Chin-Wei Huang

Chin-Wei Huang, Milad Aghajohari, Avishek Joey Bose et al.

Diffusion models are recent state-of-the-art methods for image generation and likelihood estimation. In this work, we generalize continuous-time diffusion models to arbitrary Riemannian manifolds and derive a variational framework for likelihood estimation. Computationally, we propose new methods for computing the Riemannian divergence which is needed in the likelihood estimation. Moreover, in generalizing the Euclidean case, we prove that maximizing this variational lower-bound is equivalent to Riemannian score matching. Empirically, we demonstrate the expressive power of Riemannian diffusion models on a wide spectrum of smooth manifolds, such as spheres, tori, hyperboloids, and orthogonal groups. Our proposed method achieves new state-of-the-art likelihoods on all benchmarks.

Marloes Arts, Victor Garcia Satorras, Chin-Wei Huang et al.

Coarse-grained (CG) molecular dynamics enables the study of biological processes at temporal and spatial scales that would be intractable at an atomistic resolution. However, accurately learning a CG force field remains a challenge. In this work, we leverage connections between score-based generative models, force fields and molecular dynamics to learn a CG force field without requiring any force inputs during training. Specifically, we train a diffusion generative model on protein structures from molecular dynamics simulations, and we show that its score function approximates a force field that can directly be used to simulate CG molecular dynamics. While having a vastly simplified training setup compared to previous work, we demonstrate that our approach leads to improved performance across several small- to medium-sized protein simulations, reproducing the CG equilibrium distribution, and preserving dynamics of all-atom simulations such as protein folding events.

Claudio Zeni, Robert Pinsler, Daniel Zügner et al. · cambridge

The design of functional materials with desired properties is essential in driving technological advances in areas like energy storage, catalysis, and carbon capture. Generative models provide a new paradigm for materials design by directly generating entirely novel materials given desired property constraints. Despite recent progress, current generative models have low success rate in proposing stable crystals, or can only satisfy a very limited set of property constraints. Here, we present MatterGen, a model that generates stable, diverse inorganic materials across the periodic table and can further be fine-tuned to steer the generation towards a broad range of property constraints. To enable this, we introduce a new diffusion-based generative process that produces crystalline structures by gradually refining atom types, coordinates, and the periodic lattice. We further introduce adapter modules to enable fine-tuning towards any given property constraints with a labeled dataset. Compared to prior generative models, structures produced by MatterGen are more than twice as likely to be novel and stable, and more than 15 times closer to the local energy minimum. After fine-tuning, MatterGen successfully generates stable, novel materials with desired chemistry, symmetry, as well as mechanical, electronic and magnetic properties. Finally, we demonstrate multi-property materials design capabilities by proposing structures that have both high magnetic density and a chemical composition with low supply-chain risk. We believe that the quality of generated materials and the breadth of MatterGen's capabilities represent a major advancement towards creating a universal generative model for materials design.

Giulia Luise, Chin-Wei Huang, Thijs Vogels et al.

Density Functional Theory (DFT) is the most widely used electronic structure method for predicting the properties of molecules and materials. Although DFT is, in principle, an exact reformulation of the Schrödinger equation, practical applications rely on approximations to the unknown exchange-correlation (XC) functional. Most existing XC functionals are constructed using a limited set of increasingly complex, hand-crafted features that improve accuracy at the expense of computational efficiency. Yet, no current approximation achieves the accuracy and generality for predictive modeling of laboratory experiments at chemical accuracy -- typically defined as errors below 1 kcal/mol. In this work, we present Skala, a modern deep learning-based XC functional that bypasses expensive hand-designed features by learning representations directly from data. Skala achieves chemical accuracy for atomization energies of small molecules while retaining the computational efficiency typical of semi-local DFT. This performance is enabled by training on an unprecedented volume of high-accuracy reference data generated using computationally intensive wavefunction-based methods. Notably, Skala systematically improves with additional training data covering diverse chemistry. By incorporating a modest amount of additional high-accuracy data tailored to chemistry beyond atomization energies, Skala achieves accuracy competitive with the best-performing hybrid functionals across general main group chemistry, at the cost of semi-local DFT. As the training dataset continues to expand, Skala is poised to further enhance the predictive power of first-principles simulations.

Chin-Wei Huang, Mu-Yi Shen, Kuan-Chang Shih et al.

Chest X-rays (CXRs) often display various diseases with disparate class frequencies, leading to a long-tailed, multi-label data distribution. In response to this challenge, we explore the Pruned MIMIC-CXR-LT dataset, a curated collection derived from the MIMIC-CXR dataset, specifically designed to represent a long-tailed and multi-label data scenario. We introduce LTCXNet, a novel framework that integrates the ConvNeXt model, ML-Decoder, and strategic data augmentation, further enhanced by an ensemble approach. We demonstrate that LTCXNet improves the performance of CXR interpretation across all classes, especially enhancing detection in rarer classes like `Pneumoperitoneum' and `Pneumomediastinum' by 79\% and 48\%, respectively. Beyond performance metrics, our research extends into evaluating fairness, highlighting that some methods, while improving model accuracy, could inadvertently affect fairness across different demographic groups negatively. This work contributes to advancing the understanding and management of long-tailed, multi-label data distributions in medical imaging, paving the way for more equitable and effective diagnostic tools.

Chin-Wei Huang, Jae Hyun Lim, Aaron Courville

Discrete-time diffusion-based generative models and score matching methods have shown promising results in modeling high-dimensional image data. Recently, Song et al. (2021) show that diffusion processes that transform data into noise can be reversed via learning the score function, i.e. the gradient of the log-density of the perturbed data. They propose to plug the learned score function into an inverse formula to define a generative diffusion process. Despite the empirical success, a theoretical underpinning of this procedure is still lacking. In this work, we approach the (continuous-time) generative diffusion directly and derive a variational framework for likelihood estimation, which includes continuous-time normalizing flows as a special case, and can be seen as an infinitely deep variational autoencoder. Under this framework, we show that minimizing the score-matching loss is equivalent to maximizing a lower bound of the likelihood of the plug-in reverse SDE proposed by Song et al. (2021), bridging the theoretical gap.

Chin-Wei Huang, Ricky T. Q. Chen, Christos Tsirigotis et al.

Flow-based models are powerful tools for designing probabilistic models with tractable density. This paper introduces Convex Potential Flows (CP-Flow), a natural and efficient parameterization of invertible models inspired by the optimal transport (OT) theory. CP-Flows are the gradient map of a strongly convex neural potential function. The convexity implies invertibility and allows us to resort to convex optimization to solve the convex conjugate for efficient inversion. To enable maximum likelihood training, we derive a new gradient estimator of the log-determinant of the Jacobian, which involves solving an inverse-Hessian vector product using the conjugate gradient method. The gradient estimator has constant-memory cost, and can be made effectively unbiased by reducing the error tolerance level of the convex optimization routine. Theoretically, we prove that CP-Flows are universal density approximators and are optimal in the OT sense. Our empirical results show that CP-Flow performs competitively on standard benchmarks of density estimation and variational inference.

Brady Neal, Chin-Wei Huang, Sunand Raghupathi

There are many different causal effect estimators in causal inference. However, it is unclear how to choose between these estimators because there is no ground-truth for causal effects. A commonly used option is to simulate synthetic data, where the ground-truth is known. However, the best causal estimators on synthetic data are unlikely to be the best causal estimators on real data. An ideal benchmark for causal estimators would both (a) yield ground-truth values of the causal effects and (b) be representative of real data. Using flexible generative models, we provide a benchmark that both yields ground-truth and is realistic. Using this benchmark, we evaluate over 1500 different causal estimators and provide evidence that it is rational to choose hyperparameters for causal estimators using predictive metrics.

Tianshi Cao, Chin-Wei Huang, David Yu-Tung Hui et al.

Motivation: Deep learning models deployed for use on medical tasks can be equipped with Out-of-Distribution Detection (OoDD) methods in order to avoid erroneous predictions. However it is unclear which OoDD method should be used in practice. Specific Problem: Systems trained for one particular domain of images cannot be expected to perform accurately on images of a different domain. These images should be flagged by an OoDD method prior to diagnosis. Our approach: This paper defines 3 categories of OoD examples and benchmarks popular OoDD methods in three domains of medical imaging: chest X-ray, fundus imaging, and histology slides. Results: Our experiments show that despite methods yielding good results on some categories of out-of-distribution samples, they fail to recognize images close to the training distribution. Conclusion: We find a simple binary classifier on the feature representation has the best accuracy and AUPRC on average. Users of diagnostic tools which employ these OoDD methods should still remain vigilant that images very close to the training distribution yet not in it could yield unexpected results.

Jae Hyun Lim, Aaron Courville, Christopher Pal et al.

Entropy is ubiquitous in machine learning, but it is in general intractable to compute the entropy of the distribution of an arbitrary continuous random variable. In this paper, we propose the amortized residual denoising autoencoder (AR-DAE) to approximate the gradient of the log density function, which can be used to estimate the gradient of entropy. Amortization allows us to significantly reduce the error of the gradient approximator by approaching asymptotic optimality of a regular DAE, in which case the estimation is in theory unbiased. We conduct theoretical and experimental analyses on the approximation error of the proposed method, as well as extensive studies on heuristics to ensure its robustness. Finally, using the proposed gradient approximator to estimate the gradient of entropy, we demonstrate state-of-the-art performance on density estimation with variational autoencoders and continuous control with soft actor-critic.

Chin-Wei Huang, Laurent Dinh, Aaron Courville

In this work, we propose a new family of generative flows on an augmented data space, with an aim to improve expressivity without drastically increasing the computational cost of sampling and evaluation of a lower bound on the likelihood. Theoretically, we prove the proposed flow can approximate a Hamiltonian ODE as a universal transport map. Empirically, we demonstrate state-of-the-art performance on standard benchmarks of flow-based generative modeling.

Shawn Tan, Yikang Shen, Chin-wei Huang et al.

The ability to understand logical relationships between sentences is an important task in language understanding. To aid in progress for this task, researchers have collected datasets for machine learning and evaluation of current systems. However, like in the crowdsourced Visual Question Answering (VQA) task, some biases in the data inevitably occur. In our experiments, we find that performing classification on just the hypotheses on the SNLI dataset yields an accuracy of 64%. We analyze the bias extent in the SNLI and the MultiNLI dataset, discuss its implication, and propose a simple method to reduce the biases in the datasets.

Fan-Yun Sun, Meng Qu, Jordan Hoffmann et al.

This paper focuses on two fundamental tasks of graph analysis: community detection and node representation learning, which capture the global and local structures of graphs, respectively. In the current literature, these two tasks are usually independently studied while they are actually highly correlated. We propose a probabilistic generative model called vGraph to learn community membership and node representation collaboratively. Specifically, we assume that each node can be represented as a mixture of communities, and each community is defined as a multinomial distribution over nodes. Both the mixing coefficients and the community distribution are parameterized by the low-dimensional representations of the nodes and communities. We designed an effective variational inference algorithm which regularizes the community membership of neighboring nodes to be similar in the latent space. Experimental results on multiple real-world graphs show that vGraph is very effective in both community detection and node representation learning, outperforming many competitive baselines in both tasks. We show that the framework of vGraph is quite flexible and can be easily extended to detect hierarchical communities.

Chin-Wei Huang, Ahmed Touati, Pascal Vincent et al.

Recent advances in variational inference enable the modelling of highly structured joint distributions, but are limited in their capacity to scale to the high-dimensional setting of stochastic neural networks. This limitation motivates a need for scalable parameterizations of the noise generation process, in a manner that adequately captures the dependencies among the various parameters. In this work, we address this need and present the Kronecker Flow, a generalization of the Kronecker product to invertible mappings designed for stochastic neural networks. We apply our method to variational Bayesian neural networks on predictive tasks, PAC-Bayes generalization bound estimation, and approximate Thompson sampling in contextual bandits. In all setups, our methods prove to be competitive with existing methods and better than the baselines.

Chin-Wei Huang, Aaron Courville

In this note, we study the relationship between the variational gap and the variance of the (log) likelihood ratio. We show that the gap can be upper bounded by some form of dispersion measure of the likelihood ratio, which suggests the bias of variational inference can be reduced by making the distribution of the likelihood ratio more concentrated, such as via averaging and variance reduction.

Chin-Wei Huang, Kris Sankaran, Eeshan Dhekane et al.

Importance weighted variational inference (Burda et al., 2015) uses multiple i.i.d. samples to have a tighter variational lower bound. We believe a joint proposal has the potential of reducing the number of redundant samples, and introduce a hierarchical structure to induce correlation. The hope is that the proposals would coordinate to make up for the error made by one another to reduce the variance of the importance estimator. Theoretically, we analyze the condition under which convergence of the estimator variance can be connected to convergence of the lower bound. Empirically, we confirm that maximization of the lower bound does implicitly minimize variance. Further analysis shows that this is a result of negative correlation induced by the proposed hierarchical meta sampling scheme, and performance of inference also improves when the number of samples increases.

Chin-Wei Huang, Shawn Tan, Alexandre Lacoste et al.

Despite the advances in the representational capacity of approximate distributions for variational inference, the optimization process can still limit the density that is ultimately learned. We demonstrate the drawbacks of biasing the true posterior to be unimodal, and introduce Annealed Variational Objectives (AVO) into the training of hierarchical variational methods. Inspired by Annealed Importance Sampling, the proposed method facilitates learning by incorporating energy tempering into the optimization objective. In our experiments, we demonstrate our method's robustness to deterministic warm up, and the benefits of encouraging exploration in the latent space.

Chin-Wei Huang, David Krueger, Alexandre Lacoste et al.

Normalizing flows and autoregressive models have been successfully combined to produce state-of-the-art results in density estimation, via Masked Autoregressive Flows (MAF), and to accelerate state-of-the-art WaveNet-based speech synthesis to 20x faster than real-time, via Inverse Autoregressive Flows (IAF). We unify and generalize these approaches, replacing the (conditionally) affine univariate transformations of MAF/IAF with a more general class of invertible univariate transformations expressed as monotonic neural networks. We demonstrate that the proposed neural autoregressive flows (NAF) are universal approximators for continuous probability distributions, and their greater expressivity allows them to better capture multimodal target distributions. Experimentally, NAF yields state-of-the-art performance on a suite of density estimation tasks and outperforms IAF in variational autoencoders trained on binarized MNIST.

Yikang Shen, Shawn Tan, Chin-Wei Huang et al.

Learning distributed sentence representations remains an interesting problem in the field of Natural Language Processing (NLP). We want to learn a model that approximates the conditional latent space over the representations of a logical antecedent of the given statement. In our paper, we propose an approach to generating sentences, conditioned on an input sentence and a logical inference label. We do this by modeling the different possibilities for the output sentence as a distribution over the latent representation, which we train using an adversarial objective. We evaluate the model using two state-of-the-art models for the Recognizing Textual Entailment (RTE) task, and measure the BLEU scores against the actual sentences as a probe for the diversity of sentences produced by our model. The experiment results show that, given our framework, we have clear ways to improve the quality and diversity of generated sentences.

Yikang Shen, Zhouhan Lin, Chin-Wei Huang et al.

We propose a neural language model capable of unsupervised syntactic structure induction. The model leverages the structure information to form better semantic representations and better language modeling. Standard recurrent neural networks are limited by their structure and fail to efficiently use syntactic information. On the other hand, tree-structured recursive networks usually require additional structural supervision at the cost of human expert annotation. In this paper, We propose a novel neural language model, called the Parsing-Reading-Predict Networks (PRPN), that can simultaneously induce the syntactic structure from unannotated sentences and leverage the inferred structure to learn a better language model. In our model, the gradient can be directly back-propagated from the language model loss into the neural parsing network. Experiments show that the proposed model can discover the underlying syntactic structure and achieve state-of-the-art performance on word/character-level language model tasks.

David Krueger, Chin-Wei Huang, Riashat Islam et al.

We study Bayesian hypernetworks: a framework for approximate Bayesian inference in neural networks. A Bayesian hypernetwork $\h$ is a neural network which learns to transform a simple noise distribution, $p(\vecε) = \N(\vec 0,\mat I)$, to a distribution $q(\pp) := q(h(\vecε))$ over the parameters $\pp$ of another neural network (the "primary network")\@. We train $q$ with variational inference, using an invertible $\h$ to enable efficient estimation of the variational lower bound on the posterior $p(\pp | \D)$ via sampling. In contrast to most methods for Bayesian deep learning, Bayesian hypernets can represent a complex multimodal approximate posterior with correlations between parameters, while enabling cheap iid sampling of~$q(\pp)$. In practice, Bayesian hypernets can provide a better defense against adversarial examples than dropout, and also exhibit competitive performance on a suite of tasks which evaluate model uncertainty, including regularization, active learning, and anomaly detection.

Chin-Wei Huang, Ahmed Touati, Laurent Dinh et al.

In this paper, we study two aspects of the variational autoencoder (VAE): the prior distribution over the latent variables and its corresponding posterior. First, we decompose the learning of VAEs into layerwise density estimation, and argue that having a flexible prior is beneficial to both sample generation and inference. Second, we analyze the family of inverse autoregressive flows (inverse AF) and show that with further improvement, inverse AF could be used as universal approximation to any complicated posterior. Our analysis results in a unified approach to parameterizing a VAE, without the need to restrict ourselves to use factorial Gaussians in the latent real space.