We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Integrative analysis of 111 reference human epigenomes

General Topology-I

Deep learning is at the heart of the current rise of artificial intelligence. In the field of computer vision, it has become the workhorse for applications ranging from self-driving cars to surveillance and security. Whereas, deep neural networks have demonstrated phenomenal success (often beyond human capabilities) in solving complex problems, recent studies show that they are vulnerable to adversarial attacks in the form of subtle perturbations to inputs that lead a model to predict incorrect outputs. For images, such perturbations are often too small to be perceptible, yet they completely fool the deep learning models. Adversarial attacks pose a serious threat to the success of deep learning in practice. This fact has recently led to a large influx of contributions in this direction. This paper presents the first comprehensive survey on adversarial attacks on deep learning in computer vision. We review the works that design adversarial attacks, analyze the existence of such attacks and propose defenses against them. To emphasize that adversarial attacks are possible in practical conditions, we separately review the contributions that evaluate adversarial attacks in the real-world scenarios. Finally, drawing on the reviewed literature, we provide a broader outlook of this research direction.

Threat of Adversarial Attacks on Deep Learning in Computer Vision: A Survey

Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.

https://royalsocietypublishing.org/doi/pdf/10.1098/rsif.2017.0387

Opportunities and obstacles for deep learning in biology and medicine.

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.

/pdf/deep-motif-dashboard-visualizing-and-understanding-genomic-x5uxic58ir.pdf

Deep motif dashboard: visualizing and understanding genomic sequences using deep neural networks.

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.

/pdf/deepcloak-masking-deep-neural-network-models-for-robustness-uo95xpsgmz.pdf

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

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.

Beilun Wang

Papers

Deep motif dashboard: visualizing and understanding genomic sequences using deep neural networks.

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

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

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

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