30 accepted papers
Markov Chain Monte Carlo (MCMC) algorithms are essential tools in computational statistics for sampling from unnormalised probability distributions, but can be fragile when targeting high-dimensional, multimodal, or complex target distributions. Parallel Tempering (PT) enhances MCMC's sample efficie…
Inference-time control of diffusion models aims to steer model outputs to satisfy new constraints without retraining. Previous approaches have mostly relied on heuristic guidance or have been coupled with Sequential Monte Carlo (SMC) for bias correction. In this paper, we propose a flexible alternat…
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 e…
Large language models are increasingly used to accelerate scientific discovery, especially in iteratively searching scientific hypotheses. Yet in many discovery settings the goal is not to identify a single ``best'' hypothesis: validation is noisy and expensive, multiple hypotheses can remain plausi…
Addressing real-world optimization problems becomes particularly challenging when analytic objective functions or constraints are unavailable. While numerous studies have addressed the issue of unknown objectives, limited research has focused on scenarios where feasibility constraints are not given…
Molecular discovery, when formulated as an optimization problem, presents significant computational challenges because optimization objectives can be non-differentiable. Evolutionary Algorithms (EAs), often used to optimize black-box objectives in molecular discovery, traverse chemical space by perf…
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 esc…
Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternativ…
Retrosynthesis, the process of breaking down a target molecule into simpler precursors through a series of valid reactions, stands at the core of organic chemistry and drug development. Although recent machine learning (ML) research has advanced single-step retrosynthetic modeling and subsequent rou…
Solving stochastic optimal control problems with quadratic control costs can be viewed as approximating a target path space measure, e.g. via gradient-based optimization. In practice, however, this optimization is challenging in particular if the target measure differs substantially from the prior.…
Aligning large language models (LLMs) with human objectives is crucial for real-world applications. However, fine-tuning LLMs for alignment often suffers from unstable training and requires substantial computing resources. Test-time alignment techniques, such as prompting and guided decoding, do not…
Rare event sampling in dynamical systems is a fundamental problem arising in the natural sciences, which poses significant computational challenges due to an exponentially large space of trajectories. For settings where the dynamical system of interest follows a Brownian motion with known drift, the…
Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D molecular graph or a single 3D structure, existing works often…
Recent progress of deep generative models in the vision and language domain has stimulated significant interest in more structured data generation such as molecules. However, beyond generating new random molecules, efficient exploration and a comprehensive understanding of the vast chemical space ar…
Denoising diffusion (score-based) generative models have become a popular choice for modeling complex data. Recently, a deep connection between forward-backward stochastic differential equations (SDEs) and diffusion-based models has been established, leading to the development of new SDE variants su…
Deep learning has achieved remarkable success in learning representations for molecules, which is crucial for various biochemical applications, ranging from property prediction to drug design. However, training Deep Neural Networks (DNNs) from scratch often requires abundant labeled molecules, which…
Geometric deep learning enables the encoding of physical symmetries in modeling 3D objects. Despite rapid progress in encoding 3D symmetries into Graph Neural Networks (GNNs), a comprehensive evaluation of the expressiveness of these network architectures through a local-to-global analysis lacks tod…
We introduce GAUCHE, an open-source library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine learning, affording particular advantages for uncertainty quantification and Bayesian optimisation. Extending Gaussian processes to molecular repr…
We introduce M$^2$Hub, a toolkit for advancing machine learning in materials discovery. Machine learning has achieved remarkable progress in modeling molecular structures, especially biomolecules for drug discovery. However, the development of machine learning approaches for modeling materials struc…
Self-supervised training methods for transformers have demonstrated remarkable performance across various domains. Previous transformer-based models, such as masked autoencoders (MAE), typically utilize a single normalization layer for both the [CLS] symbol and the tokens. We propose in this paper a…
We consider the problem of sampling transition paths between two given metastable states of a molecular system, eg. a folded and unfolded protein or products and reactants of a chemical reaction. Due to the existence of high energy barriers separating the states, these transition paths are unlikely…
Molecular Representation Learning (MRL) has emerged as a powerful tool for drug and materials discovery in a variety of tasks such as virtual screening and inverse design. While there has been a surge of interest in advancing model-centric techniques, the influence of both data quantity and quality…
The top-$k$ classification accuracy is a crucial metric in machine learning and is often used to evaluate the performance of deep neural networks. These networks are typically trained using the cross-entropy loss, which optimizes for top-$1$ classification and is considered optimal in the case of in…
Co-speech gesture is crucial for human-machine interaction and digital entertainment. While previous works mostly map speech audio to human skeletons (e.g., 2D keypoints), directly generating speakers' gestures in the image domain remains unsolved. In this work, we formally define and study this cha…
Spatiotemporal graph represents a crucial data structure where the nodes and edges are embedded in a geometric space and their attribute values can evolve dynamically over time. Nowadays, spatiotemporal graph data is becoming increasingly popular and important, ranging from microscale (e.g. protein…
Geometric deep learning has broad applications in biology, a domain where relational structure in data is often intrinsic to modelling the underlying phenomena. Currently, efforts in both geometric deep learning and, more broadly, deep learning applied to biomolecular tasks have been hampered by a…
Developing deep generative models has been an emerging field due to the ability to model and generate complex data for various purposes, such as image synthesis and molecular design. However, the advance of deep generative models is limited by the challenges to generate objects that possess multiple…
Group equivariance (e.g. SE(3) equivariance) is a critical physical symmetry in science, from classical and quantum physics to computational biology. It enables robust and accurate prediction under arbitrary reference transformations. In light of this, great efforts have been put on encoding this sy…
Graph generation has shown great potential in applications like network design and mobility synthesis and is one of the fastest-growing domains in machine learning for graphs. Despite the success of graph generation, the corresponding real-world datasets are few and limited to areas such as molecule…
Deep generative models have made important progress towards modeling complex, high dimensional data via learning latent representations. Their usefulness is nevertheless often limited by a lack of control over the generative process or a poor understanding of the latent representation. To overcome t…