arXiv subjects

Chang-Yu Hsieh

Publications and source records attributed to Chang-Yu Hsieh.

At least 37 records · Page 2Linked to original sources

arXiv2024

Token-Mol 1.0: Tokenized drug design with large language model

Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery lack the ability to comprehend three-dimensional (3D) structures, thereby limiting their effectiveness in tasks that explicitly involve molecular conformations. In this study, we introduced Token-Mol, a token-only 3D drug design model. This model encodes all molecular information, including 2D and 3D structures, as well as molecular property data, into tokens, which transforms classification and regression tasks in drug discovery into probabilistic prediction problems, thereby enabling learning through a unified paradigm. Token-Mol is built on the transformer decoder architecture and trained using random causal masking techniques. Additionally, we proposed the Gaussian cross-entropy (GCE) loss function to overcome the challenges in regression tasks, significantly enhancing the capacity of LLMs to learn continuous numerical values. Through a combination of fine-tuning and reinforcement learning (RL), Token-Mol achieves performance comparable to or surpassing existing task-specific methods across various downstream tasks, including pocket-based molecular generation, conformation generation, and molecular property prediction. Compared to existing molecular pre-trained models, Token-Mol exhibits superior proficiency in handling a wider range of downstream tasks essential for drug design. Notably, our approach improves regression task accuracy by approximately 30% compared to similar token-only methods. Token-Mol overcomes the precision limitations of token-only models and has the potential to integrate seamlessly with general models such as ChatGPT, paving the way for the development of a universal artificial intelligence drug design model that facilitates rapid and high-quality drug design by experts.

q-bio.BM↗

arXiv2024

Multi-Modal CLIP-Informed Protein Editing

Proteins govern most biological functions essential for life, but achieving controllable protein discovery and optimization remains challenging. Recently, machine learning-assisted protein editing (MLPE) has shown promise in accelerating optimization cycles and reducing experimental workloads. However, current methods struggle with the vast combinatorial space of potential protein edits and cannot explicitly conduct protein editing using biotext instructions, limiting their interactivity with human feedback. To fill these gaps, we propose a novel method called ProtET for efficient CLIP-informed protein editing through multi-modality learning. Our approach comprises two stages: in the pretraining stage, contrastive learning aligns protein-biotext representations encoded by two large language models (LLMs), respectively. Subsequently, during the protein editing stage, the fused features from editing instruction texts and original protein sequences serve as the final editing condition for generating target protein sequences. Comprehensive experiments demonstrated the superiority of ProtET in editing proteins to enhance human-expected functionality across multiple attribute domains, including enzyme catalytic activity, protein stability and antibody specific binding ability. And ProtET improves the state-of-the-art results by a large margin, leading to significant stability improvements of 16.67% and 16.90%. This capability positions ProtET to advance real-world artificial protein editing, potentially addressing unmet academic, industrial, and clinical needs.

cs.AI↗

arXiv2024

Human-level molecular optimization driven by mol-gene evolution

De novo molecule generation allows the search for more drug-like hits across a vast chemical space. However, lead optimization is still required, and the process of optimizing molecular structures faces the challenge of balancing structural novelty with pharmacological properties. This study introduces the Deep Genetic Molecular Modification Algorithm (DGMM), which brings structure modification to the level of medicinal chemists. A discrete variational autoencoder (D-VAE) is used in DGMM to encode molecules as quantization code, mol-gene, which incorporates deep learning into genetic algorithms for flexible structural optimization. The mol-gene allows for the discovery of pharmacologically similar but structurally distinct compounds, and reveals the trade-offs of structural optimization in drug discovery. We demonstrate the effectiveness of the DGMM in several applications.

cs.LG↗

arXiv2024

Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation

Most earlier 3D structure-based molecular generation approaches follow an atom-wise paradigm, incrementally adding atoms to a partially built molecular fragment within protein pockets. These methods, while effective in designing tightly bound ligands, often overlook other essential properties such as synthesizability. The fragment-wise generation paradigm offers a promising solution. However, a common challenge across both atom-wise and fragment-wise methods lies in their limited ability to co-design plausible chemical and geometrical structures, resulting in distorted conformations. In response to this challenge, we introduce the Deep Geometry Handling protocol, a more abstract design that extends the design focus beyond the model architecture. Through a comprehensive review of existing geometry-related models and their protocols, we propose a novel hybrid strategy, culminating in the development of FragGen - a geometry-reliable, fragment-wise molecular generation method. FragGen marks a significant leap forward in the quality of generated geometry and the synthesis accessibility of molecules. The efficacy of FragGen is further validated by its successful application in designing type II kinase inhibitors at the nanomolar level.

physics.chem-ph↗

arXiv2024

Generative AI for Controllable Protein Sequence Design: A Survey

The design of novel protein sequences with targeted functionalities underpins a central theme in protein engineering, impacting diverse fields such as drug discovery and enzymatic engineering. However, navigating this vast combinatorial search space remains a severe challenge due to time and financial constraints. This scenario is rapidly evolving as the transformative advancements in AI, particularly in the realm of generative models and optimization algorithms, have been propelling the protein design field towards an unprecedented revolution. In this survey, we systematically review recent advances in generative AI for controllable protein sequence design. To set the stage, we first outline the foundational tasks in protein sequence design in terms of the constraints involved and present key generative models and optimization algorithms. We then offer in-depth reviews of each design task and discuss the pertinent applications. Finally, we identify the unresolved challenges and highlight research opportunities that merit deeper exploration.

q-bio.BM↗

arXiv2024

Variational post-selection for ground states and thermal states simulation

Variational quantum algorithms (VQAs), as one of the most promising routes in the noisy intermediate-scale quantum (NISQ) era, offer various potential applications while also confront severe challenges due to near-term quantum hardware restrictions. In this work, we propose a framework to enhance the expressiveness of variational quantum ansatz by incorporating variational post-selection techniques. These techniques apply variational modules and neural network post-processing on ancilla qubits, which are compatible with the current generation of quantum devices. Equipped with variational post-selection, we demonstrate that the accuracy of the variational ground state and thermal state preparation for both quantum spin and molecule systems is substantially improved. Notably, in the case of estimating the local properties of a thermalized quantum system, we present a scalable approach that outperforms previous methods through the combination of neural post-selection and a new optimization objective.

quant-ph↗

arXiv2023

Sample-efficient Multi-objective Molecular Optimization with GFlowNets

Many crucial scientific problems involve designing novel molecules with desired properties, which can be formulated as a black-box optimization problem over the discrete chemical space. In practice, multiple conflicting objectives and costly evaluations (e.g., wet-lab experiments) make the diversity of candidates paramount. Computational methods have achieved initial success but still struggle with considering diversity in both objective and search space. To fill this gap, we propose a multi-objective Bayesian optimization (MOBO) algorithm leveraging the hypernetwork-based GFlowNets (HN-GFN) as an acquisition function optimizer, with the purpose of sampling a diverse batch of candidate molecular graphs from an approximate Pareto front. Using a single preference-conditioned hypernetwork, HN-GFN learns to explore various trade-offs between objectives. We further propose a hindsight-like off-policy strategy to share high-performing molecules among different preferences in order to speed up learning for HN-GFN. We empirically illustrate that HN-GFN has adequate capacity to generalize over preferences. Moreover, experiments in various real-world MOBO settings demonstrate that our framework predominantly outperforms existing methods in terms of candidate quality and sample efficiency. The code is available at https://github.com/violet-sto/HN-GFN.

cs.LG↗

arXiv2023

Variational Quantum-Neural Hybrid Error Mitigation

Quantum error mitigation (QEM) is crucial for obtaining reliable results on quantum computers by suppressing quantum noise with moderate resources. It is a key factor for successful and practical quantum algorithm implementations in the noisy intermediate scale quantum (NISQ) era. Since quantum-classical hybrid algorithms can be executed with moderate and noisy quantum resources, combining QEM with quantum-classical hybrid schemes is one of the most promising directions toward practical quantum advantages. In this work, we show how the variational quantum-neural hybrid eigensolver (VQNHE) algorithm, which seamlessly combines the expressive power of a parameterized quantum circuit with a neural network, is inherently noise resilient with a unique QEM capacity, which is absent in vanilla variational quantum eigensolvers (VQE). We carefully analyze and elucidate the asymptotic scaling of this unique QEM capacity in VQNHE from both theoretical and experimental perspectives. Finally, we propose a variational basis transformation for the Hamiltonian to be measured under the VQNHE framework, yielding a powerful tri-optimization setup, dubbed as VQNHE++. VQNHE++ can further enhance the quantum-neural hybrid expressive power and error mitigation capacity.

quant-ph↗

arXiv2023

Protein-Ligand Complex Generator & Drug Screening via Tiered Tensor Transform

The generation of small molecule candidate (ligand) binding poses in its target protein pocket is important for computer-aided drug discovery. Typical rigid-body docking methods ignore the pocket flexibility of protein, while the more accurate pose generation using molecular dynamics is hindered by slow protein dynamics. We develop a tiered tensor transform (3T) algorithm to rapidly generate diverse protein-ligand complex conformations for both pose and affinity estimation in drug screening, requiring neither machine learning training nor lengthy dynamics computation, while maintaining both coarse-grain-like coordinated protein dynamics and atomistic-level details of the complex pocket. The 3T conformation structures we generate achieve significantly higher accuracy in active ligand classification than traditional ensemble docking using hundreds of experimental protein conformations. Furthermore, we demonstrate that 3T can be used to explore distant protein-ligand binding poses within the protein pocket. 3T structure transformation is decoupled from the system physics, making future usage in other computational scientific domains possible.

cs.NE↗

arXiv2023

Neural network encoded variational quantum algorithms

We introduce a general framework called neural network (NN) encoded variational quantum algorithms (VQAs), or NN-VQA for short, to address the challenges of implementing VQAs on noisy intermediate-scale quantum (NISQ) computers. Specifically, NN-VQA feeds input (such as parameters of a Hamiltonian) from a given problem to a neural network and uses its outputs to parameterize an ansatz circuit for the standard VQA. Combining the strengths of NN and parameterized quantum circuits, NN-VQA can dramatically accelerate the training process of VQAs and handle a broad family of related problems with varying input parameters with the pre-trained NN. To concretely illustrate the merits of NN-VQA, we present results on NN-variational quantum eigensolver (VQE) for solving the ground state of parameterized XXZ spin models. Our results demonstrate that NN-VQE is able to estimate the ground-state energies of parameterized Hamiltonians with high precision without fine-tuning, and significantly reduce the overall training cost to estimate ground-state properties across the phases of XXZ Hamiltonian. We also employ an active-learning strategy to further increase the training efficiency while maintaining prediction accuracy. These encouraging results demonstrate that NN-VQAs offer a new hybrid quantum-classical paradigm to utilize NISQ resources for solving more realistic and challenging computational problems.

quant-ph↗

arXiv2023

Highly accurate and efficient deep learning paradigm for full-atom protein loop modeling with KarmaLoop

Protein loop modeling is the most challenging yet highly non-trivial task in protein structure prediction. Despite recent progress, existing methods including knowledge-based, ab initio, hybrid and deep learning (DL) methods fall significantly short of either atomic accuracy or computational efficiency. Moreover, an overarching focus on backbone atoms has resulted in a dearth of attention given to side-chain conformation, a critical aspect in a host of downstream applications including ligand docking, molecular dynamics simulation and drug design. To overcome these limitations, we present KarmaLoop, a novel paradigm that distinguishes itself as the first DL method centered on full-atom (encompassing both backbone and side-chain heavy atoms) protein loop modeling. Our results demonstrate that KarmaLoop considerably outperforms conventional and DL-based methods of loop modeling in terms of both accuracy and efficiency, with the average RMSD improved by over two-fold compared to the second-best baseline method across different tasks, and manifests at least two orders of magnitude speedup in general. Consequently, our comprehensive evaluations indicate that KarmaLoop provides a state-of-the-art DL solution for protein loop modeling, with the potential to hasten the advancement of protein engineering, antibody-antigen recognition, and drug design.

q-bio.BM↗

arXiv2023

MolHF: A Hierarchical Normalizing Flow for Molecular Graph Generation

Molecular de novo design is a critical yet challenging task in scientific fields, aiming to design novel molecular structures with desired property profiles. Significant progress has been made by resorting to generative models for graphs. However, limited attention is paid to hierarchical generative models, which can exploit the inherent hierarchical structure (with rich semantic information) of the molecular graphs and generate complex molecules of larger size that we shall demonstrate to be difficult for most existing models. The primary challenge to hierarchical generation is the non-differentiable issue caused by the generation of intermediate discrete coarsened graph structures. To sidestep this issue, we cast the tricky hierarchical generation problem over discrete spaces as the reverse process of hierarchical representation learning and propose MolHF, a new hierarchical flow-based model that generates molecular graphs in a coarse-to-fine manner. Specifically, MolHF first generates bonds through a multi-scale architecture, then generates atoms based on the coarsened graph structure at each scale. We demonstrate that MolHF achieves state-of-the-art performance in random generation and property optimization, implying its high capacity to model data distribution. Furthermore, MolHF is the first flow-based model that can be applied to model larger molecules (polymer) with more than 100 heavy atoms. The code and models are available at https://github.com/violet-sto/MolHF.

cs.LG↗

arXiv2023

An Equivariant Generative Framework for Molecular Graph-Structure Co-Design

Designing molecules with desirable physiochemical properties and functionalities is a long-standing challenge in chemistry, material science, and drug discovery. Recently, machine learning-based generative models have emerged as promising approaches for \emph{de novo} molecule design. However, further refinement of methodology is highly desired as most existing methods lack unified modeling of 2D topology and 3D geometry information and fail to effectively learn the structure-property relationship for molecule design. Here we present MolCode, a roto-translation equivariant generative framework for \underline{Mol}ecular graph-structure \underline{Co-de}sign. In MolCode, 3D geometric information empowers the molecular 2D graph generation, which in turn helps guide the prediction of molecular 3D structure. Extensive experimental results show that MolCode outperforms previous methods on a series of challenging tasks including \emph{de novo} molecule design, targeted molecule discovery, and structure-based drug design. Particularly, MolCode not only consistently generates valid (99.95$\%$ Validity) and diverse (98.75$\%$ Uniqueness) molecular graphs/structures with desirable properties, but also generate drug-like molecules with high affinity to target proteins (61.8$\%$ high-affinity ratio), which demonstrates MolCode's potential applications in material design and drug discovery. Our extensive investigation reveals that the 2D topology and 3D geometry contain intrinsically complementary information in molecule design, and provide new insights into machine learning-based molecule representation and generation.

q-bio.BM↗

arXiv2023

Discrete time crystal enabled by Stark many-body localization

Discrete time crystal (DTC) has recently attracted increasing attention, but most DTC models and their properties are only revealed after disorder average. In this Letter, we propose a simple disorder-free periodically driven model that exhibits nontrivial DTC order stabilized by Stark many-body localization (MBL). We demonstrate the existence of DTC phase by analytical analysis from perturbation theory and convincing numerical evidence from observable dynamics. The new DTC model paves a new promising way for further experiments and deepens our understanding of DTC. Since the DTC order doesn't require special quantum state preparation and the strong disorder average, it can be naturally realized on the noisy intermediate-scale quantum (NISQ) hardware with much fewer resources and repetitions. Moreover, besides the robust subharmonic response, there are other novel robust beating oscillations in Stark-MBL DTC phase which are absent in random or quasi-periodic MBL DTC.

cond-mat.str-el↗

arXiv2023

Probing many-body localization by excited-state VQE

Non-equilibrium physics including many-body localization (MBL) has attracted increasing attentions, but theoretical approaches of reliably studying non-equilibrium properties remain quite limited. In this Letter, we propose a systematic approach to probe MBL phases via the excited-state variational quantum eigensolver (VQE) and demonstrate convincing results of MBL on a quantum hardware, which we believe paves a promising way for future simulations of non-equilibrium systems beyond the reach of classical computations in the noisy intermediate-scale quantum (NISQ) era. Moreover, the MBL probing protocol based on excited-state VQE is NISQ-friendly, as it can successfully differentiate the MBL phase from thermal phases with relatively-shallow quantum circuits, and it is also robust against the effect of quantum noises.

quant-ph↗

arXiv2023

TensorCircuit: a Quantum Software Framework for the NISQ Era

TensorCircuit is an open source quantum circuit simulator based on tensor network contraction, designed for speed, flexibility and code efficiency. Written purely in Python, and built on top of industry-standard machine learning frameworks, TensorCircuit supports automatic differentiation, just-in-time compilation, vectorized parallelism and hardware acceleration. These features allow TensorCircuit to simulate larger and more complex quantum circuits than existing simulators, and are especially suited to variational algorithms based on parameterized quantum circuits. TensorCircuit enables orders of magnitude speedup for various quantum simulation tasks compared to other common quantum software, and can simulate up to 600 qubits with moderate circuit depth and low-dimensional connectivity. With its time and space efficiency, flexible and extensible architecture and compact, user-friendly API, TensorCircuit has been built to facilitate the design, simulation and analysis of quantum algorithms in the Noisy Intermediate-Scale Quantum (NISQ) era.

quant-ph↗

arXiv2022

Variational quantum simulation of the imaginary-time Lyapunov control for accelerating the ground-state preparation

Quantum computers have been widely speculated to offer significant advantages in obtaining the ground state of difficult Hamiltonian in chemistry and physics. In this work, we first propose a Lyapunov control-inspired strategy to accelerate the well-established imaginary-time method for ground-state preparation. We also dig for the source of acceleration of the imaginary-time process under Lyapunov control with theoretical understanding and dynamic process visualization. To make the method accessible in the noisy intermediate-scale quantum era, we further propose a variational form of the algorithm that could work with shallow quantum circuits. Through numerical experiments on a broad spectrum of realistic models, including molecular systems, 2D Heisenberg models, and Sherrington-Kirkpatrick models, we show that imaginary-time control may substantially accelerate the imaginary time evolution for all systems and even generate orders of magnitude acceleration (suggesting exponential-like acceleration) for challenging molecular Hamiltonians involving small energy gaps as impressive special cases. Finally, with a proper selection of the control Hamiltonian, the new variational quantum algorithm does not incur additional measurement costs compared to the original variational quantum imaginary-time algorithm.

quant-ph↗

arXiv2022

A non-Hermitian Ground State Searching Algorithm Enhanced by Variational Toolbox

Ground-state preparation for a given Hamiltonian is a common quantum-computing task of great importance and has relevant applications in quantum chemistry, computational material modeling, and combinatorial optimization. We consider an approach to simulate dissipative non-Hermitian Hamiltonian quantum dynamics using Hamiltonian simulation techniques to efficiently recover the ground state of a target Hamiltonian. The proposed method facilitates the energy transfer by repeatedly projecting ancilla qubits to the desired state, rendering the effective non-Hermitian Hamiltonian evolution on the system qubits. To make the method more resource friendly in the noisy intermediate-scale quantum (NISQ) and early fault-tolerant era, we combine the non-Hermitian projection algorithm with multiple variational gadgets, including variational module enhancement and variational state recording, to reduce the required circuit depth and avoid the exponentially vanishing success probability for post-selections. We compare our method, the non-Hermitian-variational algorithm, with a pure variational method -- QAOA for solving the 3-SAT problem and preparing the ground state for the transverse-field Ising model. As demonstrated by numerical evidence, the non-Hermitian-variational algorithm outperforms QAOA in convergence speed with improved quantum resource efficiency.

quant-ph↗