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}.

Feature Squeezing Mitigates and Detects Carlini/Wagner Adversarial Examples

Feature squeezing is a recently-introduced framework for mitigating and detecting adversarial examples. In previous work, we showed that it is effective against several earlier methods for generating adversarial examples. In this short note, we report on recent results showing that simple feature squeezing techniques also make deep learning models significantly more robust against the Carlini/Wagner attacks, which are the best known adversarial methods discovered to date.

Style Transfer Generative Adversarial Networks: Learning to Play Chess Differently

The idea of style transfer has largely only been explored in image-based tasks, which we attribute in part to the specific nature of loss functions used for style transfer. We propose a general formulation of style transfer as an extension of generative adversarial networks, by using a discriminator to regularize a generator with an otherwise separate loss function. We apply our approach to the task of learning to play chess in the style of a specific player, and present empirical evidence for the viability of our approach.

DeepCloak: Masking Deep Neural Network Models for Robustness Against Adversarial Samples

Recent studies have shown that deep neural networks (DNN) are vulnerable to adversarial samples: maliciously-perturbed samples crafted to yield incorrect model outputs. Such attacks can severely undermine DNN systems, particularly in security-sensitive settings. It was observed that an adversary could easily generate adversarial samples by making a small perturbation on irrelevant feature dimensions that are unnecessary for the current classification task. To overcome this problem, we introduce a defensive mechanism called DeepCloak. By identifying and removing unnecessary features in a DNN model, DeepCloak limits the capacity an attacker can use generating adversarial samples and therefore increase the robustness against such inputs. Comparing with other defensive approaches, DeepCloak is easy to implement and computationally efficient. Experimental results show that DeepCloak can increase the performance of state-of-the-art DNN models against adversarial samples.

Memory Matching Networks for Genomic Sequence Classification

When analyzing the genome, researchers have discovered that proteins bind to DNA based on certain patterns of the DNA sequence known as "motifs". However, it is difficult to manually construct motifs due to their complexity. Recently, externally learned memory models have proven to be effective methods for reasoning over inputs and supporting sets. In this work, we present memory matching networks (MMN) for classifying DNA sequences as protein binding sites. Our model learns a memory bank of encoded motifs, which are dynamic memory modules, and then matches a new test sequence to each of the motifs to classify the sequence as a binding or nonbinding site.

Deep Motif Dashboard: Visualizing and Understanding Genomic Sequences Using Deep Neural Networks

Deep neural network (DNN) models have recently obtained state-of-the-art prediction accuracy for the transcription factor binding (TFBS) site classification task. However, it remains unclear how these approaches identify meaningful DNA sequence signals and give insights as to why TFs bind to certain locations. In this paper, we propose a toolkit called the Deep Motif Dashboard (DeMo Dashboard) which provides a suite of visualization strategies to extract motifs, or sequence patterns from deep neural network models for TFBS classification. We demonstrate how to visualize and understand three important DNN models: convolutional, recurrent, and convolutional-recurrent networks. Our first visualization method is finding a test sequence's saliency map which uses first-order derivatives to describe the importance of each nucleotide in making the final prediction. Second, considering recurrent models make predictions in a temporal manner (from one end of a TFBS sequence to the other), we introduce temporal output scores, indicating the prediction score of a model over time for a sequential input. Lastly, a class-specific visualization strategy finds the optimal input sequence for a given TFBS positive class via stochastic gradient optimization. Our experimental results indicate that a convolutional-recurrent architecture performs the best among the three architectures. The visualization techniques indicate that CNN-RNN makes predictions by modeling both motifs as well as dependencies among them.