arXiv subjects

Chang-Yu Hsieh

Publications and source records attributed to Chang-Yu Hsieh.

At least 55 records · Page 3Linked to original sources

arXiv2022

The prospects of Monte Carlo antibody loop modelling on a fault-tolerant quantum computer

Quantum computing for the biological sciences is an area of rapidly growing interest, but specific industrial applications remain elusive. Quantum Markov chain Monte Carlo has been proposed as a method for accelerating a broad class of computational problems, including problems of pharmaceutical interest. Here we investigate the prospects of quantum advantage via this approach, by applying it to the problem of modelling antibody structure, a crucial task in drug development. To minimize the resources required while maintaining pharmaceutical-level accuracy, we propose a specific encoding of molecular dihedral angles into registers of qubits and a method for implementing, in quantum superposition, a Markov chain Monte Carlo update step based on a classical all-atom force field. We give the first detailed analysis of the resources required to solve a problem of industrial size and relevance and find that, though the time and space requirements of using a quantum computer in this way are considerable, continued technological improvements could bring the required resources within reach in the future.

quant-ph↗

arXiv2022

Variational Quantum Simulations of Finite-Temperature Dynamical Properties via Thermofield Dynamics

The recent advancement of quantum computer hardware offers the potential to simulate quantum many-body systems beyond the capability of its classical counterparts. However, most current works focus on simulating the ground-state properties or pure-state quantum dynamics of quantum systems. Finite-temperature physics are much less explored, and existing literature mainly consider equilibrium properties. Here we present a variational quantum simulation protocol based on the thermofield dynamics formalism to simulate the dynamical and non-equilibrium finite-temperature properties of quantum systems with near-term quantum computers. Compared to previous approaches in computing the equilibrium dynamical properties, our approach does not require the computationally expensive initial state sampling. More importantly, our approach is capable of simulating non-equilibrium phenomena which have not been previously explored with quantum computers. Numerical simulations of molecular absorption spectrum and spin quenched dynamics affirm the capability of our method.

quant-ph↗

arXiv2022

Retroformer: Pushing the Limits of Interpretable End-to-end Retrosynthesis Transformer

Retrosynthesis prediction is one of the fundamental challenges in organic synthesis. The task is to predict the reactants given a core product. With the advancement of machine learning, computer-aided synthesis planning has gained increasing interest. Numerous methods were proposed to solve this problem with different levels of dependency on additional chemical knowledge. In this paper, we propose Retroformer, a novel Transformer-based architecture for retrosynthesis prediction without relying on any cheminformatics tools for molecule editing. Via the proposed local attention head, the model can jointly encode the molecular sequence and graph, and efficiently exchange information between the local reactive region and the global reaction context. Retroformer reaches the new state-of-the-art accuracy for the end-to-end template-free retrosynthesis, and improves over many strong baselines on better molecule and reaction validity. In addition, its generative procedure is highly interpretable and controllable. Overall, Retroformer pushes the limits of the reaction reasoning ability of deep generative models.

physics.chem-ph↗

arXiv2022

Optimizing Quantum Annealing Schedules with Monte Carlo Tree Search enhanced with neural networks

Quantum annealing is a practical approach to approximately implement the adiabatic quantum computational model under a real-world setting. The goal of an adiabatic algorithm is to prepare the ground state of a problem-encoded Hamiltonian at the end of an annealing path. This is typically achieved by driving the dynamical evolution of a quantum system slowly to enforce adiabaticity. Properly optimized annealing schedules often significantly accelerate the computational process. Inspired by the recent success of deep reinforcement learning such as DeepMind's AlphaZero, we propose a Monte Carlo Tree Search (MCTS) algorithm and its enhanced version boosted with neural networks, which we name QuantumZero (QZero), to automate the design of annealing schedules in a hybrid quantum-classical framework. Both the MCTS and QZero algorithms perform remarkably well in discovering effective annealing schedules even when the annealing time is short for the 3-SAT examples we consider in this study. Furthermore, the flexibility of neural networks allows us to apply transfer-learning techniques to boost QZero's performance. We demonstrate in benchmark studies, that MCTS and QZero perform more efficiently than other reinforcement learning algorithms in designing annealing schedules.

quant-ph↗

arXiv2021

Modeling Protein Using Large-scale Pretrain Language Model

Protein is linked to almost every life process. Therefore, analyzing the biological structure and property of protein sequences is critical to the exploration of life, as well as disease detection and drug discovery. Traditional protein analysis methods tend to be labor-intensive and time-consuming. The emergence of deep learning models makes modeling data patterns in large quantities of data possible. Interdisciplinary researchers have begun to leverage deep learning methods to model large biological datasets, e.g. using long short-term memory and convolutional neural network for protein sequence classification. After millions of years of evolution, evolutionary information is encoded in protein sequences. Inspired by the similarity between natural language and protein sequences, we use large-scale language models to model evolutionary-scale protein sequences, encoding protein biology information in representation. Significant improvements are observed in both token-level and sequence-level tasks, demonstrating that our large-scale model can accurately capture evolution information from pretraining on evolutionary-scale individual sequences. Our code and model are available at https://github.com/THUDM/ProteinLM.

cs.LG↗

arXiv2021

Graph Self-Supervised Learning for Optoelectronic Properties of Organic Semiconductors

The search for new high-performance organic semiconducting molecules is challenging due to the vastness of the chemical space, machine learning methods, particularly deep learning models like graph neural networks (GNNs), have shown promising potential to address such challenge. However, practical applications of GNNs for chemistry are often limited by the availability of labelled data. Meanwhile, unlabelled molecular data is abundant and could potentially be utilized to alleviate the scarcity issue of labelled data. Here, we advocate the use of self-supervised learning to improve the performance of GNNs by pre-training them with unlabeled molecular data. We investigate regression problems involving ground and excited state properties, both relevant for optoelectronic properties of organic semiconductors. Additionally, we extend the self-supervised learning strategy to molecules in non-equilibrium configurations which are important for studying the effects of disorder. In all cases, we obtain considerable performance improvement over results without pre-training, in particular when labelled training data is limited, and such improvement is attributed to the capability of self-supervised learning in identifying structural similarity among unlabeled molecules.

physics.chem-ph↗

arXiv2021

Differentiable Quantum Architecture Search

Quantum architecture search (QAS) is the process of automating architecture engineering of quantum circuits. It has been desired to construct a powerful and general QAS platform which can significantly accelerate current efforts to identify quantum advantages of error-prone and depth-limited quantum circuits in the NISQ era. Hereby, we propose a general framework of differentiable quantum architecture search (DQAS), which enables automated designs of quantum circuits in an end-to-end differentiable fashion. We present several examples of circuit design problems to demonstrate the power of DQAS. For instance, unitary operations are decomposed into quantum gates, noisy circuits are re-designed to improve accuracy, and circuit layouts for quantum approximation optimization algorithm are automatically discovered and upgraded for combinatorial optimization problems. These results not only manifest the vast potential of DQAS being an essential tool for the NISQ application developments, but also present an interesting research topic from the theoretical perspective as it draws inspirations from the newly emerging interdisciplinary paradigms of differentiable programming, probabilistic programming, and quantum programming.

quant-ph↗

arXiv2021

Variational Quantum Simulation of Chemical Dynamics with Quantum Computers

Classical simulation of real-space quantum dynamics is challenging due to the exponential scaling of computational cost with system dimensions. Quantum computer offers the potential to simulate quantum dynamics with polynomial complexity; however, existing quantum algorithms based on the split-operator techniques require large-scale fault-tolerant quantum computers that remain elusive in the near future. Here we present variational simulations of real-space quantum dynamics suitable for implementation in Noisy Intermediate-Scale Quantum (NISQ) devices. The Hamiltonian is first encoded onto qubits using a discrete variable representation (DVR) and binary encoding scheme. We show that direct application of real-time variational quantum algorithm based on the McLachlan's principle is inefficient as the measurement cost grows exponentially with the qubit number for general potential energy and extremely small time-step size is required to achieve accurate results. Motivated by the insights that most chemical dynamics occur in the low energy subspace, we propose a subspace expansion method by projecting the total Hamiltonian, including the time-dependent driving field, onto the system low-energy eigenstate subspace using quantum computers, the exact quantum dynamics within the subspace can then be solved classically. We show that the measurement cost of the subspace approach grows polynomially with dimensionality for general potential energy. Our numerical examples demonstrate the capability of our approach, even under intense laser fields. Our work opens the possibility of simulating chemical dynamics with NISQ hardware.

quant-ph↗

arXiv2021

Fast Extraction of Word Embedding from Q-contexts

The notion of word embedding plays a fundamental role in natural language processing (NLP). However, pre-training word embedding for very large-scale vocabulary is computationally challenging for most existing methods. In this work, we show that with merely a small fraction of contexts (Q-contexts)which are typical in the whole corpus (and their mutual information with words), one can construct high-quality word embedding with negligible errors. Mutual information between contexts and words can be encoded canonically as a sampling state, thus, Q-contexts can be fast constructed. Furthermore, we present an efficient and effective WEQ method, which is capable of extracting word embedding directly from these typical contexts. In practical scenarios, our algorithm runs 11$\sim$13 times faster than well-established methods. By comparing with well-known methods such as matrix factorization, word2vec, GloVeand fasttext, we demonstrate that our method achieves comparable performance on a variety of downstream NLP tasks, and in the meanwhile maintains run-time and resource advantages over all these baselines.

cs.CL↗

arXiv2021

Simulation of Condensed-Phase Spectroscopy with Near-term Digital Quantum Computer

Spectroscopy is an indispensable tool in understanding the structures and dynamics of molecular systems. However computational modelling of spectroscopy is challenging due to the exponential scaling of computational complexity with system sizes unless drastic approximations are made. Quantum computer could potentially overcome these classically intractable computational tasks, but existing approaches using quantum computers to simulate spectroscopy can only handle isolated and static molecules. In this work we develop a workflow that combines multi-scale modeling and time-dependent variational quantum algorithm to compute the linear spectroscopy of systems interacting with their condensed-phase environment via the relevant time correlation function. We demonstrate the feasibility of our approach by numerically simulating the UV-Vis absorption spectra of organic semiconductors. We show that our dynamical approach captures several spectral features that are otherwise overlooked by static methods. Our method can be directly used for other linear condensed-phase spectroscopy and could potentially be extended to nonlinear multi-dimensional spectroscopy.

quant-ph↗

arXiv2021

Variational Quantum-Neural Hybrid Eigensolver

The variational quantum eigensolver (VQE) is one of the most representative quantum algorithms in the noisy intermediate-size quantum (NISQ) era, and is generally speculated to deliver one of the first quantum advantages for the ground-state simulations of some non-trivial Hamiltonians. However, short quantum coherence time and limited availability of quantum hardware resources in the NISQ hardware strongly restrain the capacity and expressiveness of VQEs. In this Letter, we introduce the variational quantum-neural hybrid eigensolver (VQNHE) in which the shallow-circuit quantum ansatz can be further enhanced by classical post-processing with neural networks. We show that VQNHE consistently and significantly outperforms VQE in simulating ground-state energies of quantum spins and molecules given the same amount of quantum resources. More importantly, we demonstrate that for arbitrary post-processing neural functions, VQNHE only incurs an polynomial overhead of processing time and represents the first scalable method to exponentially accelerate VQE with non-unitary post-processing that can be efficiently implemented in the NISQ era.

quant-ph↗

arXiv2021

A Neural-Network Variational Quantum Algorithm for Many-Body Dynamics

We propose a neural-network variational quantum algorithm to simulate the time evolution of quantum many-body systems. Based on a modified restricted Boltzmann machine (RBM) wavefunction ansatz, the proposed algorithm can be efficiently implemented in near-term quantum computers with low measurement cost. Using a qubit recycling strategy, only one ancilla qubit is required to represent all the hidden spins in an RBM architecture. The variational algorithm is extended to open quantum systems by employing a stochastic Schrodinger equation approach. Numerical simulations of spin-lattice models demonstrate that our algorithm is capable of capturing the dynamics of closed and open quantum many-body systems with high accuracy without suffering from the vanishing gradient (or 'barren plateau') issue for the considered system sizes.

quant-ph↗

arXiv2021

Neural Predictor based Quantum Architecture Search

Variational quantum algorithms (VQAs) are widely speculated to deliver quantum advantages for practical problems under the quantum-classical hybrid computational paradigm in the near term. Both theoretical and practical developments of VQAs share many similarities with those of deep learning. For instance, a key component of VQAs is the design of task-dependent parameterized quantum circuits (PQCs) as in the case of designing a good neural architecture in deep learning. Partly inspired by the recent success of AutoML and neural architecture search (NAS), quantum architecture search (QAS) is a collection of methods devised to engineer an optimal task-specific PQC. It has been proven that QAS-designed VQAs can outperform expert-crafted VQAs under various scenarios. In this work, we propose to use a neural network based predictor as the evaluation policy for QAS. We demonstrate a neural predictor guided QAS can discover powerful PQCs, yielding state-of-the-art results for various examples from quantum simulation and quantum machine learning. Notably, neural predictor guided QAS provides a better solution than that by the random-search baseline while using an order of magnitude less of circuit evaluations. Moreover, the predictor for QAS as well as the optimal ansatz found by QAS can both be transferred and generalized to address similar problems.

quant-ph↗

arXiv2020

Spectral Transfer Tensor Method for Non-Markovian Noise Characterization

With continuing improvements on the quality of fabricated quantum devices, it becomes increasingly crucial to analyze noisy quantum process in greater details such as characterizing the non-Markovianity in a quantitative manner. In this work, we propose an experimental protocol, termed Spectral Transfer Tensor Maps (SpecTTM), to accurately predict the RHP non-Markovian measure of any Pauli channels without state-preparation and measurement (SPAM) errors. In fact, for Pauli channels, SpecTTM even allows the reconstruction of highly-precised noise power spectrum for qubits. At last, we also discuss how SpecTTM can be useful to approximately characterize non-Markovianity of non-Pauli channels via Pauli twirling in an optimal basis.

quant-ph↗

arXiv2020

A quantum extension of SVM-perf for training nonlinear SVMs in almost linear time

We propose a quantum algorithm for training nonlinear support vector machines (SVM) for feature space learning where classical input data is encoded in the amplitudes of quantum states. Based on the classical SVM-perf algorithm of Joachims, our algorithm has a running time which scales linearly in the number of training examples $m$ (up to polylogarithmic factors) and applies to the standard soft-margin $\ell_1$-SVM model. In contrast, while classical SVM-perf has demonstrated impressive performance on both linear and nonlinear SVMs, its efficiency is guaranteed only in certain cases: it achieves linear $m$ scaling only for linear SVMs, where classification is performed in the original input data space, or for the special cases of low-rank or shift-invariant kernels. Similarly, previously proposed quantum algorithms either have super-linear scaling in $m$, or else apply to different SVM models such as the hard-margin or least squares $\ell_2$-SVM which lack certain desirable properties of the soft-margin $\ell_1$-SVM model. We classically simulate our algorithm and give evidence that it can perform well in practice, and not only for asymptotically large data sets.

quant-ph↗

arXiv2019

Deep Learning for Optoelectronic Properties of Organic Semiconductors

Atomistic modeling of energetic disorder in organic semiconductors (OSCs) and its effects on the optoelectronic properties of OSCs requires a large number of excited-state electronic-structure calculations, a computationally daunting task for many OSC applications. In this work, we advocate the use of deep learning to address this challenge and demonstrate that state-of-the-art deep neural networks (DNNs) are capable of predicting the electronic properties of OSCs at an accuracy comparable with the quantum chemistry methods used for generating training data. We extensively investigate the performances of four recent DNNs (deep tensor neural network, SchNet, message passing neural network, and multilevel graph convolutional neural network) in predicting various electronic properties of an important class of OSCs, i.e., oligothiophenes (OTs), including their HOMO and LUMO energies, excited-state energies and associated transition dipole moments. We find that SchNet shows the best performance for OTs of different sizes (from bithiophene to sexithiophene), achieving average prediction errors in the range of 20-80meV compared to the results from (time-dependent) density functional theory. We show that SchNet also consistently outperforms shallow feed-forward neural networks, especially in difficult cases with large molecules or limited training data. We further show that SchNet could predict the transition dipole moment accurately, a task previously known to be difficult for feed-forward neural networks, and we ascribe the relatively large errors in transition dipole prediction seen for some OT configurations to the charge-transfer character of their excited states. Finally, we demonstrate the effectiveness of SchNet by modeling the UV-Vis absorption spectra of OTs in dichloromethane and a good agreement is observed between the calculated and experimental spectra.

physics.chem-ph↗

arXiv2019

Quantum algorithms for feedforward neural networks

Quantum machine learning has the potential for broad industrial applications, and the development of quantum algorithms for improving the performance of neural networks is of particular interest given the central role they play in machine learning today. In this paper we present quantum algorithms for training and evaluating feedforward neural networks based on the canonical classical feedforward and backpropagation algorithms. Our algorithms rely on an efficient quantum subroutine for approximating the inner products between vectors in a robust way, and on implicitly storing large intermediate values in quantum random access memory for fast retrieval at later stages. The running times of our algorithms can be quadratically faster in the size of the network than their standard classical counterparts since they depend linearly on the number of neurons in the network, as opposed to the number of connections between neurons as in the classical case. This makes our algorithms suited for large-scale, highly-connected networks where the number of edges in the network dominates the classical algorithmic running time. Furthermore, networks trained by our quantum algorithm may have an intrinsic resilience to overfitting, as the algorithm naturally mimics the effects of classical techniques such as drop-out used to regularize networks. Our algorithms can also be used as the basis for new quantum-inspired classical algorithms which have the same dependence on the network dimensions as their quantum counterparts, but with quadratic overhead in other parameters that makes them relatively impractical.

quant-ph↗

arXiv2019

Unusual Transport Properties with Non-Commutative System-Bath Coupling Operators

Understanding non-equilibrium heat transport is crucial for controling heat flow in nano-scale systems. We study thermal energy transfer in a generalized non-equilibrium spin-boson model (NESB) with non-commutative system-bath coupling operators and discover unusual transport properties. Compared to the conventional NESB, the heat current is greatly enhanced by rotating the coupling operators. Constructive contribution to thermal rectification can be optimized when two sources of asymmetry, system-bath coupling strength and coupling operators, coexist. At the weak coupling and the adiabatic limit, the scaling dependence of heat current on the coupling strength and the system energy gap changes drastically when the coupling operators become non-commutative. These scaling relations can further be explained analytically by the non-equilibrium polaron-transformed Redfield equation. These novel transport properties, arising from the pure quantum effect of non-commutative coupling operators, should generally appear in other non-equilibrium set-ups and driven-systems.

cond-mat.stat-mech↗