arXiv subjects

Pin-Yu Chen

Publications and source records attributed to Pin-Yu Chen.

At least 235 records · Page 13Linked to original sources

arXiv2022

Learning Geometrically Disentangled Representations of Protein Folding Simulations

Massive molecular simulations of drug-target proteins have been used as a tool to understand disease mechanism and develop therapeutics. This work focuses on learning a generative neural network on a structural ensemble of a drug-target protein, e.g. SARS-CoV-2 Spike protein, obtained from computationally expensive molecular simulations. Model tasks involve characterizing the distinct structural fluctuations of the protein bound to various drug molecules, as well as efficient generation of protein conformations that can serve as an complement of a molecular simulation engine. Specifically, we present a geometric autoencoder framework to learn separate latent space encodings of the intrinsic and extrinsic geometries of the protein structure. For this purpose, the proposed Protein Geometric AutoEncoder (ProGAE) model is trained on the protein contact map and the orientation of the backbone bonds of the protein. Using ProGAE latent embeddings, we reconstruct and generate the conformational ensemble of a protein at or near the experimental resolution, while gaining better interpretability and controllability in term of protein structure generation from the learned latent space. Additionally, ProGAE models are transferable to a different state of the same protein or to a new protein of different size, where only the dense layer decoding from the latent representation needs to be retrained. Results show that our geometric learning-based method enjoys both accuracy and efficiency for generating complex structural variations, charting the path toward scalable and improved approaches for analyzing and enhancing high-cost simulations of drug-target proteins.

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arXiv2022

Evaluating the Adversarial Robustness for Fourier Neural Operators

In recent years, Machine-Learning (ML)-driven approaches have been widely used in scientific discovery domains. Among them, the Fourier Neural Operator (FNO) was the first to simulate turbulent flow with zero-shot super-resolution and superior accuracy, which significantly improves the speed when compared to traditional partial differential equation (PDE) solvers. To inspect the trustworthiness, we provide the first study on the adversarial robustness of scientific discovery models by generating adversarial examples for FNO, based on norm-bounded data input perturbations. Evaluated on the mean squared error between the FNO model's output and the PDE solver's output, our results show that the model's robustness degrades rapidly with increasing perturbation levels, particularly in non-simplistic cases like the 2D Darcy and the Navier cases. Our research provides a sensitivity analysis tool and evaluation principles for assessing the adversarial robustness of ML-based scientific discovery models.

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arXiv2022

Auto-Transfer: Learning to Route Transferrable Representations

Knowledge transfer between heterogeneous source and target networks and tasks has received a lot of attention in recent times as large amounts of quality labeled data can be difficult to obtain in many applications. Existing approaches typically constrain the target deep neural network (DNN) feature representations to be close to the source DNNs feature representations, which can be limiting. We, in this paper, propose a novel adversarial multi-armed bandit approach that automatically learns to route source representations to appropriate target representations following which they are combined in meaningful ways to produce accurate target models. We see upwards of 5\% accuracy improvements compared with the state-of-the-art knowledge transfer methods on four benchmark (target) image datasets CUB200, Stanford Dogs, MIT67, and Stanford40 where the source dataset is ImageNet. We qualitatively analyze the goodness of our transfer scheme by showing individual examples of the important features focused on by our target network at different layers compared with the (closest) competitors. We also observe that our improvement over other methods is higher for smaller target datasets making it an effective tool for small data applications that may benefit from transfer learning.

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arXiv2022

MAML is a Noisy Contrastive Learner in Classification

Model-agnostic meta-learning (MAML) is one of the most popular and widely adopted meta-learning algorithms, achieving remarkable success in various learning problems. Yet, with the unique design of nested inner-loop and outer-loop updates, which govern the task-specific and meta-model-centric learning, respectively, the underlying learning objective of MAML remains implicit and thus impedes a more straightforward understanding of it. In this paper, we provide a new perspective of the working mechanism of MAML. We discover that MAML is analogous to a meta-learner using a supervised contrastive objective. The query features are pulled towards the support features of the same class and against those of different classes. Such contrastiveness is experimentally verified via an analysis based on the cosine similarity. Moreover, we reveal that vanilla MAML has an undesirable interference term originating from the random initialization and the cross-task interaction. We thus propose a simple but effective technique, zeroing trick, to alleviate the interference. Extensive experiments are conducted on both mini-ImageNet and Omniglot datasets to demonstrate the consistent improvement brought by our proposed method, validating its effectiveness.

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arXiv2022

Exploiting Low-Rank Tensor-Train Deep Neural Networks Based on Riemannian Gradient Descent With Illustrations of Speech Processing

This work focuses on designing low complexity hybrid tensor networks by considering trade-offs between the model complexity and practical performance. Firstly, we exploit a low-rank tensor-train deep neural network (TT-DNN) to build an end-to-end deep learning pipeline, namely LR-TT-DNN. Secondly, a hybrid model combining LR-TT-DNN with a convolutional neural network (CNN), which is denoted as CNN+(LR-TT-DNN), is set up to boost the performance. Instead of randomly assigning large TT-ranks for TT-DNN, we leverage Riemannian gradient descent to determine a TT-DNN associated with small TT-ranks. Furthermore, CNN+(LR-TT-DNN) consists of convolutional layers at the bottom for feature extraction and several TT layers at the top to solve regression and classification problems. We separately assess the LR-TT-DNN and CNN+(LR-TT-DNN) models on speech enhancement and spoken command recognition tasks. Our empirical evidence demonstrates that the LR-TT-DNN and CNN+(LR-TT-DNN) models with fewer model parameters can outperform the TT-DNN and CNN+(TT-DNN) counterparts.

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arXiv2022

CAFE: Catastrophic Data Leakage in Vertical Federated Learning

Recent studies show that private training data can be leaked through the gradients sharing mechanism deployed in distributed machine learning systems, such as federated learning (FL). Increasing batch size to complicate data recovery is often viewed as a promising defense strategy against data leakage. In this paper, we revisit this defense premise and propose an advanced data leakage attack with theoretical justification to efficiently recover batch data from the shared aggregated gradients. We name our proposed method as catastrophic data leakage in vertical federated learning (CAFE). Comparing to existing data leakage attacks, our extensive experimental results on vertical FL settings demonstrate the effectiveness of CAFE to perform large-batch data leakage attack with improved data recovery quality. We also propose a practical countermeasure to mitigate CAFE. Our results suggest that private data participated in standard FL, especially the vertical case, have a high risk of being leaked from the training gradients. Our analysis implies unprecedented and practical data leakage risks in those learning settings. The code of our work is available at https://github.com/DeRafael/CAFE.

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arXiv2022

When BERT Meets Quantum Temporal Convolution Learning for Text Classification in Heterogeneous Computing

The rapid development of quantum computing has demonstrated many unique characteristics of quantum advantages, such as richer feature representation and more secured protection on model parameters. This work proposes a vertical federated learning architecture based on variational quantum circuits to demonstrate the competitive performance of a quantum-enhanced pre-trained BERT model for text classification. In particular, our proposed hybrid classical-quantum model consists of a novel random quantum temporal convolution (QTC) learning framework replacing some layers in the BERT-based decoder. Our experiments on intent classification show that our proposed BERT-QTC model attains competitive experimental results in the Snips and ATIS spoken language datasets. Particularly, the BERT-QTC boosts the performance of the existing quantum circuit-based language model in two text classification datasets by 1.57% and 1.52% relative improvements. Furthermore, BERT-QTC can be feasibly deployed on both existing commercial-accessible quantum computation hardware and CPU-based interface for ensuring data isolation.

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arXiv2022

How does unlabeled data improve generalization in self-training? A one-hidden-layer theoretical analysis

Self-training, a semi-supervised learning algorithm, leverages a large amount of unlabeled data to improve learning when the labeled data are limited. Despite empirical successes, its theoretical characterization remains elusive. To the best of our knowledge, this work establishes the first theoretical analysis for the known iterative self-training paradigm and proves the benefits of unlabeled data in both training convergence and generalization ability. To make our theoretical analysis feasible, we focus on the case of one-hidden-layer neural networks. However, theoretical understanding of iterative self-training is non-trivial even for a shallow neural network. One of the key challenges is that existing neural network landscape analysis built upon supervised learning no longer holds in the (semi-supervised) self-training paradigm. We address this challenge and prove that iterative self-training converges linearly with both convergence rate and generalization accuracy improved in the order of $1/\sqrt{M}$, where $M$ is the number of unlabeled samples. Experiments from shallow neural networks to deep neural networks are also provided to justify the correctness of our established theoretical insights on self-training.

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arXiv2022

Revisiting Contrastive Learning through the Lens of Neighborhood Component Analysis: an Integrated Framework

As a seminal tool in self-supervised representation learning, contrastive learning has gained unprecedented attention in recent years. In essence, contrastive learning aims to leverage pairs of positive and negative samples for representation learning, which relates to exploiting neighborhood information in a feature space. By investigating the connection between contrastive learning and neighborhood component analysis (NCA), we provide a novel stochastic nearest neighbor viewpoint of contrastive learning and subsequently propose a series of contrastive losses that outperform the existing ones. Under our proposed framework, we show a new methodology to design integrated contrastive losses that could simultaneously achieve good accuracy and robustness on downstream tasks. With the integrated framework, we achieve up to 6\% improvement on the standard accuracy and 17\% improvement on the robust accuracy.

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arXiv2022

Training a Resilient Q-Network against Observational Interference

Deep reinforcement learning (DRL) has demonstrated impressive performance in various gaming simulators and real-world applications. In practice, however, a DRL agent may receive faulty observation by abrupt interferences such as black-out, frozen-screen, and adversarial perturbation. How to design a resilient DRL algorithm against these rare but mission-critical and safety-crucial scenarios is an essential yet challenging task. In this paper, we consider a deep q-network (DQN) framework training with an auxiliary task of observational interferences such as artificial noises. Inspired by causal inference for observational interference, we propose a causal inference based DQN algorithm called causal inference Q-network (CIQ). We evaluate the performance of CIQ in several benchmark DQN environments with different types of interferences as auxiliary labels. Our experimental results show that the proposed CIQ method could achieve higher performance and more resilience against observational interferences.

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arXiv2022

Voice2Series: Reprogramming Acoustic Models for Time Series Classification

Learning to classify time series with limited data is a practical yet challenging problem. Current methods are primarily based on hand-designed feature extraction rules or domain-specific data augmentation. Motivated by the advances in deep speech processing models and the fact that voice data are univariate temporal signals, in this paper, we propose Voice2Series (V2S), a novel end-to-end approach that reprograms acoustic models for time series classification, through input transformation learning and output label mapping. Leveraging the representation learning power of a large-scale pre-trained speech processing model, on 30 different time series tasks we show that V2S performs competitive results on 19 time series classification tasks. We further provide a theoretical justification of V2S by proving its population risk is upper bounded by the source risk and a Wasserstein distance accounting for feature alignment via reprogramming. Our results offer new and effective means to time series classification.

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arXiv2022

Neural Capacitance: A New Perspective of Neural Network Selection via Edge Dynamics

Efficient model selection for identifying a suitable pre-trained neural network to a downstream task is a fundamental yet challenging task in deep learning. Current practice requires expensive computational costs in model training for performance prediction. In this paper, we propose a novel framework for neural network selection by analyzing the governing dynamics over synaptic connections (edges) during training. Our framework is built on the fact that back-propagation during neural network training is equivalent to the dynamical evolution of synaptic connections. Therefore, a converged neural network is associated with an equilibrium state of a networked system composed of those edges. To this end, we construct a network mapping $ϕ$, converting a neural network $G_A$ to a directed line graph $G_B$ that is defined on those edges in $G_A$. Next, we derive a neural capacitance metric $β_{\rm eff}$ as a predictive measure universally capturing the generalization capability of $G_A$ on the downstream task using only a handful of early training results. We carried out extensive experiments using 17 popular pre-trained ImageNet models and five benchmark datasets, including CIFAR10, CIFAR100, SVHN, Fashion MNIST and Birds, to evaluate the fine-tuning performance of our framework. Our neural capacitance metric is shown to be a powerful indicator for model selection based only on early training results and is more efficient than state-of-the-art methods.

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arXiv2022

Characterizing Speech Adversarial Examples Using Self-Attention U-Net Enhancement

Recent studies have highlighted adversarial examples as ubiquitous threats to the deep neural network (DNN) based speech recognition systems. In this work, we present a U-Net based attention model, U-Net$_{At}$, to enhance adversarial speech signals. Specifically, we evaluate the model performance by interpretable speech recognition metrics and discuss the model performance by the augmented adversarial training. Our experiments show that our proposed U-Net$_{At}$ improves the perceptual evaluation of speech quality (PESQ) from 1.13 to 2.78, speech transmission index (STI) from 0.65 to 0.75, short-term objective intelligibility (STOI) from 0.83 to 0.96 on the task of speech enhancement with adversarial speech examples. We conduct experiments on the automatic speech recognition (ASR) task with adversarial audio attacks. We find that (i) temporal features learned by the attention network are capable of enhancing the robustness of DNN based ASR models; (ii) the generalization power of DNN based ASR model could be enhanced by applying adversarial training with an additive adversarial data augmentation. The ASR metric on word-error-rates (WERs) shows that there is an absolute 2.22 $\%$ decrease under gradient-based perturbation, and an absolute 2.03 $\%$ decrease, under evolutionary-optimized perturbation, which suggests that our enhancement models with adversarial training can further secure a resilient ASR system.

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arXiv2021

Zeroth-order Optimization for Composite Problems with Functional Constraints

In many real-world problems, first-order (FO) derivative evaluations are too expensive or even inaccessible. For solving these problems, zeroth-order (ZO) methods that only need function evaluations are often more efficient than FO methods or sometimes the only options. In this paper, we propose a novel zeroth-order inexact augmented Lagrangian method (ZO-iALM) to solve black-box optimization problems, which involve a composite (i.e., smooth+nonsmooth) objective and functional constraints. Under a certain regularity condition (also assumed by several existing works on FO methods), the query complexity of our ZO-iALM is $\tilde{O}(d\varepsilon^{-3})$ to find an $\varepsilon$-KKT point for problems with a nonconvex objective and nonconvex constraints, and $\tilde{O}(d\varepsilon^{-2.5})$ for nonconvex problems with convex constraints, where $d$ is the variable dimension. This appears to be the first work that develops an iALM-based ZO method for functional constrained optimization and meanwhile achieves query complexity results matching the best-known FO complexity results up to a factor of $d$. With an extensive experimental study, we show the effectiveness of our method. The applications of our method span from classical optimization problems to practical machine learning examples such as resource allocation in sensor networks and adversarial example generation.

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arXiv2021

Formalizing Generalization and Robustness of Neural Networks to Weight Perturbations

Studying the sensitivity of weight perturbation in neural networks and its impacts on model performance, including generalization and robustness, is an active research topic due to its implications on a wide range of machine learning tasks such as model compression, generalization gap assessment, and adversarial attacks. In this paper, we provide the first integral study and analysis for feed-forward neural networks in terms of the robustness in pairwise class margin and its generalization behavior under weight perturbation. We further design a new theory-driven loss function for training generalizable and robust neural networks against weight perturbations. Empirical experiments are conducted to validate our theoretical analysis. Our results offer fundamental insights for characterizing the generalization and robustness of neural networks against weight perturbations.

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arXiv2021

Meta Adversarial Perturbations

A plethora of attack methods have been proposed to generate adversarial examples, among which the iterative methods have been demonstrated the ability to find a strong attack. However, the computation of an adversarial perturbation for a new data point requires solving a time-consuming optimization problem from scratch. To generate a stronger attack, it normally requires updating a data point with more iterations. In this paper, we show the existence of a meta adversarial perturbation (MAP), a better initialization that causes natural images to be misclassified with high probability after being updated through only a one-step gradient ascent update, and propose an algorithm for computing such perturbations. We conduct extensive experiments, and the empirical results demonstrate that state-of-the-art deep neural networks are vulnerable to meta perturbations. We further show that these perturbations are not only image-agnostic, but also model-agnostic, as a single perturbation generalizes well across unseen data points and different neural network architectures.

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arXiv2021

Network Graph Based Neural Architecture Search

Neural architecture search enables automation of architecture design. Despite its success, it is computationally costly and does not provide an insight on how to design a desirable architecture. Here we propose a new way of searching neural network where we search neural architecture by rewiring the corresponding graph and predict the architecture performance by graph properties. Because we do not perform machine learning over the entire graph space and use predicted architecture performance to search architecture, the searching process is remarkably efficient. We find graph based search can give a reasonably good prediction of desirable architecture. In addition, we find graph properties that are effective to predict architecture performance. Our work proposes a new way of searching neural architecture and provides insights on neural architecture design.

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arXiv2021

Adversarial Examples can be Effective Data Augmentation for Unsupervised Machine Learning

Adversarial examples causing evasive predictions are widely used to evaluate and improve the robustness of machine learning models. However, current studies focus on supervised learning tasks, relying on the ground-truth data label, a targeted objective, or supervision from a trained classifier. In this paper, we propose a framework of generating adversarial examples for unsupervised models and demonstrate novel applications to data augmentation. Our framework exploits a mutual information neural estimator as an information-theoretic similarity measure to generate adversarial examples without supervision. We propose a new MinMax algorithm with provable convergence guarantees for efficient generation of unsupervised adversarial examples. Our framework can also be extended to supervised adversarial examples. When using unsupervised adversarial examples as a simple plug-in data augmentation tool for model retraining, significant improvements are consistently observed across different unsupervised tasks and datasets, including data reconstruction, representation learning, and contrastive learning. Our results show novel methods and considerable advantages in studying and improving unsupervised machine learning via adversarial examples.

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