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Joey Bose
Affiliate Member
University of Oxford, Department of Computer Science
Scalable sampling of molecular states in thermodynamic equilibrium is a long-standing challenge in statistical physics. Boltzmann generators… (see more) tackle this problem by pairing powerful normalizing flows with importance sampling to obtain statistically independent samples under the target distribution. In this paper, we extend the Boltzmann generator framework and introduce Sequential Boltzmann generators (SBG) with two key improvements. The first is a highly efficient non-equivariant Transformer-based normalizing flow operating directly on all-atom Cartesian coordinates. In contrast to equivariant continuous flows of prior methods, we leverage exactly invertible non-equivariant architectures which are highly efficient both during sample generation and likelihood computation. As a result, this unlocks more sophisticated inference strategies beyond standard importance sampling. More precisely, as a second key improvement we perform inference-time scaling of flow samples using annealed Langevin dynamics which transports samples toward the target distribution leading to lower variance (annealed) importance weights which enable higher fidelity resampling with sequential Monte Carlo. SBG achieves state-of-the-art performance w.r.t. all metrics on molecular systems, demonstrating the first equilibrium sampling in Cartesian coordinates of tri, tetra, and hexapeptides that were so far intractable for prior Boltzmann generators.
The Cambrian explosion of easily accessible pre-trained diffusion models suggests a demand for methods that combine multiple different pre-t… (see more)rained diffusion models without incurring the significant computational burden of re-training a larger combined model. In this paper, we cast the problem of combining multiple pre-trained diffusion models at the generation stage under a novel proposed framework termed superposition. Theoretically, we derive superposition from rigorous first principles stemming from the celebrated continuity equation and design two novel algorithms tailor-made for combining diffusion models in SuperDiff. SuperDiff leverages a new scalable It\^o density estimator for the log likelihood of the diffusion SDE which incurs no additional overhead compared to the well-known Hutchinson's estimator needed for divergence calculations. We demonstrate that SuperDiff is scalable to large pre-trained diffusion models as superposition is performed solely through composition during inference, and also enjoys painless implementation as it combines different pre-trained vector fields through an automated re-weighting scheme. Notably, we show that SuperDiff is efficient during inference time, and mimics traditional composition operators such as the logical OR and the logical AND. We empirically demonstrate the utility of using SuperDiff for generating more diverse images on CIFAR-10, more faithful prompt conditioned image editing using Stable Diffusion, as well as improved conditional molecule generation and unconditional de novo structure design of proteins. https://github.com/necludov/super-diffusion
Predicting Drug Effects from High-Dimensional, Asymmetric Drug Datasets by Using Graph Neural Networks: A Comprehensive Analysis of Multitarget Drug Effect Prediction
Graph neural networks (GNNs) have emerged as one of the most effective ML techniques for drug effect prediction from drug molecular graphs. … (see more)Despite having immense potential, GNN models lack performance when using datasets that contain high-dimensional, asymmetrically co-occurrent drug effects as targets with complex correlations between them. Training individual learning models for each drug effect and incorporating every prediction result for a wide spectrum of drug effects are impractical. Therefore, an opportunity exists to address this challenge as multitarget prediction problems and predict all drug effects at a time. We developed standard and hybrid GNNs to perform two separate tasks: multiregression for continuous values and multilabel classification for categorical values contained in our datasets. Because multilabel classification makes the target data even more sparse and introduces asymmetric label co-occurrence, learning these models becomes difficult and heavily impacts the GNN's performance. To address these challenges, we propose a new data oversampling technique to improve multilabel classification performances on all the given imbalanced molecular graph datasets. Using the technique, we improve the data imbalance ratio of the drug effects while protecting the datasets' integrity. Finally, we evaluate the multilabel classification performance of the best-performing hybrid GNN model on all the oversampled datasets obtained from the proposed oversampling technique. In all the evaluation metrics (i.e., precision, recall, and F1 score), this model significantly outperforms other ML models, including GNN models when they are trained on the original datasets or oversampled datasets with MLSMOTE, which is a well-known oversampling technique.
2024-12-18
2024 International Conference on Machine Learning and Applications (ICMLA) (published)
Predicting Drug Effects from High-Dimensional, Asymmetric Drug Datasets by Using Graph Neural Networks: A Comprehensive Analysis of Multitarget Drug Effect Prediction
Graph neural networks (GNNs) have emerged as one of the most effective ML techniques for drug effect prediction from drug molecular graphs. … (see more)Despite having immense potential, GNN models lack performance when using datasets that contain high-dimensional, asymmetrically co-occurrent drug effects as targets with complex correlations between them. Training individual learning models for each drug effect and incorporating every prediction result for a wide spectrum of drug effects are impractical. Therefore, an opportunity exists to address this challenge as multitarget prediction problems and predict all drug effects at a time. We developed standard and hybrid GNNs to perform two separate tasks: multiregression for continuous values and multilabel classification for categorical values contained in our datasets. Because multilabel classification makes the target data even more sparse and introduces asymmetric label co-occurrence, learning these models becomes difficult and heavily impacts the GNN's performance. To address these challenges, we propose a new data oversampling technique to improve multilabel classification performances on all the given imbalanced molecular graph datasets. Using the technique, we improve the data imbalance ratio of the drug effects while protecting the datasets' integrity. Finally, we evaluate the multilabel classification performance of the best-performing hybrid GNN model on all the oversampled datasets obtained from the proposed oversampling technique. In all the evaluation metrics (i.e., precision, recall, and F1 score), this model significantly outperforms other ML models, including GNN models when they are trained on the original datasets or oversampled datasets with MLSMOTE, which is a well-known oversampling technique.
The rapid progress in generative models has resulted in impressive leaps in generation quality, blurring the lines between synthetic and rea… (see more)l data. Web-scale datasets are now prone to the inevitable contamination by synthetic data, directly impacting the training of future generated models. Already, some theoretical results on self-consuming generative models (a.k.a., iterative retraining) have emerged in the literature, showcasing that either model collapse or stability could be possible depending on the fraction of generated data used at each retraining step. However, in practice, synthetic data is often subject to human feedback and curated by users before being used and uploaded online. For instance, many interfaces of popular text-to-image generative models, such as Stable Diffusion or Midjourney, produce several variations of an image for a given query which can eventually be curated by the users. In this paper, we theoretically study the impact of data curation on iterated retraining of generative models and show that it can be seen as an \emph{implicit preference optimization mechanism}. However, unlike standard preference optimization, the generative model does not have access to the reward function or negative samples needed for pairwise comparisons. Moreover, our study doesn't require access to the density function, only to samples. We prove that, if the data is curated according to a reward model, then the expected reward of the iterative retraining procedure is maximized. We further provide theoretical results on the stability of the retraining loop when using a positive fraction of real data at each step. Finally, we conduct illustrative experiments on both synthetic datasets and on CIFAR10 showing that such a procedure amplifies biases of the reward model.
Large language models (LLMs) have garnered significant attention in both the AI community and beyond. Among these, the Generative Pre-traine… (see more)d Transformer (GPT) has emerged as the dominant architecture, spawning numerous variants. However, these variants have undergone pre-training under diverse conditions, including variations in input data, data preprocessing, and training methodologies, resulting in a lack of controlled comparative studies. Here we meticulously examine two prominent open-sourced GPT architectures, GPT-NeoX and LLaMA, leveraging the computational power of Frontier, the world’s first Exascale supercomputer. Employing the same materials science text corpus and a comprehensive end-to-end pipeline, we conduct a comparative analysis of their training and downstream performance. Our efforts culminate in achieving state-of-the-art performance on a challenging materials science benchmark. Furthermore, we investigate the computation and energy efficiency, and propose a computationally efficient method for architecture design. To our knowledge, these pre-trained models represent the largest available for materials science. Our findings provide practical guidance for building LLMs on HPC platforms.
2024-05-27
2024 IEEE International Parallel and Distributed Processing Symposium (IPDPS) (published)
Generative modeling over discrete data has recently seen numerous success stories, with applications spanning language modeling, biological … (see more)sequence design, and graph-structured molecular data. The predominant generative modeling paradigm for discrete data is still autoregressive, with more recent alternatives based on diffusion or flow-matching falling short of their impressive performance in continuous data settings, such as image or video generation. In this work, we introduce Fisher-Flow, a novel flow-matching model for discrete data. Fisher-Flow takes a manifestly geometric perspective by considering categorical distributions over discrete data as points residing on a statistical manifold equipped with its natural Riemannian metric: the
Matching objectives underpin the success of modern generative models and rely on constructing conditional paths that transform a source dist… (see more)ribution into a target distribution. Despite being a fundamental building block, conditional paths have been designed principally under the assumption of Euclidean geometry, resulting in straight interpolations. However, this can be particularly restrictive for tasks such as trajectory inference, where straight paths might lie outside the data manifold, thus failing to capture the underlying dynamics giving rise to the observed marginals. In this paper, we propose Metric Flow Matching (MFM), a novel simulation-free framework for conditional flow matching where interpolants are approximate geodesics learned by minimizing the kinetic energy of a data-induced Riemannian metric. This way, the generative model matches vector fields on the data manifold, which corresponds to lower uncertainty and more meaningful interpolations. We prescribe general metrics to instantiate MFM, independent of the task, and test it on a suite of challenging problems including LiDAR navigation, unpaired image translation, and modeling cellular dynamics. We observe that MFM outperforms the Euclidean baselines, particularly achieving SOTA on single-cell trajectory prediction.
Efficiently generating statistically independent samples from an unnormalized probability distribution, such as equilibrium samples of many-… (see more)body systems, is a foundational problem in science. In this paper, we propose Iterated Denoising Energy Matching (iDEM), an iterative algorithm that uses a novel stochastic score matching objective leveraging solely the energy function and its gradient---and no data samples---to train a diffusion-based sampler. Specifically, iDEM alternates between (I) sampling regions of high model density from a diffusion-based sampler and (II) using these samples in our stochastic matching objective to further improve the sampler. iDEM is scalable to high dimensions as the inner matching objective, is *simulation-free*, and requires no MCMC samples. Moreover, by leveraging the fast mode mixing behavior of diffusion, iDEM smooths out the energy landscape enabling efficient exploration and learning of an amortized sampler. We evaluate iDEM on a suite of tasks ranging from standard synthetic energy functions to invariant
Efficiently generating statistically independent samples from an unnormalized probability distribution, such as equilibrium samples of many-… (see more)body systems, is a foundational problem in science. In this paper, we propose Iterated Denoising Energy Matching (iDEM), an iterative algorithm that uses a novel stochastic score matching objective leveraging solely the energy function and its gradient -- and no data samples -- to train a diffusion-based sampler. Specifically, iDEM alternates between (I) sampling regions of high model density from a diffusion-based sampler and (II) using these samples in our stochastic matching objective to further improve the sampler. iDEM is scalable to high dimensions as the inner matching objective, is simulation-free, and requires no MCMC samples. Moreover, by leveraging the fast mode mixing behavior of diffusion, iDEM smooths out the energy landscape enabling efficient exploration and learning of an amortized sampler. We evaluate iDEM on a suite of tasks ranging from standard synthetic energy functions to invariant
Efficiently generating statistically independent samples from an unnormalized probability distribution, such as equilibrium samples of many-… (see more)body systems, is a foundational problem in science. In this paper, we propose Iterated Denoising Energy Matching (iDEM), an iterative algorithm that uses a novel stochastic score matching objective leveraging solely the energy function and its gradient -- and no data samples -- to train a diffusion-based sampler. Specifically, iDEM alternates between (I) sampling regions of high model density from a diffusion-based sampler and (II) using these samples in our stochastic matching objective to further improve the sampler. iDEM is scalable to high dimensions as the inner matching objective, is simulation-free, and requires no MCMC samples. Moreover, by leveraging the fast mode mixing behavior of diffusion, iDEM smooths out the energy landscape enabling efficient exploration and learning of an amortized sampler. We evaluate iDEM on a suite of tasks ranging from standard synthetic energy functions to invariant
