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

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 "jeek"

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}

Fast and Scalable Learning of Sparse Changes in High-Dimensional Gaussian Graphical Model Structure

We focus on the problem of estimating the change in the dependency structures of two $p$-dimensional Gaussian Graphical models (GGMs). Previous studies for sparse change estimation in GGMs involve expensive and difficult non-smooth optimization. We propose a novel method, DIFFEE for estimating DIFFerential networks via an Elementary Estimator under a high-dimensional situation. DIFFEE is solved through a faster and closed form solution that enables it to work in large-scale settings. We conduct a rigorous statistical analysis showing that surprisingly DIFFEE achieves the same asymptotic convergence rates as the state-of-the-art estimators that are much more difficult to compute. Our experimental results on multiple synthetic datasets and one real-world data about brain connectivity show strong performance improvements over baselines, as well as significant computational benefits.

Black-box Generation of Adversarial Text Sequences to Evade Deep Learning Classifiers

Although various techniques have been proposed to generate adversarial samples for white-box attacks on text, little attention has been paid to black-box attacks, which are more realistic scenarios. In this paper, we present a novel algorithm, DeepWordBug, to effectively generate small text perturbations in a black-box setting that forces a deep-learning classifier to misclassify a text input. We employ novel scoring strategies to identify the critical tokens that, if modified, cause the classifier to make an incorrect prediction. Simple character-level transformations are applied to the highest-ranked tokens in order to minimize the edit distance of the perturbation, yet change the original classification. We evaluated DeepWordBug on eight real-world text datasets, including text classification, sentiment analysis, and spam detection. We compare the result of DeepWordBug with two baselines: Random (Black-box) and Gradient (White-box). Our experimental results indicate that DeepWordBug reduces the prediction accuracy of current state-of-the-art deep-learning models, including a decrease of 68\% on average for a Word-LSTM model and 48\% on average for a Char-CNN model.

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.