arXiv subjects

Fei Ye

Publications and source records attributed to Fei Ye.

At least 55 records · Page 3Linked to original sources

arXiv2023

Accelerating Antimicrobial Peptide Discovery with Latent Structure

Antimicrobial peptides (AMPs) are promising therapeutic approaches against drug-resistant pathogens. Recently, deep generative models are used to discover new AMPs. However, previous studies mainly focus on peptide sequence attributes and do not consider crucial structure information. In this paper, we propose a latent sequence-structure model for designing AMPs (LSSAMP). LSSAMP exploits multi-scale vector quantization in the latent space to represent secondary structures (e.g. alpha helix and beta sheet). By sampling in the latent space, LSSAMP can simultaneously generate peptides with ideal sequence attributes and secondary structures. Experimental results show that the peptides generated by LSSAMP have a high probability of antimicrobial activity. Our wet laboratory experiments verified that two of the 21 candidates exhibit strong antimicrobial activity. The code is released at https://github.com/dqwang122/LSSAMP.

q-bio.BM↗

arXiv2023

Learning Harmonic Molecular Representations on Riemannian Manifold

Molecular representation learning plays a crucial role in AI-assisted drug discovery research. Encoding 3D molecular structures through Euclidean neural networks has become the prevailing method in the geometric deep learning community. However, the equivariance constraints and message passing in Euclidean space may limit the network expressive power. In this work, we propose a Harmonic Molecular Representation learning (HMR) framework, which represents a molecule using the Laplace-Beltrami eigenfunctions of its molecular surface. HMR offers a multi-resolution representation of molecular geometric and chemical features on 2D Riemannian manifold. We also introduce a harmonic message passing method to realize efficient spectral message passing over the surface manifold for better molecular encoding. Our proposed method shows comparable predictive power to current models in small molecule property prediction, and outperforms the state-of-the-art deep learning models for ligand-binding protein pocket classification and the rigid protein docking challenge, demonstrating its versatility in molecular representation learning.

cs.LG↗

arXiv2023

On Pre-trained Language Models for Antibody

Antibodies are vital proteins offering robust protection for the human body from pathogens. The development of general protein and antibody-specific pre-trained language models both facilitate antibody prediction tasks. However, there have been limited studies that comprehensively explore the representation capability of distinct pre-trained language models on different antibody tasks. To investigate the problem, we aim to answer several key questions in this paper, such as how pre-trained language models perform in antibody tasks with different specificity and how introducing specific biological mechanisms to the pre-training process can benefit the model. Additionally, we evaluate if the learned antibody pre-trained representations can be applied to real-world antibody problems, like drug discovery and immune process understanding. Previously, no benchmark available largely hindered the study to answer these questions. To aid in our investigation, we provide an AnTibody Understanding Evaluation (ATUE) benchmark. We comprehensively evaluate the performance of protein pre-trained language models by empirical study along with conclusions and new insights. Our ATUE and code are released at https://github.com/dqwang122/EATLM.

cs.CL↗

arXiv2022

Task-Free Continual Learning via Online Discrepancy Distance Learning

Learning from non-stationary data streams, also called Task-Free Continual Learning (TFCL) remains challenging due to the absence of explicit task information. Although recently some methods have been proposed for TFCL, they lack theoretical guarantees. Moreover, forgetting analysis during TFCL was not studied theoretically before. This paper develops a new theoretical analysis framework which provides generalization bounds based on the discrepancy distance between the visited samples and the entire information made available for training the model. This analysis gives new insights into the forgetting behaviour in classification tasks. Inspired by this theoretical model, we propose a new approach enabled by the dynamic component expansion mechanism for a mixture model, namely the Online Discrepancy Distance Learning (ODDL). ODDL estimates the discrepancy between the probabilistic representation of the current memory buffer and the already accumulated knowledge and uses it as the expansion signal to ensure a compact network architecture with optimal performance. We then propose a new sample selection approach that selectively stores the most relevant samples into the memory buffer through the discrepancy-based measure, further improving the performance. We perform several TFCL experiments with the proposed methodology, which demonstrate that the proposed approach achieves the state of the art performance.

cs.CV↗

arXiv2022

Continual Variational Autoencoder Learning via Online Cooperative Memorization

Due to their inference, data representation and reconstruction properties, Variational Autoencoders (VAE) have been successfully used in continual learning classification tasks. However, their ability to generate images with specifications corresponding to the classes and databases learned during Continual Learning (CL) is not well understood and catastrophic forgetting remains a significant challenge. In this paper, we firstly analyze the forgetting behaviour of VAEs by developing a new theoretical framework that formulates CL as a dynamic optimal transport problem. This framework proves approximate bounds to the data likelihood without requiring the task information and explains how the prior knowledge is lost during the training process. We then propose a novel memory buffering approach, namely the Online Cooperative Memorization (OCM) framework, which consists of a Short-Term Memory (STM) that continually stores recent samples to provide future information for the model, and a Long-Term Memory (LTM) aiming to preserve a wide diversity of samples. The proposed OCM transfers certain samples from STM to LTM according to the information diversity selection criterion without requiring any supervised signals. The OCM framework is then combined with a dynamic VAE expansion mixture network for further enhancing its performance.

cs.LG↗

arXiv2022

Learning an evolved mixture model for task-free continual learning

Recently, continual learning (CL) has gained significant interest because it enables deep learning models to acquire new knowledge without forgetting previously learnt information. However, most existing works require knowing the task identities and boundaries, which is not realistic in a real context. In this paper, we address a more challenging and realistic setting in CL, namely the Task-Free Continual Learning (TFCL) in which a model is trained on non-stationary data streams with no explicit task information. To address TFCL, we introduce an evolved mixture model whose network architecture is dynamically expanded to adapt to the data distribution shift. We implement this expansion mechanism by evaluating the probability distance between the knowledge stored in each mixture model component and the current memory buffer using the Hilbert Schmidt Independence Criterion (HSIC). We further introduce two simple dropout mechanisms to selectively remove stored examples in order to avoid memory overload while preserving memory diversity. Empirical results demonstrate that the proposed approach achieves excellent performance.

cs.LG↗

arXiv2022

Lattice dynamics in the charge-density-wave metal at a van-Hove-singularity filling

The charge-density-wave (CDW) order with macroscopically occupied electrons distorts the underlying lattice and usually causes the softening of the associated phonon mode. However, previous studies demonstrated that the spin-Peierls transition does not always induce an associated phonon softening, but the central-peak scenario applied in the quasi-one-dimensional compound CuGeO$_3$. We generalize the lattice-dynamics studies on the two-dimensional CDW state at van-Hove-singularity (VHS) filling and find that the CDW ordering could develop a central peak at zero frequency while the associated phonon undergoes hardening. The particle-hole scatterings between VHS points give rise to a low-energy increased charge-density susceptibility, and their coupling to the lattice dynamics induces two poles in the Green function for the CDW-associated phonon mode. The zero-frequency pole corresponds to the collective charge-density and phonon coupling mode. The high-frequency one is related to the high-temperature phonon mode that hardens as reaching the CDW transition. Our result may have the potential implication for the recently discovered Kagome metal $A$V$_3$Sb$_5$ ($A$ = K, Rb, Cs) in which no soft phonon is observed during the CDW transition.

cond-mat.str-el↗

arXiv2022

Supplemental Material: Lifelong Generative Modelling Using Dynamic Expansion Graph Model

In this article, we provide the appendix for Lifelong Generative Modelling Using Dynamic Expansion Graph Model. This appendix includes additional visual results as well as the numerical results on the challenging datasets. In addition, we also provide detailed proofs for the proposed theoretical analysis framework. The source code can be found in https://github.com/dtuzi123/Expansion-Graph-Model.

cs.LG↗

arXiv2021

Lifelong Generative Modelling Using Dynamic Expansion Graph Model

Variational Autoencoders (VAEs) suffer from degenerated performance, when learning several successive tasks. This is caused by catastrophic forgetting. In order to address the knowledge loss, VAEs are using either Generative Replay (GR) mechanisms or Expanding Network Architectures (ENA). In this paper we study the forgetting behaviour of VAEs using a joint GR and ENA methodology, by deriving an upper bound on the negative marginal log-likelihood. This theoretical analysis provides new insights into how VAEs forget the previously learnt knowledge during lifelong learning. The analysis indicates the best performance achieved when considering model mixtures, under the ENA framework, where there are no restrictions on the number of components. However, an ENA-based approach may require an excessive number of parameters. This motivates us to propose a novel Dynamic Expansion Graph Model (DEGM). DEGM expands its architecture, according to the novelty associated with each new databases, when compared to the information already learnt by the network from previous tasks. DEGM training optimizes knowledge structuring, characterizing the joint probabilistic representations corresponding to the past and more recently learned tasks. We demonstrate that DEGM guarantees optimal performance for each task while also minimizing the required number of parameters. Supplementary materials (SM) and source code are available in https://github.com/dtuzi123/Expansion-Graph-Model.

cs.LG↗

arXiv2021

Facet Dependent Topological Phase Transition in Bi4Br4

The realization of the coexistence of various topologically nontrivial surface states in one material is expected to lay a foundation for new electric applications with selective robust spin current. Here we apply the magnetoconductivity characteristic and angle-resolved photoemission spectroscopy (ARPES) to visualize the surface-selected electronic features evolution of quasi-one-dimensional material Bi4Br4. The transport measurements indicate the quantum interference correction to conductivity possesses symbolic spin rotational characteristic correlated to the value of Berry phase with the effects of weak localization and weak antilocalization for (001) and (100) surfaces, respectively. The ARPES spectra provide the experimental evidence for quasi-one-dimensional massless Dirac surface state at the side (100) surface and anisotropic massive Dirac surface state at the top (001) surface, respectively, which is highly coincide with the angle-dependent scaling behavior of magnetoconductivity. Our results reveal the facet dependent topological phases in quasi-one-dimensional Bi4Br4, stimulating the further investigations of this dual topology classes and the applications of the feasible technologies of topological spintronics.

cond-mat.mtrl-sci↗

arXiv2021

ESAD: End-to-end Deep Semi-supervised Anomaly Detection

This paper explores semi-supervised anomaly detection, a more practical setting for anomaly detection where a small additional set of labeled samples are provided. We propose a new KL-divergence based objective function for semi-supervised anomaly detection, and show that two factors: the mutual information between the data and latent representations, and the entropy of latent representations, constitute an integral objective function for anomaly detection. To resolve the contradiction in simultaneously optimizing the two factors, we propose a novel encoder-decoder-encoder structure, with the first encoder focusing on optimizing the mutual information and the second encoder focusing on optimizing the entropy. The two encoders are enforced to share similar encoding with a consistent constraint on their latent representations. Extensive experiments have revealed that the proposed method significantly outperforms several state-of-the-arts on multiple benchmark datasets, including medical diagnosis and several classic anomaly detection benchmarks.

cs.LG↗

arXiv2021

Lifelong Infinite Mixture Model Based on Knowledge-Driven Dirichlet Process

Recent research efforts in lifelong learning propose to grow a mixture of models to adapt to an increasing number of tasks. The proposed methodology shows promising results in overcoming catastrophic forgetting. However, the theory behind these successful models is still not well understood. In this paper, we perform the theoretical analysis for lifelong learning models by deriving the risk bounds based on the discrepancy distance between the probabilistic representation of data generated by the model and that corresponding to the target dataset. Inspired by the theoretical analysis, we introduce a new lifelong learning approach, namely the Lifelong Infinite Mixture (LIMix) model, which can automatically expand its network architectures or choose an appropriate component to adapt its parameters for learning a new task, while preserving its previously learnt information. We propose to incorporate the knowledge by means of Dirichlet processes by using a gating mechanism which computes the dependence between the knowledge learnt previously and stored in each component, and a new set of data. Besides, we train a compact Student model which can accumulate cross-domain representations over time and make quick inferences. The code is available at https://github.com/dtuzi123/Lifelong-infinite-mixture-model.

cs.LG↗

arXiv2021

Lifelong Mixture of Variational Autoencoders

In this paper, we propose an end-to-end lifelong learning mixture of experts. Each expert is implemented by a Variational Autoencoder (VAE). The experts in the mixture system are jointly trained by maximizing a mixture of individual component evidence lower bounds (MELBO) on the log-likelihood of the given training samples. The mixing coefficients in the mixture, control the contributions of each expert in the goal representation. These are sampled from a Dirichlet distribution whose parameters are determined through non-parametric estimation during lifelong learning. The model can learn new tasks fast when these are similar to those previously learnt. The proposed Lifelong mixture of VAE (L-MVAE) expands its architecture with new components when learning a completely new task. After the training, our model can automatically determine the relevant expert to be used when fed with new data samples. This mechanism benefits both the memory efficiency and the required computational cost as only one expert is used during the inference. The L-MVAE inference model is able to perform interpolation in the joint latent space across the data domains associated with different tasks and is shown to be efficient for disentangled learning representation.

cs.LG↗

arXiv2021

InfoVAEGAN : learning joint interpretable representations by information maximization and maximum likelihood

Learning disentangled and interpretable representations is an important step towards accomplishing comprehensive data representations on the manifold. In this paper, we propose a novel representation learning algorithm which combines the inference abilities of Variational Autoencoders (VAE) with the generalization capability of Generative Adversarial Networks (GAN). The proposed model, called InfoVAEGAN, consists of three networks~: Encoder, Generator and Discriminator. InfoVAEGAN aims to jointly learn discrete and continuous interpretable representations in an unsupervised manner by using two different data-free log-likelihood functions onto the variables sampled from the generator's distribution. We propose a two-stage algorithm for optimizing the inference network separately from the generator training. Moreover, we enforce the learning of interpretable representations through the maximization of the mutual information between the existing latent variables and those created through generative and inference processes.

cs.LG↗

arXiv2021

Lifelong Twin Generative Adversarial Networks

In this paper, we propose a new continuously learning generative model, called the Lifelong Twin Generative Adversarial Networks (LT-GANs). LT-GANs learns a sequence of tasks from several databases and its architecture consists of three components: two identical generators, namely the Teacher and Assistant, and one Discriminator. In order to allow for the LT-GANs to learn new concepts without forgetting, we introduce a new lifelong training approach, namely Lifelong Adversarial Knowledge Distillation (LAKD), which encourages the Teacher and Assistant to alternately teach each other, while learning a new database. This training approach favours transferring knowledge from a more knowledgeable player to another player which knows less information about a previously given task.

cs.CV↗

arXiv2021

Lifelong Teacher-Student Network Learning

A unique cognitive capability of humans consists in their ability to acquire new knowledge and skills from a sequence of experiences. Meanwhile, artificial intelligence systems are good at learning only the last given task without being able to remember the databases learnt in the past. We propose a novel lifelong learning methodology by employing a Teacher-Student network framework. While the Student module is trained with a new given database, the Teacher module would remind the Student about the information learnt in the past. The Teacher, implemented by a Generative Adversarial Network (GAN), is trained to preserve and replay past knowledge corresponding to the probabilistic representations of previously learn databases. Meanwhile, the Student module is implemented by a Variational Autoencoder (VAE) which infers its latent variable representation from both the output of the Teacher module as well as from the newly available database. Moreover, the Student module is trained to capture both continuous and discrete underlying data representations across different domains. The proposed lifelong learning framework is applied in supervised, semi-supervised and unsupervised training. The code is available~: \url{https://github.com/dtuzi123/Lifelong-Teacher-Student-Network-Learning}

cs.LG↗

arXiv2021

Few-Shot Bearing Fault Diagnosis Based on Model-Agnostic Meta-Learning

The rapid development of artificial intelligence and deep learning has provided many opportunities to further enhance the safety, stability, and accuracy of industrial Cyber-Physical Systems (CPS). As indispensable components to many mission-critical CPS assets and equipment, mechanical bearings need to be monitored to identify any trace of abnormal conditions. Most of the data-driven approaches applied to bearing fault diagnosis up-to-date are trained using a large amount of fault data collected a priori. In many practical applications, however, it can be unsafe and time-consuming to collect sufficient data samples for each fault category, making it challenging to train a robust classifier. In this paper, we propose a few-shot learning framework for bearing fault diagnosis based on model-agnostic meta-learning (MAML), which targets for training an effective fault classifier using limited data. In addition, it can leverage the training data and learn to identify new fault scenarios more efficiently. Case studies on the generalization to new artificial faults show that the proposed framework achieves an overall accuracy up to 25% higher than a Siamese network-based benchmark study. Finally, the robustness and the generalization capability of the proposed framework are further validated by applying it to identify real bearing damages using data from artificial damages, which compares favorably against 6 state-of-the-art few-shot learning algorithms using consistent test environments.

cs.LG↗

arXiv2021

A Survey of Deep Reinforcement Learning Algorithms for Motion Planning and Control of Autonomous Vehicles

In this survey, we systematically summarize the current literature on studies that apply reinforcement learning (RL) to the motion planning and control of autonomous vehicles. Many existing contributions can be attributed to the pipeline approach, which consists of many hand-crafted modules, each with a functionality selected for the ease of human interpretation. However, this approach does not automatically guarantee maximal performance due to the lack of a system-level optimization. Therefore, this paper also presents a growing trend of work that falls into the end-to-end approach, which typically offers better performance and smaller system scales. However, their performance also suffers from the lack of expert data and generalization issues. Finally, the remaining challenges applying deep RL algorithms on autonomous driving are summarized, and future research directions are also presented to tackle these challenges.

cs.RO↗