Author name cluster

Stephen Ra

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6 papers

2 author rows

TMLR Journal 2024 Journal Article

Blind Biological Sequence Denoising with Self-Supervised Set Learning

Nathan Hoyen Ng
Ji Won Park
Jae Hyeon Lee
Ryan Lewis Kelly
Stephen Ra
Kyunghyun Cho

Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate multiple subreads, or noisy obser- vations of the same sequence. Denoising these subreads with alignment-based approaches often fails when too few subreads are available or error rates are too high. In this paper, we propose a novel method for blindly denoising sets of sequences without directly observing clean source sequence labels. Our method, Self-Supervised Set Learning (SSSL), gathers subreads together in an embedding space and estimates a single set embedding as the mid- point of the subreads in both the latent and sequence spaces. This set embedding represents the “average” of the subreads and can be decoded into a prediction of the clean sequence. In experiments on simulated long-read DNA data, SSSL methods denoise small reads of ≤ 6 subreads with 17% fewer errors and large reads of > 6 subreads with 8% fewer errors compared to the best baseline. On a real dataset of antibody sequences, SSSL improves over baselines on two self-supervised metrics, with a significant improvement on difficult small reads that comprise over 60% of the test set. By accurately denoising these reads, SSSL promises to better realize the potential of high-throughput DNA sequencing data for downstream scientific applications.

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ICML Conference 2024 Conference Paper

BOtied: Multi-objective Bayesian optimization with tied multivariate ranks

Ji Won Park
Natasa Tagasovska
Michael Maser
Stephen Ra
Kyunghyun Cho

Many scientific and industrial applications require the joint optimization of multiple, potentially competing objectives. Multi-objective Bayesian optimization (MOBO) is a sample-efficient framework for identifying Pareto-optimal solutions. At the heart of MOBO is the acquisition function, which determines the next candidate to evaluate by navigating the best compromises among the objectives. Acquisition functions that rely on integrating over the objective space scale poorly to a large number of objectives. In this paper, we show a natural connection between the non-dominated solutions and the highest multivariate rank, which coincides with the extreme level line of the joint cumulative distribution function (CDF). Motivated by this link, we propose the CDF indicator, a Pareto-compliant metric for evaluating the quality of approximate Pareto sets, that can complement the popular hypervolume indicator. We then introduce an acquisition function based on the CDF indicator, called BOtied. BOtied can be implemented efficiently with copulas, a statistical tool for modeling complex, high-dimensional distributions. Our experiments on a variety of synthetic and real-world experiments demonstrate that BOtied outperforms state-of-the-art MOBO algorithms while being computationally efficient for many objectives.

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ICLR Conference 2024 Conference Paper

Concept Bottleneck Generative Models

Aya Abdelsalam Ismail
Julius Adebayo
Héctor Corrada Bravo
Stephen Ra
Kyunghyun Cho

We introduce a generative model with an intrinsically interpretable layer---a concept bottleneck layer---that constrains the model to encode human-understandable concepts. The concept bottleneck layer partitions the generative model into three parts: the pre-concept bottleneck portion, the CB layer, and the post-concept bottleneck portion. To train CB generative models, we complement the traditional task-based loss function for training generative models with a concept loss and an orthogonality loss. The CB layer and these loss terms are model agnostic, which we demonstrate by applying the CB layer to three different families of generative models: generative adversarial networks, variational autoencoders, and diffusion models. On multiple datasets across different types of generative models, steering a generative model, with the CB layer, outperforms all baselines---in some cases, it is \textit{10 times} more effective. In addition, we show how the CB layer can be used to interpret the output of the generative model and debug the model during or post training.

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ICLR Conference 2024 Conference Paper

Protein Discovery with Discrete Walk-Jump Sampling

Nathan C. Frey
Daniel Berenberg
Karina Zadorozhny
Joseph Kleinhenz
Julien Lafrance-Vanasse
Isidro Hötzel
Yan Wu 0027
Stephen Ra

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our $\textit{Discrete Walk-Jump Sampling}$ formalism combines the contrastive divergence training of an energy-based model and improved sample quality of a score-based model, while simplifying training and sampling by requiring only a single noise level. We evaluate the robustness of our approach on generative modeling of antibody proteins and introduce the $\textit{distributional conformity score}$ to benchmark protein generative models. By optimizing and sampling from our models for the proposed distributional conformity score, 97-100\% of generated samples are successfully expressed and purified and 70\% of functional designs show equal or improved binding affinity compared to known functional antibodies on the first attempt in a single round of laboratory experiments. We also report the first demonstration of long-run fast-mixing MCMC chains where diverse antibody protein classes are visited in a single MCMC chain.

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NeurIPS Conference 2023 Conference Paper

3D molecule generation by denoising voxel grids

Pedro O. O. Pinheiro
Joshua Rackers
Joseph Kleinhenz
Michael Maser
Omar Mahmood
Andrew Watkins
Stephen Ra
Vishnu Sresht

We propose a new score-based approach to generate 3D molecules represented as atomic densities on regular grids. First, we train a denoising neural network that learns to map from a smooth distribution of noisy molecules to the distribution of real molecules. Then, we follow the neural empirical Bayes framework [Saremi and Hyvarinen, 2019] and generate molecules in two steps: (i) sample noisy density grids from a smooth distribution via underdamped Langevin Markov chain Monte Carlo, and (ii) recover the "clean" molecule by denoising the noisy grid with a single step. Our method, VoxMol, generates molecules in a fundamentally different way than the current state of the art (ie, diffusion models applied to atom point clouds). It differs in terms of the data representation, the noise model, the network architecture and the generative modeling algorithm. Our experiments show that VoxMol captures the distribution of drug-like molecules better than state of the art, while being faster to generate samples.

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NeurIPS Conference 2023 Conference Paper

OpenProteinSet: Training data for structural biology at scale

Gustaf Ahdritz
Nazim Bouatta
Sachin Kadyan
Lukas Jarosch
Dan Berenberg
Ian Fisk
Andrew Watkins
Stephen Ra

Multiple sequence alignments (MSAs) of proteins encode rich biological information and have been workhorses in bioinformatic methods for tasks like protein design and protein structure prediction for decades. Recent breakthroughs like AlphaFold2 that use transformers to attend directly over large quantities of raw MSAs have reaffirmed their importance. Generation of MSAs is highly computationally intensive, however, and no datasets comparable to those used to train AlphaFold2 have been made available to the research community, hindering progress in machine learning for proteins. To remedy this problem, we introduce OpenProteinSet, an open-source corpus of more than 16 million MSAs, associated structural homologs from the Protein Data Bank, and AlphaFold2 protein structure predictions. We have previously demonstrated the utility of OpenProteinSet by successfully retraining AlphaFold2 on it. We expect OpenProteinSet to be broadly useful as training and validation data for 1) diverse tasks focused on protein structure, function, and design and 2) large-scale multimodal machine learning research.

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