Deep learning is one of the most recent and advanced topics in machine learning, with several applications in many fields. It shows promising results in many areas, from computer vision to drug discovery and stock market prediction. There are many books and articles in deep learning that discuss its algorithms, theories, and applications. Also, because of its capabilities and potentials in solving different problems by deploying different data types, many researchers and people who are not in computer science or related fields are interested in learning and using deep learning architectures in their projects. This course gives you some fundamentals of artificial neural networks and deep learning and then has focused on Generative Adversarial Network and its applications with some coding examples to understand the concepts better.

Researchers are developing a deep learning network capable of detecting disease biomarkers with a much higher degree of accuracy. Experts at the University of Waterloo's Cheriton School of Computer Science have created a deep neural network that achieves 98 per cent detection of peptide features in a dataset. That means scientists and medical practitioners have a greater chance of discovering possible diseases through tissue sample analysis. There are multiple existing techniques for detecting diseases by analyzing the protein structure of bio-samples. Computer programs increasingly play a part in this process by examining the large amount of data produced in such tests to pinpoint specific markers of disease.

As a hereditary disease, breast cancer has affected hundreds of families throughout the state. Annually, an average of 1,190 women are diagnosed with breast cancer in Hawaiʻi. As October approaches in recognition of National Breast Cancer Awareness Month, new public impact research from the University of Hawaiʻi Cancer Center is using artificial intelligence (AI) to improve risk assessment for breast cancer to aid in prevention and early detection, improving breast cancer outcomes for women all over the world. To reduce unnecessary imaging for breast cancer and costs associated with it, UH Cancer Center Researcher John Shepherd and his colleagues found that AI is able to distinguish between the mammograms of women who are more likely to develop breast cancer later on, and those who are not. The study was published in Radiology.

Mixed-signal analog/digital circuits emulate spiking neurons and synapses with extremely high energy efficiency, an approach known as "neuromorphic engineering". However, analog circuits are sensitive to process-induced variation among transistors in a chip ("device mismatch"). For neuromorphic implementation of Spiking Neural Networks (SNNs), mismatch causes parameter variation between identically-configured neurons and synapses. Each chip exhibits a different distribution of neural parameters, causing deployed networks to respond differently between chips. Current solutions to mitigate mismatch based on per-chip calibration or on-chip learning entail increased design complexity, area and cost, making deployment of neuromorphic devices expensive and difficult. Here we present a supervised learning approach that produces SNNs with high robustness to mismatch and other common sources of noise. Our method trains SNNs to perform temporal classification tasks by mimicking a pre-trained dynamical system, using a local learning rule from non-linear control theory. We demonstrate our method on two tasks requiring memory, and measure the robustness of our approach to several forms of noise and mismatch. We show that our approach is more robust than common alternatives for training SNNs. Our method provides robust deployment of pre-trained networks on mixed-signal neuromorphic hardware, without requiring per-device training or calibration.

We develop a framework for comparing data manifolds, aimed, in particular, towards the evaluation of deep generative models. We describe a novel tool, Cross-Barcode(P,Q), that, given a pair of distributions in a high-dimensional space, tracks multiscale topology spacial discrepancies between manifolds on which the distributions are concentrated. Based on the Cross-Barcode, we introduce the Manifold Topology Divergence score (MTop-Divergence) and apply it to assess the performance of deep generative models in various domains: images, 3D-shapes, time-series, and on different datasets: MNIST, Fashion MNIST, SVHN, CIFAR10, FFHQ, chest X-ray images, market stock data, ShapeNet. We demonstrate that the MTop-Divergence accurately detects various degrees of mode-dropping, intra-mode collapse, mode invention, and image disturbance. Our algorithm scales well (essentially linearly) with the increase of the dimension of the ambient high-dimensional space. It is one of the first TDA-based practical methodologies that can be applied universally to datasets of different sizes and dimensions, including the ones on which the most recent GANs in the visual domain are trained. The proposed method is domain agnostic and does not rely on pre-trained networks.

The task of image captioning aims to generate captions directly from images via the automatically learned cross-modal generator. To build a well-performing generator, existing approaches usually need a large number of described images, which requires a huge effects on manual labeling. However, in real-world applications, a more general scenario is that we only have limited amount of described images and a large number of undescribed images. Therefore, a resulting challenge is how to effectively combine the undescribed images into the learning of cross-modal generator. To solve this problem, we propose a novel image captioning method by exploiting the Cross-modal Prediction and Relation Consistency (CPRC), which aims to utilize the raw image input to constrain the generated sentence in the commonly semantic space. In detail, considering that the heterogeneous gap between modalities always leads to the supervision difficulty of using the global embedding directly, CPRC turns to transform both the raw image and corresponding generated sentence into the shared semantic space, and measure the generated sentence from two aspects: 1) Prediction consistency. CPRC utilizes the prediction of raw image as soft label to distill useful supervision for the generated sentence, rather than employing the traditional pseudo labeling; 2) Relation consistency. CPRC develops a novel relation consistency between augmented images and corresponding generated sentences to retain the important relational knowledge. In result, CPRC supervises the generated sentence from both the informativeness and representativeness perspectives, and can reasonably use the undescribed images to learn a more effective generator under the semi-supervised scenario.

Deep neural networks (DNNs) are proved to be vulnerable against backdoor attacks. A backdoor is often embedded in the target DNNs through injecting a backdoor trigger into training examples, which can cause the target DNNs misclassify an input attached with the backdoor trigger. Existing backdoor detection methods often require the access to the original poisoned training data, the parameters of the target DNNs, or the predictive confidence for each given input, which are impractical in many real-world applications, e.g., on-device deployed DNNs. We address the black-box hard-label backdoor detection problem where the DNN is fully black-box and only its final output label is accessible. We approach this problem from the optimization perspective and show that the objective of backdoor detection is bounded by an adversarial objective. Further theoretical and empirical studies reveal that this adversarial objective leads to a solution with highly skewed distribution; a singularity is often observed in the adversarial map of a backdoorinfected example, which we call the adversarial singularity phenomenon. Based on this observation, we propose the adversarial extreme value analysis (AEVA) to detect backdoors in black-box neural networks. AEVA is based on an extreme value analysis of the adversarial map, computed from the monte-carlo gradient estimation. Evidenced by extensive experiments across multiple popular tasks and backdoor attacks, our approach is shown effective in detecting backdoor attacks under the black-box hard-label scenarios. Deep Neural Networks (DNNs) have pervasively been used in a wide range of applications such as facial recognition (Masi et al., 2018), object detection (Szegedy et al., 2013), autonomous driving (Okuyama et al., 2018), and home assistants (Singh et al., 2020). In the meanwhile, DNNs become increasingly complex. Training state-of-the-art models requires enormous data and expensive computation.

We consider human activity recognition (HAR) from wearable sensor data in manual-work processes, like warehouse order-picking. Such structured domains can often be partitioned into distinct process steps, e.g., packaging or transporting. Each process step can have a different prior distribution over activity classes, e.g., standing or walking, and different system dynamics. Here, we show how such context information can be integrated systematically into a deep neural network-based HAR system. Specifically, we propose a hybrid architecture that combines a deep neural network-that estimates high-level movement descriptors, attributes, from the raw-sensor data-and a shallow classifier, which predicts activity classes from the estimated attributes and (optional) context information, like the currently executed process step. We empirically show that our proposed architecture increases HAR performance, compared to state-of-the-art methods. Additionally, we show that HAR performance can be further increased when information about process steps is incorporated, even when that information is only partially correct.

The field of machine learning for drug discovery is witnessing an explosion of novel methods. These methods are often benchmarked on simple physicochemical properties such as solubility or general druglikeness, which can be readily computed. However, these properties are poor representatives of objective functions in drug design, mainly because they do not depend on the candidate's interaction with the target. By contrast, molecular docking is a widely successful method in drug discovery to estimate binding affinities. However, docking simulations require a significant amount of domain knowledge to set up correctly which hampers adoption. To this end, we present DOCKSTRING, a bundle for meaningful and robust comparison of ML models consisting of three components: (1) an open-source Python package for straightforward computation of docking scores; (2) an extensive dataset of docking scores and poses of more than 260K ligands for 58 medically-relevant targets; and (3) a set of pharmaceutically-relevant benchmark tasks including regression, virtual screening, and de novo design. The Python package implements a robust ligand and target preparation protocol that allows non-experts to obtain meaningful docking scores. Our dataset is the first to include docking poses, as well as the first of its size that is a full matrix, thus facilitating experiments in multiobjective optimization and transfer learning. Overall, our results indicate that docking scores are a more appropriate evaluation objective than simple physicochemical properties, yielding more realistic benchmark tasks and molecular candidates.

Discovering a solution in a combinatorial space is prevalent in many real-world problems but it is also challenging due to diverse complex constraints and the vast number of possible combinations. To address such a problem, we introduce a novel formulation, combinatorial construction, which requires a building agent to assemble unit primitives (i.e., LEGO bricks) sequentially -- every connection between two bricks must follow a fixed rule, while no bricks mutually overlap. To construct a target object, we provide incomplete knowledge about the desired target (i.e., 2D images) instead of exact and explicit volumetric information to the agent. This problem requires a comprehensive understanding of partial information and long-term planning to append a brick sequentially, which leads us to employ reinforcement learning. The approach has to consider a variable-sized action space where a large number of invalid actions, which would cause overlap between bricks, exist. To resolve these issues, our model, dubbed Brick-by-Brick, adopts an action validity prediction network that efficiently filters invalid actions for an actor-critic network. We demonstrate that the proposed method successfully learns to construct an unseen object conditioned on a single image or multiple views of a target object.