranging from forecasting to inverse problems, such as data assimilation. However, most previous numerical and machine learning approaches that target forecasting cannot be applied out-of-the-box for data assimilation. Recently, diffusion models have emerged as a powerful tool for conditional generation, being able to flexibly incorporate observations without retraining. In this work, we perform a comparative study of score-based diffusion models for forecasting and assimilation of sparse observations. In particular, we focus on diffusion models that are either trained in a conditional manner, or conditioned after unconditional training. We address the shortcomings of existing models by proposing 1) an autoregressive sampling approach that significantly improves performance in forecasting, 2) a new training strategy for conditional score-based models that achieves stable performance over a range of history lengths, and 3) a hybrid model which employs flexible pre-training conditioning on initial conditions and flexible post-training conditioning to handle data assimilation. We empirically show that these modifications are crucial for successfully tackling the combination of forecasting and data assimilation, a task commonly encountered in real-world scenarios.

Jiajun He, Yuanqi Du, Francisco Vargas et al. · cambridge

We consider the sampling problem, where the aim is to draw samples from a distribution whose density is known only up to a normalization constant. Recent breakthroughs in generative modeling to approximate a high-dimensional data distribution have sparked significant interest in developing neural network-based methods for this challenging problem. However, neural samplers typically incur heavy computational overhead due to simulating trajectories during training. This motivates the pursuit of simulation-free training procedures of neural samplers. In this work, we propose an elegant modification to previous methods, which allows simulation-free training with the help of a time-dependent normalizing flow. However, it ultimately suffers from severe mode collapse. On closer inspection, we find that nearly all successful neural samplers rely on Langevin preconditioning to avoid mode collapsing. We systematically analyze several popular methods with various objective functions and demonstrate that, in the absence of Langevin preconditioning, most of them fail to adequately cover even a simple target. Finally, we draw attention to a strong baseline by combining the state-of-the-art MCMC method, Parallel Tempering (PT), with an additional generative model to shed light on future explorations of neural samplers.

Wenlin Chen, Mingtian Zhang, Brooks Paige et al. · cambridge

The inadequate mixing of conventional Markov Chain Monte Carlo (MCMC) methods for multi-modal distributions presents a significant challenge in practical applications such as Bayesian inference and molecular dynamics. Addressing this, we propose Diffusive Gibbs Sampling (DiGS), an innovative family of sampling methods designed for effective sampling from distributions characterized by distant and disconnected modes. DiGS integrates recent developments in diffusion models, leveraging Gaussian convolution to create an auxiliary noisy distribution that bridges isolated modes in the original space and applying Gibbs sampling to alternately draw samples from both spaces. A novel Metropolis-within-Gibbs scheme is proposed to enhance mixing in the denoising sampling step. DiGS exhibits a better mixing property for sampling multi-modal distributions than state-of-the-art methods such as parallel tempering, attaining substantially improved performance across various tasks, including mixtures of Gaussians, Bayesian neural networks and molecular dynamics.

Jiajun He, Wenlin Chen, Mingtian Zhang et al. · cambridge

Training generative models to sample from unnormalized density functions is an important and challenging task in machine learning. Traditional training methods often rely on the reverse Kullback-Leibler (KL) divergence due to its tractability. However, the mode-seeking behavior of reverse KL hinders effective approximation of multi-modal target distributions. To address this, we propose to minimize the reverse KL along diffusion trajectories of both model and target densities. We refer to this objective as the reverse diffusive KL divergence, which allows the model to capture multiple modes. Leveraging this objective, we train neural samplers that can efficiently generate samples from the target distribution in one step. We demonstrate that our method enhances sampling performance across various Boltzmann distributions, including both synthetic multi-modal densities and n-body particle systems.

James Urquhart Allingham, Bruno Kacper Mlodozeniec, Shreyas Padhy et al.

Correctly capturing the symmetry transformations of data can lead to efficient models with strong generalization capabilities, though methods incorporating symmetries often require prior knowledge. While recent advancements have been made in learning those symmetries directly from the dataset, most of this work has focused on the discriminative setting. In this paper, we take inspiration from group theoretic ideas to construct a generative model that explicitly aims to capture the data's approximate symmetries. This results in a model that, given a prespecified but broad set of possible symmetries, learns to what extent, if at all, those symmetries are actually present. Our model can be seen as a generative process for data augmentation. We provide a simple algorithm for learning our generative model and empirically demonstrate its ability to capture symmetries under affine and color transformations, in an interpretable way. Combining our symmetry model with standard generative models results in higher marginal test-log-likelihoods and improved data efficiency.

Maksym Korablyov, Cheng-Hao Liu, Moksh Jain et al. · mila

Despite substantial progress in machine learning for scientific discovery in recent years, truly de novo design of small molecules which exhibit a property of interest remains a significant challenge. We introduce LambdaZero, a generative active learning approach to search for synthesizable molecules. Powered by deep reinforcement learning, LambdaZero learns to search over the vast space of molecules to discover candidates with a desired property. We apply LambdaZero with molecular docking to design novel small molecules that inhibit the enzyme soluble Epoxide Hydrolase 2 (sEH), while enforcing constraints on synthesizability and drug-likeliness. LambdaZero provides an exponential speedup in terms of the number of calls to the expensive molecular docking oracle, and LambdaZero de novo designed molecules reach docking scores that would otherwise require the virtual screening of a hundred billion molecules. Importantly, LambdaZero discovers novel scaffolds of synthesizable, drug-like inhibitors for sEH. In in vitro experimental validation, a series of ligands from a generated quinazoline-based scaffold were synthesized, and the lead inhibitor N-(4,6-di(pyrrolidin-1-yl)quinazolin-2-yl)-N-methylbenzamide (UM0152893) displayed sub-micromolar enzyme inhibition of sEH.

Severi Rissanen, RuiKang OuYang, Jiajun He et al. · cambridge

Recent research has focused on designing neural samplers that amortize the process of sampling from unnormalized densities. However, despite significant advancements, they still fall short of the state-of-the-art MCMC approach, Parallel Tempering (PT), when it comes to the efficiency of target evaluations. On the other hand, unlike a well-trained neural sampler, PT yields only dependent samples and needs to be rerun -- at considerable computational cost -- whenever new samples are required. To address these weaknesses, we propose the Progressive Tempering Sampler with Diffusion (PTSD), which trains diffusion models sequentially across temperatures, leveraging the advantages of PT to improve the training of neural samplers. We also introduce a novel method to combine high-temperature diffusion models to generate approximate lower-temperature samples, which are minimally refined using MCMC and used to train the next diffusion model. PTSD enables efficient reuse of sample information across temperature levels while generating well-mixed, uncorrelated samples. Our method significantly improves target evaluation efficiency, outperforming diffusion-based neural samplers.

Mingtian Zhang, Wenlin Chen, Jiajun He et al. · cambridge

Recent advances in training one-step diffusion models typically follow a two-stage pipeline: first training a teacher diffusion model and then distilling it into a one-step student model. This process often depends on both the teacher's score function for supervision and its weights for initializing the student model. In this paper, we explore whether one-step diffusion models can be trained directly without this distillation procedure. We introduce a family of new training methods that entirely forgo teacher score supervision, yet outperforms most teacher-guided distillation approaches. This suggests that score supervision is not essential for effective training of one-step diffusion models. However, we find that initializing the student model with the teacher's weights remains critical. Surprisingly, the key advantage of teacher initialization is not due to better latent-to-output mappings, but rather the rich set of feature representations across different noise levels that the teacher diffusion model provides. These insights take us one step closer towards training one-step diffusion models without distillation and provide a better understanding of the roles of teacher supervision and initialization in the distillation process.

Antonio Almudévar, José Miguel Hernández-Lobato, Sameer Khurana et al. · mit

Contrastive losses have been extensively used as a tool for multimodal representation learning. However, it has been empirically observed that their use is not effective to learn an aligned representation space. In this paper, we argue that this phenomenon is caused by the presence of modality-specific information in the representation space. Although some of the most widely used contrastive losses maximize the mutual information between representations of both modalities, they are not designed to remove the modality-specific information. We give a theoretical description of this problem through the lens of the Information Bottleneck Principle. We also empirically analyze how different hyperparameters affect the emergence of this phenomenon in a controlled experimental setup. Finally, we propose a regularization term in the loss function that is derived by means of a variational approximation and aims to increase the representational alignment. We analyze in a set of controlled experiments and real-world applications the advantages of including this regularization term.

Fengzhe Zhang, Laurence I. Midgley, José Miguel Hernández-Lobato

Score-based diffusion models (SBDMs) are powerful amortized samplers for Boltzmann distributions; however, imperfect score estimates bias downstream Monte Carlo estimates. Classical importance sampling (IS) can correct this bias, but computing exact likelihoods requires solving the probability-flow ordinary differential equation (PF-ODE), a procedure that is prohibitively costly and scales poorly with dimensionality. We introduce Variance-Tuned Diffusion Importance Sampling (VT-DIS), a lightweight post-training method that adapts the per-step noise covariance of a pretrained SBDM by minimizing the $α$-divergence ($α=2$) between its forward diffusion and reverse denoising trajectories. VT-DIS assigns a single trajectory-wise importance weight to the joint forward-reverse process, yielding unbiased expectation estimates at test time with negligible overhead compared to standard sampling. On the DW-4, LJ-13, and alanine-dipeptide benchmarks, VT-DIS achieves effective sample sizes of approximately 80 %, 35 %, and 3.5 %, respectively, while using only a fraction of the computational budget required by vanilla diffusion + IS or PF-ODE-based IS.

Weilin Chen, Ruichu Cai, Junjie Wan et al.

Long-term causal inference has drawn increasing attention in many scientific domains. Existing methods mainly focus on estimating average long-term causal effects by combining long-term observational data and short-term experimental data. However, it is still understudied how to robustly and effectively estimate heterogeneous long-term causal effects, significantly limiting practical applications. In this paper, we propose several two-stage style nonparametric estimators for heterogeneous long-term causal effect estimation, including propensity-based, regression-based, and multiple robust estimators. We conduct a comprehensive theoretical analysis of their asymptotic properties under mild assumptions, with the ultimate goal of building a better understanding of the conditions under which some estimators can be expected to perform better. Extensive experiments across several semi-synthetic and real-world datasets validate the theoretical results and demonstrate the effectiveness of the proposed estimators.

Yuxuan Ou, Jingyi Zhao, Austin Tripp et al.

Lipid nanoparticles (LNPs) are vital in modern biomedicine, enabling the effective delivery of mRNA for vaccines and therapies by protecting it from rapid degradation. Among the components of LNPs, ionizable lipids play a key role in RNA protection and facilitate its delivery into the cytoplasm. However, designing ionizable lipids is complex. Deep generative models can accelerate this process and explore a larger candidate space compared to traditional methods. Due to the structural differences between lipids and small molecules, existing generative models used for small molecule generation are unsuitable for lipid generation. To address this, we developed a deep generative model specifically tailored for the discovery of ionizable lipids. Our model generates novel ionizable lipid structures and provides synthesis paths using synthetically accessible building blocks, addressing synthesizability. This advancement holds promise for streamlining the development of lipid-based delivery systems, potentially accelerating the deployment of new therapeutic agents, including mRNA vaccines and gene therapies.

Jiajun He, Gergely Flamich, José Miguel Hernández-Lobato · cambridge

Relative entropy coding (REC) algorithms encode a random sample following a target distribution $Q$, using a coding distribution $P$ shared between the sender and receiver. Sadly, general REC algorithms suffer from prohibitive encoding times, at least on the order of $2^{D_{\text{KL}}[Q||P]}$, and faster algorithms are limited to very specific settings. This work addresses this issue by introducing a REC scheme utilizing space partitioning to reduce runtime in practical scenarios. We provide theoretical analyses of our method and demonstrate its effectiveness with both toy examples and practical applications. Notably, our method successfully handles REC tasks with $D_{\text{KL}}[Q||P]$ about three times greater than what previous methods can manage, and reduces the bitrate by approximately 5-15% in VAE-based lossless compression on MNIST and INR-based lossy compression on CIFAR-10, compared to previous methods, significantly improving the practicality of REC for neural compression.

Weilin Chen, Ruichu Cai, Yuguang Yan et al.

Long-term causal inference is an important but challenging problem across various scientific domains. To solve the latent confounding problem in long-term observational studies, existing methods leverage short-term experimental data. Ghassami et al. propose an approach based on the Conditional Additive Equi-Confounding Bias (CAECB) assumption, which asserts that the confounding bias in the short-term outcome is equal to that in the long-term outcome, so that the long-term confounding bias and the causal effects can be identified. While effective in certain cases, this assumption is limited to scenarios where there is only one short-term outcome with the same scale as the long-term outcome. In this paper, we introduce a novel assumption that extends the CAECB assumption to accommodate temporal short-term outcomes. Our proposed assumption states a functional relationship between sequential confounding biases across temporal short-term outcomes, under which we theoretically establish the identification of long-term causal effects. Based on the identification result, we develop an estimator and conduct a theoretical analysis of its asymptotic properties. Extensive experiments validate our theoretical results and demonstrate the effectiveness of the proposed method.

Louis Grenioux, RuiKang OuYang, José Miguel Hernández-Lobato

Score-based generative models have recently achieved remarkable success. While they are usually parameterized by the score, an alternative way is to use a series of time-dependent energy-based models (EBMs), where the score is obtained from the negative input-gradient of the energy. Crucially, EBMs can be leveraged not only for generation, but also for tasks such as compositional sampling or building Boltzmann Generators via Monte Carlo methods. However, training EBMs remains challenging. Direct maximum likelihood is computationally prohibitive due to the need for nested sampling, while score matching, though efficient, suffers from mode blindness. To address these issues, we introduce the Diffusive Classification (DiffCLF) objective, a simple method that avoids blindness while remaining computationally efficient. DiffCLF reframes EBM learning as a supervised classification problem across noise levels, and can be seamlessly combined with standard score-based objectives. We validate the effectiveness of DiffCLF by comparing the estimated energies against ground truth in analytical Gaussian mixture cases, and by applying the trained models to tasks such as model composition and Boltzmann Generator sampling. Our results show that DiffCLF enables EBMs with higher fidelity and broader applicability than existing approaches.

Jiajun He, Zongyu Guo, Zhaoyang Jia et al.

Modern visual generative models acquire rich visual knowledge through large-scale training, yet existing visual representations (such as pixels, latents, or tokens) remain external to the model and cannot directly exploit this knowledge for compact storage or reuse. In this work, we introduce a new visual representation framework that encodes a signal as a function, which is parametrized by low-rank adaptations attached to a frozen visual generative model. Such implicit representations of visual signals, \textit{e.g.}, an 81-frame video, can further be hashed into a single compact vector, achieving strong perceptual video compression at extremely low bitrates. Beyond basic compression, the functional nature of this representation enables inference-time scaling and control, allowing additional refinement on the compression performance. More broadly, as the implicit representations directly act as a function of the generation process, this suggests a unified framework bridging visual compression and generation.

Alan Yufei Dong, Jihao Andreas Lin, José Miguel Hernández-Lobato

Scalable Gaussian process (GP) inference is essential for sequential decision-making tasks, yet improving GP scalability remains a challenging problem with many open avenues of research. This paper focuses on iterative GPs, where iterative linear solvers, such as conjugate gradients, stochastic gradient descent or alternative projections, are used to approximate the GP posterior. We propose a new method which improves solver convergence of a large linear system by leveraging the known solution to a smaller system contained within. This is significant for tasks with incremental data additions, and we show that our technique achieves speed-ups when solving to tolerance, as well as improved Bayesian optimisation performance under a fixed compute budget.