A Fast and Scalable Joint Estimator for Learning Multiple Related Sparse Gaussian Graphical Models

Estimating multiple sparse Gaussian Graphical Models (sGGMs) jointly for many related tasks (large $K$) under a high-dimensional (large $p$) situation is an important task. Most previous studies for the joint estimation of multiple sGGMs rely on penalized log-likelihood estimators that involve expensive and difficult non-smooth optimizations. We propose a novel approach, FASJEM for \underline{fa}st and \underline{s}calable \underline{j}oint structure-\underline{e}stimation of \underline{m}ultiple sGGMs at a large scale. As the first study of joint sGGM using the Elementary Estimator framework, our work has three major contributions: (1) We solve FASJEM through an entry-wise manner which is parallelizable. (2) We choose a proximal algorithm to optimize FASJEM. This improves the computational efficiency from $O(Kp^3)$ to $O(Kp^2)$ and reduces the memory requirement from $O(Kp^2)$ to $O(K)$. (3) We theoretically prove that FASJEM achieves a consistent estimation with a convergence rate of $O(\log(Kp)/n_{tot})$. On several synthetic and four real-world datasets, FASJEM shows significant improvements over baselines on accuracy, computational complexity, and memory costs.

Feature Squeezing: Detecting Adversarial Examples in Deep Neural Networks

Although deep neural networks (DNNs) have achieved great success in many tasks, they can often be fooled by \emph{adversarial examples} that are generated by adding small but purposeful distortions to natural examples. Previous studies to defend against adversarial examples mostly focused on refining the DNN models, but have either shown limited success or required expensive computation. We propose a new strategy, \emph{feature squeezing}, that can be used to harden DNN models by detecting adversarial examples. Feature squeezing reduces the search space available to an adversary by coalescing samples that correspond to many different feature vectors in the original space into a single sample. By comparing a DNN model's prediction on the original input with that on squeezed inputs, feature squeezing detects adversarial examples with high accuracy and few false positives. This paper explores two feature squeezing methods: reducing the color bit depth of each pixel and spatial smoothing. These simple strategies are inexpensive and complementary to other defenses, and can be combined in a joint detection framework to achieve high detection rates against state-of-the-art attacks.

Prototype Matching Networks for Large-Scale Multi-label Genomic Sequence Classification

One of the fundamental tasks in understanding genomics is the problem of predicting Transcription Factor Binding Sites (TFBSs). With more than hundreds of Transcription Factors (TFs) as labels, genomic-sequence based TFBS prediction is a challenging multi-label classification task. There are two major biological mechanisms for TF binding: (1) sequence-specific binding patterns on genomes known as "motifs" and (2) interactions among TFs known as co-binding effects. In this paper, we propose a novel deep architecture, the Prototype Matching Network (PMN) to mimic the TF binding mechanisms. Our PMN model automatically extracts prototypes ("motif"-like features) for each TF through a novel prototype-matching loss. Borrowing ideas from few-shot matching models, we use the notion of support set of prototypes and an LSTM to learn how TFs interact and bind to genomic sequences. On a reference TFBS dataset with $2.1$ $million$ genomic sequences, PMN significantly outperforms baselines and validates our design choices empirically. To our knowledge, this is the first deep learning architecture that introduces prototype learning and considers TF-TF interactions for large-scale TFBS prediction. Not only is the proposed architecture accurate, but it also models the underlying biology.

Attend and Predict: Understanding Gene Regulation by Selective Attention on Chromatin

The past decade has seen a revolution in genomic technologies that enable a flood of genome-wide profiling of chromatin marks. Recent literature tried to understand gene regulation by predicting gene expression from large-scale chromatin measurements. Two fundamental challenges exist for such learning tasks: (1) genome-wide chromatin signals are spatially structured, high-dimensional and highly modular; and (2) the core aim is to understand what are the relevant factors and how they work together? Previous studies either failed to model complex dependencies among input signals or relied on separate feature analysis to explain the decisions. This paper presents an attention-based deep learning approach; we call AttentiveChrome, that uses a unified architecture to model and to interpret dependencies among chromatin factors for controlling gene regulation. AttentiveChrome uses a hierarchy of multiple Long short-term memory (LSTM) modules to encode the input signals and to model how various chromatin marks cooperate automatically. AttentiveChrome trains two levels of attention jointly with the target prediction, enabling it to attend differentially to relevant marks and to locate important positions per mark. We evaluate the model across 56 different cell types (tasks) in human. Not only is the proposed architecture more accurate, but its attention scores also provide a better interpretation than state-of-the-art feature visualization methods such as saliency map. Code and data are shared at www.deepchrome.org

A Theoretical Framework for Robustness of (Deep) Classifiers against Adversarial Examples

Most machine learning classifiers, including deep neural networks, are vulnerable to adversarial examples. Such inputs are typically generated by adding small but purposeful modifications that lead to incorrect outputs while imperceptible to human eyes. The goal of this paper is not to introduce a single method, but to make theoretical steps towards fully understanding adversarial examples. By using concepts from topology, our theoretical analysis brings forth the key reasons why an adversarial example can fool a classifier ($f_1$) and adds its oracle ($f_2$, like human eyes) in such analysis. By investigating the topological relationship between two (pseudo)metric spaces corresponding to predictor $f_1$ and oracle $f_2$, we develop necessary and sufficient conditions that can determine if $f_1$ is always robust (strong-robust) against adversarial examples according to $f_2$. Interestingly our theorems indicate that just one unnecessary feature can make $f_1$ not strong-robust, and the right feature representation learning is the key to getting a classifier that is both accurate and strong-robust.

A Constrained, Weighted-L1 Minimization Approach for Joint Discovery of Heterogeneous Neural Connectivity Graphs

Determining functional brain connectivity is crucial to understanding the brain and neural differences underlying disorders such as autism. Recent studies have used Gaussian graphical models to learn brain connectivity via statistical dependencies across brain regions from neuroimaging. However, previous studies often fail to properly incorporate priors tailored to neuroscience, such as preferring shorter connections. To remedy this problem, the paper here introduces a novel, weighted-$\ell_1$, multi-task graphical model (W-SIMULE). This model elegantly incorporates a flexible prior, along with a parallelizable formulation. Additionally, W-SIMULE extends the often-used Gaussian assumption, leading to considerable performance increases. Here, applications to fMRI data show that W-SIMULE succeeds in determining functional connectivity in terms of (1) log-likelihood, (2) finding edges that differentiate groups, and (3) classifying different groups based on their connectivity, achieving 58.6\% accuracy on the ABIDE dataset. Having established W-SIMULE's effectiveness, it links four key areas to autism, all of which are consistent with the literature. Due to its elegant domain adaptivity, W-SIMULE can be readily applied to various data types to effectively estimate connectivity.

GaKCo: a Fast GApped k-mer string Kernel using COunting

String Kernel (SK) techniques, especially those using gapped $k$-mers as features (gk), have obtained great success in classifying sequences like DNA, protein, and text. However, the state-of-the-art gk-SK runs extremely slow when we increase the dictionary size ($\Sigma$) or allow more mismatches ($M$). This is because current gk-SK uses a trie-based algorithm to calculate co-occurrence of mismatched substrings resulting in a time cost proportional to $O(\Sigma^{M})$. We propose a \textbf{fast} algorithm for calculating \underline{Ga}pped $k$-mer \underline{K}ernel using \underline{Co}unting (GaKCo). GaKCo uses associative arrays to calculate the co-occurrence of substrings using cumulative counting. This algorithm is fast, scalable to larger $\Sigma$ and $M$, and naturally parallelizable. We provide a rigorous asymptotic analysis that compares GaKCo with the state-of-the-art gk-SK. Theoretically, the time cost of GaKCo is independent of the $\Sigma^{M}$ term that slows down the trie-based approach. Experimentally, we observe that GaKCo achieves the same accuracy as the state-of-the-art and outperforms its speed by factors of 2, 100, and 4, on classifying sequences of DNA (5 datasets), protein (12 datasets), and character-based English text (2 datasets), respectively. GaKCo is shared as an open source tool at \url{https://github.com/QData/GaKCo-SVM}

A constrained L1 minimization approach for estimating multiple Sparse Gaussian or Nonparanormal Graphical Models

Identifying context-specific entity networks from aggregated data is an important task, arising often in bioinformatics and neuroimaging. Computationally, this task can be formulated as jointly estimating multiple different, but related, sparse Undirected Graphical Models (UGM) from aggregated samples across several contexts. Previous joint-UGM studies have mostly focused on sparse Gaussian Graphical Models (sGGMs) and can't identify context-specific edge patterns directly. We, therefore, propose a novel approach, SIMULE (detecting Shared and Individual parts of MULtiple graphs Explicitly) to learn multi-UGM via a constrained L1 minimization. SIMULE automatically infers both specific edge patterns that are unique to each context and shared interactions preserved among all the contexts. Through the L1 constrained formulation, this problem is cast as multiple independent subtasks of linear programming that can be solved efficiently in parallel. In addition to Gaussian data, SIMULE can also handle multivariate Nonparanormal data that greatly relaxes the normality assumption that many real-world applications do not follow. We provide a novel theoretical proof showing that SIMULE achieves a consistent result at the rate O(log(Kp)/n_{tot}). On multiple synthetic datasets and two biomedical datasets, SIMULE shows significant improvement over state-of-the-art multi-sGGM and single-UGM baselines.

Adversarial-Playground: A Visualization Suite Showing How Adversarial Examples Fool Deep Learning

Recent studies have shown that attackers can force deep learning models to misclassify so-called "adversarial examples": maliciously generated images formed by making imperceptible modifications to pixel values. With growing interest in deep learning for security applications, it is important for security experts and users of machine learning to recognize how learning systems may be attacked. Due to the complex nature of deep learning, it is challenging to understand how deep models can be fooled by adversarial examples. Thus, we present a web-based visualization tool, Adversarial-Playground, to demonstrate the efficacy of common adversarial methods against a convolutional neural network (CNN) system. Adversarial-Playground is educational, modular and interactive. (1) It enables non-experts to compare examples visually and to understand why an adversarial example can fool a CNN-based image classifier. (2) It can help security experts explore more vulnerability of deep learning as a software module. (3) Building an interactive visualization is challenging in this domain due to the large feature space of image classification (generating adversarial examples is slow in general and visualizing images are costly). Through multiple novel design choices, our tool can provide fast and accurate responses to user requests. Empirically, we find that our client-server division strategy reduced the response time by an average of 1.5 seconds per sample. Our other innovation, a faster variant of JSMA evasion algorithm, empirically performed twice as fast as JSMA and yet maintains a comparable evasion rate. Project source code and data from our experiments available at: https://github.com/QData/AdversarialDNN-Playground

Adversarial-Playground: A Visualization Suite for Adversarial Sample Generation

With growing interest in adversarial machine learning, it is important for machine learning practitioners and users to understand how their models may be attacked. We propose a web-based visualization tool, Adversarial-Playground, to demonstrate the efficacy of common adversarial methods against a deep neural network (DNN) model, built on top of the TensorFlow library. Adversarial-Playground provides users an efficient and effective experience in exploring techniques generating adversarial examples, which are inputs crafted by an adversary to fool a machine learning system. To enable Adversarial-Playground to generate quick and accurate responses for users, we use two primary tactics: (1) We propose a faster variant of the state-of-the-art Jacobian saliency map approach that maintains a comparable evasion rate. (2) Our visualization does not transmit the generated adversarial images to the client, but rather only the matrix describing the sample and the vector representing classification likelihoods. The source code along with the data from all of our experiments are available at \url{https://github.com/QData/AdversarialDNN-Playground}.