Fei Ye

Danqing Wang, Zeyu Wen, Fei Ye et al. · cmu

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.

Danqing Wang, Fei Ye, Hao Zhou

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.

Yiqun Wang, Yuning Shen, Shi Chen et al. · tsinghua

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.

Fei Ye, Adrian G. Bors

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.

Zaixiang Zheng, Yifan Deng, Dongyu Xue et al.

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

Fei Ye, Adrian G. Bors

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.

Fei Ye, Adrian G. Bors

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.

Xinyou Wang, Zaixiang Zheng, Fei Ye et al.

This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences. We first pre-train scalable DPLMs from evolutionary-scale protein sequences within a generative self-supervised discrete diffusion probabilistic framework, which generalizes language modeling for proteins in a principled way. After pre-training, DPLM exhibits the ability to generate structurally plausible, novel, and diverse protein sequences for unconditional generation. We further demonstrate the proposed diffusion generative pre-training makes DPLM possess a better understanding of proteins, making it a superior representation learner, which can be fine-tuned for various predictive tasks, comparing favorably to ESM2 (Lin et al., 2022). Moreover, DPLM can be tailored for various needs, which showcases its prowess of conditional generation in several ways: (1) conditioning on partial peptide sequences, e.g., generating scaffolds for functional motifs with high success rate; (2) incorporating other modalities as conditioner, e.g., structure-conditioned generation for inverse folding; and (3) steering sequence generation towards desired properties, e.g., satisfying specified secondary structures, through a plug-and-play classifier guidance. Code is released at \url{https://github.com/bytedance/dplm}.

Fei Ye, Zaixiang Zheng, Dongyu Xue et al.

Recent years have witnessed a surge in the development of protein foundation models, significantly improving performance in protein prediction and generative tasks ranging from 3D structure prediction and protein design to conformational dynamics. However, the capabilities and limitations associated with these models remain poorly understood due to the absence of a unified evaluation framework. To fill this gap, we introduce ProteinBench, a holistic evaluation framework designed to enhance the transparency of protein foundation models. Our approach consists of three key components: (i) A taxonomic classification of tasks that broadly encompass the main challenges in the protein domain, based on the relationships between different protein modalities; (ii) A multi-metric evaluation approach that assesses performance across four key dimensions: quality, novelty, diversity, and robustness; and (iii) In-depth analyses from various user objectives, providing a holistic view of model performance. Our comprehensive evaluation of protein foundation models reveals several key findings that shed light on their current capabilities and limitations. To promote transparency and facilitate further research, we release the evaluation dataset, code, and a public leaderboard publicly for further analysis and a general modular toolkit. We intend for ProteinBench to be a living benchmark for establishing a standardized, in-depth evaluation framework for protein foundation models, driving their development and application while fostering collaboration within the field.

Zipeng Qi, Guoxi Huang, Chenyang Liu et al.

This paper introduces innovative solutions to enhance spatial controllability in diffusion models reliant on text queries. We first introduce vision guidance as a foundational spatial cue within the perturbed distribution. This significantly refines the search space in a zero-shot paradigm to focus on the image sampling process adhering to the spatial layout conditions. To precisely control the spatial layouts of multiple visual concepts with the employment of vision guidance, we propose a universal framework, Layered Rendering Diffusion (LRDiff), which constructs an image-rendering process with multiple layers, each of which applies the vision guidance to instructively estimate the denoising direction for a single object. Such a layered rendering strategy effectively prevents issues like unintended conceptual blending or mismatches while allowing for more coherent and contextually accurate image synthesis. The proposed method offers a more efficient and accurate means of synthesising images that align with specific layout and contextual requirements. Through experiments, we demonstrate that our method outperforms existing techniques, both quantitatively and qualitatively, in two specific layout-to-image tasks: bounding box-to-image and instance maskto-image. Furthermore, we extend the proposed framework to enable spatially controllable editing

Titouan Duston, Shuo Xin, Yang Sun et al.

We introduce AInsteinBench, a large-scale benchmark for evaluating whether large language model (LLM) agents can operate as scientific computing development agents within real research software ecosystems. Unlike existing scientific reasoning benchmarks which focus on conceptual knowledge, or software engineering benchmarks that emphasize generic feature implementation and issue resolving, AInsteinBench evaluates models in end-to-end scientific development settings grounded in production-grade scientific repositories. The benchmark consists of tasks derived from maintainer-authored pull requests across six widely used scientific codebases, spanning quantum chemistry, quantum computing, molecular dynamics, numerical relativity, fluid dynamics, and cheminformatics. All benchmark tasks are carefully curated through multi-stage filtering and expert review to ensure scientific challenge, adequate test coverage, and well-calibrated difficulty. By leveraging evaluation in executable environments, scientifically meaningful failure modes, and test-driven verification, AInsteinBench measures a model's ability to move beyond surface-level code generation toward the core competencies required for computational scientific research.

Fei Ye, Adrian G. Bors

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.

Fei Ye, Adrian G. Bors

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.

Fei Ye, Adrian G. Bors

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.

Fei Ye, Adrian G. Bors

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}

Xinyou Wang, Zaixiang Zheng, Fei Ye et al.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Cheng-Yen Hsieh, Xinyou Wang, Daiheng Zhang et al.

Multimodal protein language models (PLMs) integrate sequence and token-based structural information, serving as a powerful foundation for protein modeling, generation, and design. However, the reliance on tokenizing 3D structures into discrete tokens causes substantial loss of fidelity about fine-grained structural details and correlations. In this paper, we systematically elucidate the design space of multimodal PLMs to overcome their limitations. We identify tokenization loss and inaccurate structure token predictions by the PLMs as major bottlenecks. To address these, our proposed design space covers improved generative modeling, structure-aware architectures and representation learning, and data exploration. Our advancements approach finer-grained supervision, demonstrating that token-based multimodal PLMs can achieve robust structural modeling. The effective design methods dramatically improve the structure generation diversity, and notably, folding abilities of our 650M model by reducing the RMSD from 5.52 to 2.36 on PDB testset, even outperforming 3B baselines and on par with the specialized folding models. Project page and code: https://bytedance.github.io/dplm/dplm-2.1/.

Guoxi Huang, Nantheera Anantrasirichai, Fei Ye et al.

In image enhancement tasks, such as low-light and underwater image enhancement, a degraded image can correspond to multiple plausible target images due to dynamic photography conditions, such as variations in illumination. This naturally results in a one-to-many mapping challenge. To address this, we propose a Bayesian Enhancement Model (BEM) that incorporates Bayesian Neural Networks (BNNs) to capture data uncertainty and produce diverse outputs. To achieve real-time inference, we introduce a two-stage approach: Stage I employs a BNN to model the one-to-many mappings in the low-dimensional space, while Stage II refines fine-grained image details using a Deterministic Neural Network (DNN). To accelerate BNN training and convergence, we introduce a dynamic Momentum Prior. Extensive experiments on multiple low-light and underwater image enhancement benchmarks demonstrate the superiority of our method over deterministic models.

Runqing Wu, Fei Ye, Qihe Liu et al.

Continual Learning seeks to develop a model capable of incrementally assimilating new information while retaining prior knowledge. However, current research predominantly addresses a straightforward learning context, wherein all data samples originate from a singular data domain. This paper shifts focus to a more complex and realistic learning environment, characterized by data samples sourced from multiple distinct domains. We tackle this intricate learning challenge by introducing a novel methodology, termed the Multi-Source Dynamic Expansion Model (MSDEM), which leverages various pre-trained models as backbones and progressively establishes new experts based on them to adapt to emerging tasks. Additionally, we propose an innovative dynamic expandable attention mechanism designed to selectively harness knowledge from multiple backbones, thereby accelerating the new task learning. Moreover, we introduce a dynamic graph weight router that strategically reuses all previously acquired parameters and representations for new task learning, maximizing the positive knowledge transfer effect, which further improves generalization performance. We conduct a comprehensive series of experiments, and the empirical findings indicate that our proposed approach achieves state-of-the-art performance.

RunQing Wu, KaiHui Huang, HanYi Zhang et al.

Continuously acquiring new knowledge from a dynamic environment is a fundamental capability for animals, facilitating their survival and ability to address various challenges. This capability is referred to as continual learning, which focuses on the ability to learn a sequence of tasks without the detriment of previous knowledge. A prevalent strategy to tackle continual learning involves selecting and storing numerous essential data samples from prior tasks within a fixed-size memory buffer. However, the majority of current memory-based techniques typically utilize a single memory buffer, which poses challenges in concurrently managing newly acquired and previously learned samples. Drawing inspiration from the Complementary Learning Systems (CLS) theory, which defines rapid and gradual learning mechanisms for processing information, we propose an innovative dual memory system called the Information-Theoretic Dual Memory System (ITDMS). This system comprises a fast memory buffer designed to retain temporary and novel samples, alongside a slow memory buffer dedicated to preserving critical and informative samples. The fast memory buffer is optimized employing an efficient reservoir sampling process. Furthermore, we introduce a novel information-theoretic memory optimization strategy that selectively identifies and retains diverse and informative data samples for the slow memory buffer. Additionally, we propose a novel balanced sample selection procedure that automatically identifies and eliminates redundant memorized samples, thus freeing up memory capacity for new data acquisitions, which can deal with a growing array of tasks. Our methodology is rigorously assessed through a series of continual learning experiments, with empirical results underscoring the effectiveness of the proposed system.

Lingfei Zeng, Fengdi Che, Xuhan Huang et al.

Formal verification is the next frontier for ensuring the correctness of code generated by Large Language Models (LLMs). While methods that co-generate code and formal specifications in formal languages, like Dafny, can, in principle, prove alignment with user intent, progress is bottlenecked by specification quality evaluation. Current benchmarks rely on matching against ground-truth specifications, a manual and expertise-intensive process that has limited existing datasets to a few hundred simple problems and also suffers from a reliability issue. To address this, we introduce VeriEquivBench, a new benchmark with $2,389$ complex algorithmic problems that probe the limitations of current models in both code generation and formal reasoning. Our evaluation framework replaces ground-truth matching with a formally grounded metric, the equivalence score, and rigorously verifies the quality of generated specifications and code. Our results show that generating formally verifiable code remains a profound challenge for state-of-the-art LLMs. This underscores both the difficulty of the task and the need for benchmarks like VeriEquivBench to drive progress toward scalable and reliable coding agents.

Ruihao Zhang, Mao chen, Fei Ye et al.

T cell receptor (TCR) repertoires encode critical immunological signatures for autoimmune diseases, yet their clinical application remains limited by sequence sparsity and low witness rates. We developed EAMil, a multi-instance deep learning framework that leverages TCR sequencing data to diagnose systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) with exceptional accuracy. By integrating PrimeSeq feature extraction with ESMonehot encoding and enhanced gate attention mechanisms, our model achieved state-of-the-art performance with AUCs of 98.95% for SLE and 97.76% for RA. EAMil successfully identified disease-associated genes with over 90% concordance with established differential analyses and effectively distinguished disease-specific TCR genes. The model demonstrated robustness in classifying multiple disease categories, utilizing the SLEDAI score to stratify SLE patients by disease severity as well as to diagnose the site of damage in SLE patients, and effectively controlling for confounding factors such as age and gender. This interpretable framework for immune receptor analysis provides new insights for autoimmune disease detection and classification with broad potential clinical applications across immune-mediated conditions.

Congren Dai, Huichi Zhou, Jiahao Huang et al.

Online Continual Learning (OCL) presents a complex learning environment in which new data arrives in a batch-to-batch online format, and the risk of catastrophic forgetting can significantly impair model efficacy. In this study, we address OCL by introducing an innovative memory framework that incorporates a short-term memory system to retain dynamic information and a long-term memory system to archive enduring knowledge. Specifically, the long-term memory system comprises a collection of sub-memory buffers, each linked to a cluster prototype and designed to retain data samples from distinct categories. We propose a novel $K$-means-based sample selection method to identify cluster prototypes for each encountered category. To safeguard essential and critical samples, we introduce a novel memory optimisation strategy that selectively retains samples in the appropriate sub-memory buffer by evaluating each cluster prototype against incoming samples through an optimal transportation mechanism. This approach specifically promotes each sub-memory buffer to retain data samples that exhibit significant discrepancies from the corresponding cluster prototype, thereby ensuring the preservation of semantically rich information. In addition, we propose a novel Divide-and-Conquer (DAC) approach that formulates the memory updating as an optimisation problem and divides it into several subproblems. As a result, the proposed DAC approach can solve these subproblems separately and thus can significantly reduce computations of the proposed memory updating process. We conduct a series of experiments across standard and imbalanced learning settings, and the empirical findings indicate that the proposed memory framework achieves state-of-the-art performance in both learning contexts.

Runqing Wu, Kaihui Huang, Hanyi Zhang et al.

Continual Learning (CL) epitomizes an advanced training paradigm wherein prior data samples remain inaccessible during the acquisition of new tasks. Numerous investigations have delved into leveraging a pre-trained Vision Transformer (ViT) to enhance model efficacy in continual learning. Nonetheless, these approaches typically utilize a singular, static backbone, which inadequately adapts to novel tasks, particularly when engaging with diverse data domains, due to a substantial number of inactive parameters. This paper addresses this limitation by introducing an innovative Self-Controlled Dynamic Expansion Model (SCDEM), which orchestrates multiple distinct trainable pre-trained ViT backbones to furnish diverse and semantically enriched representations. Specifically, by employing the multi-backbone architecture as a shared module, the proposed SCDEM dynamically generates a new expert with minimal parameters to accommodate a new task. A novel Collaborative Optimization Mechanism (COM) is introduced to synergistically optimize multiple backbones by harnessing prediction signals from historical experts, thereby facilitating new task learning without erasing previously acquired knowledge. Additionally, a novel Feature Distribution Consistency (FDC) approach is proposed to align semantic similarity between previously and currently learned representations through an optimal transport distance-based mechanism, effectively mitigating negative knowledge transfer effects. Furthermore, to alleviate over-regularization challenges, this paper presents a novel Dynamic Layer-Wise Feature Attention Mechanism (DLWFAM) to autonomously determine the penalization intensity on each trainable representation layer. An extensive series of experiments have been conducted to evaluate the proposed methodology's efficacy, with empirical results corroborating that the approach attains state-of-the-art performance.

KaiHui Huang, RunQing Wu, JinHui Shen et al.

Continual learning has emerged as a pivotal area of research, primarily due to its advantageous characteristic that allows models to persistently acquire and retain information. However, catastrophic forgetting can severely impair model performance. In this study, we address network forgetting by introducing a novel framework termed Optimally-Weighted Maximum Mean Discrepancy (OWMMD), which imposes penalties on representation alterations via a Multi-Level Feature Matching Mechanism (MLFMM). Furthermore, we propose an Adaptive Regularization Optimization (ARO) strategy to refine the adaptive weight vectors, which autonomously assess the significance of each feature layer throughout the optimization process, The proposed ARO approach can relieve the over-regularization problem and promote the future task learning. We conduct a comprehensive series of experiments, benchmarking our proposed method against several established baselines. The empirical findings indicate that our approach achieves state-of-the-art performance.

Yiming Ma, Fei Ye, Yi Zhou et al.

Nature creates diverse proteins through a 'divide and assembly' strategy. Inspired by this idea, we introduce ProteinWeaver, a two-stage framework for protein backbone design. Our method first generates individual protein domains and then employs an SE(3) diffusion model to flexibly assemble these domains. A key challenge lies in the assembling step, given the complex and rugged nature of the inter-domain interaction landscape. To address this challenge, we employ preference alignment to discern complex relationships between structure and interaction landscapes through comparative analysis of generated samples. Comprehensive experiments demonstrate that ProteinWeaver: (1) generates high-quality, novel protein backbones through versatile domain assembly; (2) outperforms RFdiffusion, the current state-of-the-art in backbone design, by 13\% and 39\% for long-chain proteins; (3) shows the potential for cooperative function design through illustrative case studies. To sum up, by introducing a `divide-and-assembly' paradigm, ProteinWeaver advances protein engineering and opens new avenues for functional protein design.

Fei Ye, Adrian G. Bors

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.

Fei Ye, Adrian G. Bors

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.

Fei Ye, Adrian G. Bors

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.

Fei Ye, Shen Zhang, Pin Wang et al.

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.

Chaoqin Huang, Fei Ye, Peisen Zhao et al.

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.

Fei Ye, Huangjie Zheng, Chaoqin Huang et al.

Surrogate task based methods have recently shown great promise for unsupervised image anomaly detection. However, there is no guarantee that the surrogate tasks share the consistent optimization direction with anomaly detection. In this paper, we return to a direct objective function for anomaly detection with information theory, which maximizes the distance between normal and anomalous data in terms of the joint distribution of images and their representation. Unfortunately, this objective function is not directly optimizable under the unsupervised setting where no anomalous data is provided during training. Through mathematical analysis of the above objective function, we manage to decompose it into four components. In order to optimize in an unsupervised fashion, we show that, under the assumption that distribution of the normal and anomalous data are separable in the latent space, its lower bound can be considered as a function which weights the trade-off between mutual information and entropy. This objective function is able to explain why the surrogate task based methods are effective for anomaly detection and further point out the potential direction of improvement. Based on this object function we introduce a novel information theoretic framework for unsupervised image anomaly detection. Extensive experiments have demonstrated that the proposed framework significantly outperforms several state-of-the-arts on multiple benchmark data sets.

Fei Ye, Pin Wang, Ching-Yao Chan et al.

Recent advances in supervised learning and reinforcement learning have provided new opportunities to apply related methodologies to automated driving. However, there are still challenges to achieve automated driving maneuvers in dynamically changing environments. Supervised learning algorithms such as imitation learning can generalize to new environments by training on a large amount of labeled data, however, it can be often impractical or cost-prohibitive to obtain sufficient data for each new environment. Although reinforcement learning methods can mitigate this data-dependency issue by training the agent in a trial-and-error way, they still need to re-train policies from scratch when adapting to new environments. In this paper, we thus propose a meta reinforcement learning (MRL) method to improve the agent's generalization capabilities to make automated lane-changing maneuvers at different traffic environments, which are formulated as different traffic congestion levels. Specifically, we train the model at light to moderate traffic densities and test it at a new heavy traffic density condition. We use both collision rate and success rate to quantify the safety and effectiveness of the proposed model. A benchmark model is developed based on a pretraining method, which uses the same network structure and training tasks as our proposed model for fair comparison. The simulation results shows that the proposed method achieves an overall success rate up to 20% higher than the benchmark model when it is generalized to the new environment of heavy traffic density. The collision rate is also reduced by up to 18% than the benchmark model. Finally, the proposed model shows more stable and efficient generalization capabilities adapting to the new environment, and it can achieve 100% successful rate and 0% collision rate with only a few steps of gradient updates.

Shen Zhang, Fei Ye, Bingnan Wang et al.

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.

Fei Ye, Adrian G. Bors

The problem of catastrophic forgetting occurs in deep learning models trained on multiple databases in a sequential manner. Recently, generative replay mechanisms (GRM), have been proposed to reproduce previously learned knowledge aiming to reduce the forgetting. However, such approaches lack an appropriate inference model and therefore can not provide latent representations of data. In this paper, we propose a novel lifelong learning approach, namely the Lifelong VAEGAN (L-VAEGAN), which not only induces a powerful generative replay network but also learns meaningful latent representations, benefiting representation learning. L-VAEGAN can allow to automatically embed the information associated with different domains into several clusters in the latent space, while also capturing semantically meaningful shared latent variables, across different data domains. The proposed model supports many downstream tasks that traditional generative replay methods can not, including interpolation and inference across different data domains.

Fei Ye, Xuxin Cheng, Pin Wang et al.

Lane-change maneuvers are commonly executed by drivers to follow a certain routing plan, overtake a slower vehicle, adapt to a merging lane ahead, etc. However, improper lane change behaviors can be a major cause of traffic flow disruptions and even crashes. While many rule-based methods have been proposed to solve lane change problems for autonomous driving, they tend to exhibit limited performance due to the uncertainty and complexity of the driving environment. Machine learning-based methods offer an alternative approach, as Deep reinforcement learning (DRL) has shown promising success in many application domains including robotic manipulation, navigation, and playing video games. However, applying DRL to autonomous driving still faces many practical challenges in terms of slow learning rates, sample inefficiency, and safety concerns. In this study, we propose an automated lane change strategy using proximal policy optimization-based deep reinforcement learning, which shows great advantages in learning efficiency while still maintaining stable performance. The trained agent is able to learn a smooth, safe, and efficient driving policy to make lane-change decisions (i.e. when and how) in a challenging situation such as dense traffic scenarios. The effectiveness of the proposed policy is validated by using metrics of task success rate and collision rate. The simulation results demonstrate the lane change maneuvers can be efficiently learned and executed in a safe, smooth, and efficient manner.

Shen Zhang, Fei Ye, Bingnan Wang et al.

Most of the data-driven approaches applied to bearing fault diagnosis up to date are established in the supervised learning paradigm, which usually requires a large set of labeled data collected a priori. In practical applications, however, obtaining accurate labels based on real-time bearing conditions can be far more challenging than simply collecting a huge amount of unlabeled data using various sensors. In this paper, we thus propose a semi-supervised learning approach for bearing anomaly detection using variational autoencoder (VAE) based deep generative models, which allows for effective utilization of dataset when only a small subset of data have labels. Finally, a series of experiments is performed using both the Case Western Reserve University (CWRU) bearing dataset and the University of Cincinnati's Center for Intelligent Maintenance Systems (IMS) dataset. The experimental results demonstrate that the proposed semi-supervised learning scheme greatly outperforms two mainstream semi-supervised learning approaches and a baseline supervised convolutional neural network approach, with the overall accuracy improvement ranging between 3% to 30% using different proportions of labeled samples.

Chaoqin Huang, Fei Ye, Jinkun Cao et al.

With the recent advances in deep neural networks, anomaly detection in multimedia has received much attention in the computer vision community. While reconstruction-based methods have recently shown great promise for anomaly detection, the information equivalence among input and supervision for reconstruction tasks can not effectively force the network to learn semantic feature embeddings. We here propose to break this equivalence by erasing selected attributes from the original data and reformulate it as a restoration task, where the normal and the anomalous data are expected to be distinguishable based on restoration errors. Through forcing the network to restore the original image, the semantic feature embeddings related to the erased attributes are learned by the network. During testing phases, because anomalous data are restored with the attribute learned from the normal data, the restoration error is expected to be large. Extensive experiments have demonstrated that the proposed method significantly outperforms several state-of-the-arts on multiple benchmark datasets, especially on ImageNet, increasing the AUROC of the top-performing baseline by 10.1%. We also evaluate our method on a real-world anomaly detection dataset MVTec AD and a video anomaly detection dataset ShanghaiTech.

Haiyang Wang, Yong Tang, Ziyang Jia et al.

Recent researches have shown that deep forest ensemble achieves a considerable increase in classification accuracy compared with the general ensemble learning methods, especially when the training set is small. In this paper, we take advantage of deep forest ensemble and introduce the Dense Adaptive Cascade Forest (daForest). Our model has a better performance than the original Cascade Forest with three major features: first, we apply SAMME.R boosting algorithm to improve the performance of the model. It guarantees the improvement as the number of layers increases. Second, our model connects each layer to the subsequent ones in a feed-forward fashion, which enhances the capability of the model to resist performance degeneration. Third, we add a hyper-parameters optimization layer before the first classification layer, making our model spend less time to set up and find the optimal hyper-parameters. Experimental results show that daForest performs significantly well, and in some cases, even outperforms neural networks and achieves state-of-the-art results.

Gol Kim, Fei Ye

The feature of our method different from other fuzzy grey relation method for supermixed multiple attribute group decision-making is that all of the subjective and objective weights are obtained by interval grey number and that the group decisionmaking is performed based on the relative approach degree of grey TOPSIS, the relative approach degree of grey incidence and the relative membership degree of grey incidence using 4-dimensional Euclidean distance. The weighted Borda method is used to obtain final rank by using the results of four methods. An example shows the applicability of the proposed approach.