Prashant Emani works at Yale University.

Posts

A Quantum Variational Autoencoder Utilizing Regularized Mixed-state Latent Representations

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A major challenge in near-term quantum computing is its application to large real-world datasets due to scarce quantum hardware resources. One approach to enabling tractable quantum models for such datasets involves finding low-dimensional representations that preserve essential information for downstream analysis. Inclassical machine learning, variational autoencoders (VAEs) facilitate efficient data compression, representationlearning for subsequent tasks, and novel data generation. However, no quantum model has been proposed thatexactly captures all of these features for direct application to quantum data on quantum computers. Some existingquantum models for data compression lack regularization of latent representations, thus preventing direct use forgeneration and control of generalization. Others are hybrid models with only some internal quantum components,impeding direct training on quantum data. To address this, we present a fully quantum framework, ?-QVAE,which encompasses all the capabilities of classical VAEs and can be directly applied to map both classicaland quantum data to a lower-dimensional space, while effectively reconstructing much of the original statefrom it. Our model utilizes regularized mixed states to attain optimal latent representations. It accommodatesvarious divergences for reconstruction and regularization. Furthermore, by accommodating mixed states at everystage, it can utilize the full data density matrix and allow for a training objective defined on probabilisticmixtures of input data. Doing so, in turn, makes efficient optimization possible and has potential implications forprivate and federated learning. In addition to exploring the theoretical properties of ?-QVAE, we demonstrateits performance on representative genomics and synthetic data. Our results indicate that ?-QVAE consistentlylearns representations that better utilize the capacity of the latent space and exhibits similar or better performancecompared with matched classical models.

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Binding Peptide Generation for MHC Class I Proteins with Deep Reinforcement Learning

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Motivation: MHC Class I protein plays an important role in immunotherapy by presenting immunogenic peptides to anti-tumor immune cells. The repertoires of peptides for various MHC Class I proteins are distinct, which can be reflected by their diverse binding motifs. To characterize binding motifs for MHC Class I proteins, in vitro experiments have been conducted to screen peptides with high binding affinities to hundreds of given MHC Class I proteins. However, considering tens of thousands of known MHC Class I proteins, conducting in vitro experiments for extensive MHC proteins is infeasible, and thus a more efficient and scalable way to characterize binding motifs is needed.Results: We presented a de novo generation framework, coined PepPPO, to characterize binding motif for any given MHC Class I proteins via generating repertoires of peptides presented by them. PepPPO leverages a reinforcement learning agent with a mutation policy to mutate random input peptides into positive presented ones. Using PepPPO, we characterized binding motifs for around 10 000 known human MHC Class I proteins with and without experimental for the rapid screening of neoantigens at a much lower time cost than previous deep-learning methods.

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