arXiv subjects

Yanjun Qi

Publications and source records attributed to Yanjun Qi.

At least 55 records · Page 3Linked to original sources

arXiv2022

Evolving Image Compositions for Feature Representation Learning

Convolutional neural networks for visual recognition require large amounts of training samples and usually benefit from data augmentation. This paper proposes PatchMix, a data augmentation method that creates new samples by composing patches from pairs of images in a grid-like pattern. These new samples are assigned label scores that are proportional to the number of patches borrowed from each image. We then add a set of additional losses at the patch-level to regularize and to encourage good representations at both the patch and image levels. A ResNet-50 model trained on ImageNet using PatchMix exhibits superior transfer learning capabilities across a wide array of benchmarks. Although PatchMix can rely on random pairings and random grid-like patterns for mixing, we explore evolutionary search as a guiding strategy to jointly discover optimal grid-like patterns and image pairings. For this purpose, we conceive a fitness function that bypasses the need to re-train a model to evaluate each possible choice. In this way, PatchMix outperforms a base model on CIFAR-10 (+1.91), CIFAR-100 (+5.31), Tiny Imagenet (+3.52), and ImageNet (+1.16).

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arXiv2021

Reevaluating Adversarial Examples in Natural Language

State-of-the-art attacks on NLP models lack a shared definition of a what constitutes a successful attack. We distill ideas from past work into a unified framework: a successful natural language adversarial example is a perturbation that fools the model and follows some linguistic constraints. We then analyze the outputs of two state-of-the-art synonym substitution attacks. We find that their perturbations often do not preserve semantics, and 38% introduce grammatical errors. Human surveys reveal that to successfully preserve semantics, we need to significantly increase the minimum cosine similarities between the embeddings of swapped words and between the sentence encodings of original and perturbed sentences.With constraints adjusted to better preserve semantics and grammaticality, the attack success rate drops by over 70 percentage points.

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arXiv2021

Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure

The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19). While this viral species was unknown prior to January 2020, its similarity to other coronaviruses that infect humans has allowed for rapid insight into the mechanisms that it uses to infect human hosts, as well as the ways in which the human immune system can respond. Here, we contextualize SARS-CoV-2 among other coronaviruses and identify what is known and what can be inferred about its behavior once inside a human host. Because the genomic content of coronaviruses, which specifies the virus's structure, is highly conserved, early genomic analysis provided a significant head start in predicting viral pathogenesis and in understanding potential differences among variants. The pathogenesis of the virus offers insights into symptomatology, transmission, and individual susceptibility. Additionally, prior research into interactions between the human immune system and coronaviruses has identified how these viruses can evade the immune system's protective mechanisms. We also explore systems-level research into the regulatory and proteomic effects of SARS-CoV-2 infection and the immune response. Understanding the structure and behavior of the virus serves to contextualize the many facets of the COVID-19 pandemic and can influence efforts to control the virus and treat the disease.

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arXiv2021

Towards Automatic Actor-Critic Solutions to Continuous Control

Model-free off-policy actor-critic methods are an efficient solution to complex continuous control tasks. However, these algorithms rely on a number of design tricks and hyperparameters, making their application to new domains difficult and computationally expensive. This paper creates an evolutionary approach that automatically tunes these design decisions and eliminates the RL-specific hyperparameters from the Soft Actor-Critic algorithm. Our design is sample efficient and provides practical advantages over baseline approaches, including improved exploration, generalization over multiple control frequencies, and a robust ensemble of high-performance policies. Empirically, we show that our agent outperforms well-tuned hyperparameter settings in popular benchmarks from the DeepMind Control Suite. We then apply it to less common control tasks outside of simulated robotics to find high-performance solutions with minimal compute and research effort.

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arXiv2021

ST-MAML: A Stochastic-Task based Method for Task-Heterogeneous Meta-Learning

Optimization-based meta-learning typically assumes tasks are sampled from a single distribution - an assumption oversimplifies and limits the diversity of tasks that meta-learning can model. Handling tasks from multiple different distributions is challenging for meta-learning due to a so-called task ambiguity issue. This paper proposes a novel method, ST-MAML, that empowers model-agnostic meta-learning (MAML) to learn from multiple task distributions. ST-MAML encodes tasks using a stochastic neural network module, that summarizes every task with a stochastic representation. The proposed Stochastic Task (ST) strategy allows a meta-model to get tailored for the current task and enables us to learn a distribution of solutions for an ambiguous task. ST-MAML also propagates the task representation to revise the encoding of input variables. Empirically, we demonstrate that ST-MAML matches or outperforms the state-of-the-art on two few-shot image classification tasks, one curve regression benchmark, one image completion problem, and a real-world temperature prediction application. To the best of authors' knowledge, this is the first time optimization-based meta-learning method being applied on a large-scale real-world task.

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arXiv2021

Perturbing Inputs for Fragile Interpretations in Deep Natural Language Processing

Interpretability methods like Integrated Gradient and LIME are popular choices for explaining natural language model predictions with relative word importance scores. These interpretations need to be robust for trustworthy NLP applications in high-stake areas like medicine or finance. Our paper demonstrates how interpretations can be manipulated by making simple word perturbations on an input text. Via a small portion of word-level swaps, these adversarial perturbations aim to make the resulting text semantically and spatially similar to its seed input (therefore sharing similar interpretations). Simultaneously, the generated examples achieve the same prediction label as the seed yet are given a substantially different explanation by the interpretation methods. Our experiments generate fragile interpretations to attack two SOTA interpretation methods, across three popular Transformer models and on two different NLP datasets. We observe that the rank order correlation drops by over 20% when less than 10% of words are perturbed on average. Further, rank-order correlation keeps decreasing as more words get perturbed. Furthermore, we demonstrate that candidates generated from our method have good quality metrics.

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arXiv2021

Towards Improving Adversarial Training of NLP Models

Adversarial training, a method for learning robust deep neural networks, constructs adversarial examples during training. However, recent methods for generating NLP adversarial examples involve combinatorial search and expensive sentence encoders for constraining the generated instances. As a result, it remains challenging to use vanilla adversarial training to improve NLP models' performance, and the benefits are mainly uninvestigated. This paper proposes a simple and improved vanilla adversarial training process for NLP models, which we name Attacking to Training (A2T). The core part of A2T is a new and cheaper word substitution attack optimized for vanilla adversarial training. We use A2T to train BERT and RoBERTa models on IMDB, Rotten Tomatoes, Yelp, and SNLI datasets. Our results empirically show that it is possible to train robust NLP models using a much cheaper adversary. We demonstrate that vanilla adversarial training with A2T can improve an NLP model's robustness to the attack it was originally trained with and also defend the model against other types of word substitution attacks. Furthermore, we show that A2T can improve NLP models' standard accuracy, cross-domain generalization, and interpretability. Code is available at https://github.com/QData/Textattack-A2T .

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arXiv2021

Identification and Development of Therapeutics for COVID-19

After emerging in China in late 2019, the novel Severe acute respiratory syndrome-like coronavirus 2 (SARS-CoV-2) spread worldwide and as of early 2021, continues to significantly impact most countries. Only a small number of coronaviruses are known to infect humans, and only two are associated with the severe outcomes associated with SARS-CoV-2: Severe acute respiratory syndrome-related coronavirus, a closely related species of SARS-CoV-2 that emerged in 2002, and Middle East respiratory syndrome-related coronavirus, which emerged in 2012. Both of these previous epidemics were controlled fairly rapidly through public health measures, and no vaccines or robust therapeutic interventions were identified. However, previous insights into the immune response to coronaviruses gained during the outbreaks of severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) have proved beneficial to identifying approaches to the treatment and prophylaxis of novel coronavirus disease 2019 (COVID-19). A number of potential therapeutics against SARS-CoV-2 and the resultant COVID-19 illness were rapidly identified, leading to a large number of clinical trials investigating a variety of possible therapeutic approaches being initiated early on in the pandemic. As a result, a small number of therapeutics have already been authorized by regulatory agencies such as the Food and Drug Administration (FDA) in the United States, and many other therapeutics remain under investigation. Here, we describe a range of approaches for the treatment of COVID-19, along with their proposed mechanisms of action and the current status of clinical investigation into each candidate. The status of these investigations will continue to evolve, and this review will be updated as progress is made.

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arXiv2021

Relate and Predict: Structure-Aware Prediction with Jointly Optimized Neural DAG

Understanding relationships between feature variables is one important way humans use to make decisions. However, state-of-the-art deep learning studies either focus on task-agnostic statistical dependency learning or do not model explicit feature dependencies during prediction. We propose a deep neural network framework, dGAP, to learn neural dependency Graph and optimize structure-Aware target Prediction simultaneously. dGAP trains towards a structure self-supervision loss and a target prediction loss jointly. Our method leads to an interpretable model that can disentangle sparse feature relationships, informing the user how relevant dependencies impact the target task. We empirically evaluate dGAP on multiple simulated and real datasets. dGAP is not only more accurate, but can also recover correct dependency structure.

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arXiv2020

Curriculum Labeling: Revisiting Pseudo-Labeling for Semi-Supervised Learning

In this paper we revisit the idea of pseudo-labeling in the context of semi-supervised learning where a learning algorithm has access to a small set of labeled samples and a large set of unlabeled samples. Pseudo-labeling works by applying pseudo-labels to samples in the unlabeled set by using a model trained on the combination of the labeled samples and any previously pseudo-labeled samples, and iteratively repeating this process in a self-training cycle. Current methods seem to have abandoned this approach in favor of consistency regularization methods that train models under a combination of different styles of self-supervised losses on the unlabeled samples and standard supervised losses on the labeled samples. We empirically demonstrate that pseudo-labeling can in fact be competitive with the state-of-the-art, while being more resilient to out-of-distribution samples in the unlabeled set. We identify two key factors that allow pseudo-labeling to achieve such remarkable results (1) applying curriculum learning principles and (2) avoiding concept drift by restarting model parameters before each self-training cycle. We obtain 94.91% accuracy on CIFAR-10 using only 4,000 labeled samples, and 68.87% top-1 accuracy on Imagenet-ILSVRC using only 10% of the labeled samples. The code is available at https://github.com/uvavision/Curriculum-Labeling

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arXiv2020

Measuring Visual Generalization in Continuous Control from Pixels

Self-supervised learning and data augmentation have significantly reduced the performance gap between state and image-based reinforcement learning agents in continuous control tasks. However, it is still unclear whether current techniques can face a variety of visual conditions required by real-world environments. We propose a challenging benchmark that tests agents' visual generalization by adding graphical variety to existing continuous control domains. Our empirical analysis shows that current methods struggle to generalize across a diverse set of visual changes, and we examine the specific factors of variation that make these tasks difficult. We find that data augmentation techniques outperform self-supervised learning approaches and that more significant image transformations provide better visual generalization \footnote{The benchmark and our augmented actor-critic implementation are open-sourced @ https://github.com/QData/dmc_remastered)

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arXiv2020

General Multi-label Image Classification with Transformers

Multi-label image classification is the task of predicting a set of labels corresponding to objects, attributes or other entities present in an image. In this work we propose the Classification Transformer (C-Tran), a general framework for multi-label image classification that leverages Transformers to exploit the complex dependencies among visual features and labels. Our approach consists of a Transformer encoder trained to predict a set of target labels given an input set of masked labels, and visual features from a convolutional neural network. A key ingredient of our method is a label mask training objective that uses a ternary encoding scheme to represent the state of the labels as positive, negative, or unknown during training. Our model shows state-of-the-art performance on challenging datasets such as COCO and Visual Genome. Moreover, because our model explicitly represents the uncertainty of labels during training, it is more general by allowing us to produce improved results for images with partial or extra label annotations during inference. We demonstrate this additional capability in the COCO, Visual Genome, News500, and CUB image datasets.

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arXiv2020

Searching for a Search Method: Benchmarking Search Algorithms for Generating NLP Adversarial Examples

We study the behavior of several black-box search algorithms used for generating adversarial examples for natural language processing (NLP) tasks. We perform a fine-grained analysis of three elements relevant to search: search algorithm, search space, and search budget. When new search algorithms are proposed in past work, the attack search space is often modified alongside the search algorithm. Without ablation studies benchmarking the search algorithm change with the search space held constant, one cannot tell if an increase in attack success rate is a result of an improved search algorithm or a less restrictive search space. Additionally, many previous studies fail to properly consider the search algorithms' run-time cost, which is essential for downstream tasks like adversarial training. Our experiments provide a reproducible benchmark of search algorithms across a variety of search spaces and query budgets to guide future research in adversarial NLP. Based on our experiments, we recommend greedy attacks with word importance ranking when under a time constraint or attacking long inputs, and either beam search or particle swarm optimization otherwise. Code implementation shared via https://github.com/QData/TextAttack-Search-Benchmark

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arXiv2020

TextAttack: A Framework for Adversarial Attacks, Data Augmentation, and Adversarial Training in NLP

While there has been substantial research using adversarial attacks to analyze NLP models, each attack is implemented in its own code repository. It remains challenging to develop NLP attacks and utilize them to improve model performance. This paper introduces TextAttack, a Python framework for adversarial attacks, data augmentation, and adversarial training in NLP. TextAttack builds attacks from four components: a goal function, a set of constraints, a transformation, and a search method. TextAttack's modular design enables researchers to easily construct attacks from combinations of novel and existing components. TextAttack provides implementations of 16 adversarial attacks from the literature and supports a variety of models and datasets, including BERT and other transformers, and all GLUE tasks. TextAttack also includes data augmentation and adversarial training modules for using components of adversarial attacks to improve model accuracy and robustness. TextAttack is democratizing NLP: anyone can try data augmentation and adversarial training on any model or dataset, with just a few lines of code. Code and tutorials are available at https://github.com/QData/TextAttack.

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arXiv2020

TextAttack: Lessons learned in designing Python frameworks for NLP

TextAttack is an open-source Python toolkit for adversarial attacks, adversarial training, and data augmentation in NLP. TextAttack unites 15+ papers from the NLP adversarial attack literature into a single framework, with many components reused across attacks. This framework allows both researchers and developers to test and study the weaknesses of their NLP models. To build such an open-source NLP toolkit requires solving some common problems: How do we enable users to supply models from different deep learning frameworks? How can we build tools to support as many different datasets as possible? We share our insights into developing a well-written, well-documented NLP Python framework in hope that they can aid future development of similar packages.

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arXiv2019

Neural Message Passing for Multi-Label Classification

Multi-label classification (MLC) is the task of assigning a set of target labels for a given sample. Modeling the combinatorial label interactions in MLC has been a long-haul challenge. We propose Label Message Passing (LaMP) Neural Networks to efficiently model the joint prediction of multiple labels. LaMP treats labels as nodes on a label-interaction graph and computes the hidden representation of each label node conditioned on the input using attention-based neural message passing. Attention enables LaMP to assign different importance to neighbor nodes per label, learning how labels interact (implicitly). The proposed models are simple, accurate, interpretable, structure-agnostic, and applicable for predicting dense labels since LaMP is incredibly parallelizable. We validate the benefits of LaMP on seven real-world MLC datasets, covering a broad spectrum of input/output types and outperforming the state-of-the-art results. Notably, LaMP enables intuitive interpretation of how classifying each label depends on the elements of a sample and at the same time rely on its interaction with other labels. We provide our code and datasets at https://github.com/QData/LaMP

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arXiv2019

A Fast and Scalable Joint Estimator for Integrating Additional Knowledge in Learning Multiple Related Sparse Gaussian Graphical Models

We consider the problem of including additional knowledge in estimating sparse Gaussian graphical models (sGGMs) from aggregated samples, arising often in bioinformatics and neuroimaging applications. Previous joint sGGM estimators either fail to use existing knowledge or cannot scale-up to many tasks (large $K$) under a high-dimensional (large $p$) situation. In this paper, we propose a novel \underline{J}oint \underline{E}lementary \underline{E}stimator incorporating additional \underline{K}nowledge (JEEK) to infer multiple related sparse Gaussian Graphical models from large-scale heterogeneous data. Using domain knowledge as weights, we design a novel hybrid norm as the minimization objective to enforce the superposition of two weighted sparsity constraints, one on the shared interactions and the other on the task-specific structural patterns. This enables JEEK to elegantly consider various forms of existing knowledge based on the domain at hand and avoid the need to design knowledge-specific optimization. JEEK is solved through a fast and entry-wise parallelizable solution that largely improves the computational efficiency of the state-of-the-art $O(p^5K^4)$ to $O(p^2K^4)$. We conduct a rigorous statistical analysis showing that JEEK achieves the same convergence rate $O(\log(Kp)/n_{tot})$ as the state-of-the-art estimators that are much harder to compute. Empirically, on multiple synthetic datasets and two real-world data, JEEK outperforms the speed of the state-of-arts significantly while achieving the same level of prediction accuracy. Available as R tool @ http://jointnets.org/

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arXiv2018

DeepDiff: Deep-learning for predicting Differential gene expression from histone modifications

Computational methods that predict differential gene expression from histone modification signals are highly desirable for understanding how histone modifications control the functional heterogeneity of cells through influencing differential gene regulation. Recent studies either failed to capture combinatorial effects on differential prediction or primarily only focused on cell type-specific analysis. In this paper, we develop a novel attention-based deep learning architecture, DeepDiff, that provides a unified and end-to-end solution to model and to interpret how dependencies among histone modifications control the differential patterns of gene regulation. DeepDiff uses a hierarchy of multiple Long short-term memory (LSTM) modules to encode the spatial structure of input signals and to model how various histone modifications cooperate automatically. We introduce and train two levels of attention jointly with the target prediction, enabling DeepDiff to attend differentially to relevant modifications and to locate important genome positions for each modification. Additionally, DeepDiff introduces a novel deep-learning based multi-task formulation to use the cell-type-specific gene expression predictions as auxiliary tasks, encouraging richer feature embeddings in our primary task of differential expression prediction. Using data from Roadmap Epigenomics Project (REMC) for ten different pairs of cell types, we show that DeepDiff significantly outperforms the state-of-the-art baselines for differential gene expression prediction. The learned attention weights are validated by observations from previous studies about how epigenetic mechanisms connect to differential gene expression. Codes and results are available at \url{deepchrome.org}

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