Opportunities and obstacles for deep learning in biology and medicine

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\u27s 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

Multi-objective Robust Machine Learning For Critical Systems With Scarce Data

With the heavy reliance on Information Technologies in every aspect of our daily lives, Machine Learning (ML) models have become a cornerstone of these technologies’ rapid growth and pervasiveness. In particular, the most critical and fundamental technologies that handle our economic systems, transportation, health, and even privacy. However, while these systems are becoming more effective, their complexity inherently decreases our ability to understand, test, and assess the dependability and trustworthiness of these systems. This problem becomes even more challenging under a multi-objective framework: When the ML model is required to learn multiple tasks together, behave under constrained inputs or fulfill contradicting concomitant objectives. Our dissertation focuses on the context of robust ML under limited training data, i.e., use cases where it is costly to collect additional training data and/or label it. We will study this topic under the prism of three real use cases: Fraud detection, pandemic forecasting, and chest x-ray diagnosis. Each use-case covers one of the challenges of robust ML with limited data, (1) robustness to imperceptible perturbations, or (2) robustness to confounding variables. We provide a study of the challenges for each case and propose novel techniques to achieve robust learning. As the first contribution of this dissertation, we collaborate with BGL BNP Paribas. We demonstrate that their overdraft and fraud detection systems are prima facie robust to adversarial attacks because of the complexity of their feature engineering and domain constraints. However, we show that gray-box attacks that take into account domain knowledge can easily break their defense. We propose, CoEva2 adversarial fine-tuning, a new defense mechanism based on multi-objective evolutionary algorithms to augment the training data and mitigate the system’s vulnerabilities. Next, we investigate how domain knowledge can protect against adversarial attacks through multi-task learning. We show that adding domain constraints in the form of additional tasks can significantly improve the robustness of models to adversarial attacks, particularly for the robot navigation use case. We propose a new set of adaptive attacks and demonstrate that adversarial training combined with such attacks can improve robustness. While the raw data available in the BGL or Robot Navigation is vast, it is heavily cleaned, feature-engineered, and annotated by domain experts (which are expensive), and the end training data is scarce. In contrast, raw data is scarce when dealing with an outbreak, and designing robust ML systems to predict, forecast, and recommend mitigation policies is challenging. In particular, for small countries like Luxembourg. Contrary to common techniques that forecast new cases based on previous data in time series, we propose a novel surrogate-based optimization as an integrated loop. It combines a neural network prediction of the infection rate based on mobility attributes and a model-based simulation that predicts the cases and deaths. Our approach has been used by the Luxembourg government’s task force and has been recognized with a best paper award at KDD2020. Our following work focuses on the challenges that pose cofounding factors to the robustness and generalization of Chest X-ray (CXR) classification. We first investigate the robustness and generalization of multi-task models, then demonstrate that multi-task learning, leveraging the cofounding variables, can significantly improve the generalization and robustness of CXR classification models. Our results suggest that task augmentation with additional knowledge (like extraneous variables) outperforms state-of-art data augmentation techniques in improving test and robust performances. Overall, this dissertation provides insights into the importance of domain knowledge in the robustness and generalization of models. It shows that instead of building data-hungry ML models, particularly for critical systems, a better understanding of the system as a whole and its domain constraints yields improved robustness and generalization performances. This dissertation also proposes theorems, algorithms, and frameworks to effectively assess and improve the robustness of ML systems for real-world cases and applications

On the Design, Implementation and Application of Novel Multi-disciplinary Techniques for explaining Artificial Intelligence Models

284 p.Artificial Intelligence is a non-stopping field of research that has experienced some incredible growth lastdecades. Some of the reasons for this apparently exponential growth are the improvements incomputational power, sensing capabilities and data storage which results in a huge increment on dataavailability. However, this growth has been mostly led by a performance-based mindset that has pushedmodels towards a black-box nature. The performance prowess of these methods along with the risingdemand for their implementation has triggered the birth of a new research field. Explainable ArtificialIntelligence. As any new field, XAI falls short in cohesiveness. Added the consequences of dealing withconcepts that are not from natural sciences (explanations) the tumultuous scene is palpable. This thesiscontributes to the field from two different perspectives. A theoretical one and a practical one. The formeris based on a profound literature review that resulted in two main contributions: 1) the proposition of anew definition for Explainable Artificial Intelligence and 2) the creation of a new taxonomy for the field.The latter is composed of two XAI frameworks that accommodate in some of the raging gaps found field,namely: 1) XAI framework for Echo State Networks and 2) XAI framework for the generation ofcounterfactual. The first accounts for the gap concerning Randomized neural networks since they havenever been considered within the field of XAI. Unfortunately, choosing the right parameters to initializethese reservoirs falls a bit on the side of luck and past experience of the scientist and less on that of soundreasoning. The current approach for assessing whether a reservoir is suited for a particular task is toobserve if it yields accurate results, either by handcrafting the values of the reservoir parameters or byautomating their configuration via an external optimizer. All in all, this poses tough questions to addresswhen developing an ESN for a certain application, since knowing whether the created structure is optimalfor the problem at hand is not possible without actually training it. However, some of the main concernsfor not pursuing their application is related to the mistrust generated by their black-box" nature. Thesecond presents a new paradigm to treat counterfactual generation. Among the alternatives to reach auniversal understanding of model explanations, counterfactual examples is arguably the one that bestconforms to human understanding principles when faced with unknown phenomena. Indeed, discerningwhat would happen should the initial conditions differ in a plausible fashion is a mechanism oftenadopted by human when attempting at understanding any unknown. The search for counterfactualsproposed in this thesis is governed by three different objectives. Opposed to the classical approach inwhich counterfactuals are just generated following a minimum distance approach of some type, thisframework allows for an in-depth analysis of a target model by means of counterfactuals responding to:Adversarial Power, Plausibility and Change Intensity

Deep Neural Networks and Data for Automated Driving

This open access book brings together the latest developments from industry and research on automated driving and artificial intelligence. Environment perception for highly automated driving heavily employs deep neural networks, facing many challenges. How much data do we need for training and testing? How to use synthetic data to save labeling costs for training? How do we increase robustness and decrease memory usage? For inevitably poor conditions: How do we know that the network is uncertain about its decisions? Can we understand a bit more about what actually happens inside neural networks? This leads to a very practical problem particularly for DNNs employed in automated driving: What are useful validation techniques and how about safety? This book unites the views from both academia and industry, where computer vision and machine learning meet environment perception for highly automated driving. Naturally, aspects of data, robustness, uncertainty quantification, and, last but not least, safety are at the core of it. This book is unique: In its first part, an extended survey of all the relevant aspects is provided. The second part contains the detailed technical elaboration of the various questions mentioned above

Towards Interpretability and Robustness of Machine Learning Models

Modern machine learning models can be difficult to probe and understand after they have been trained. This is a major problem for the field, with consequences for trustworthiness, diagnostics, debugging, robustness, and a range of other engineering and human interaction issues surrounding the deployment of a model. Another problem of modern machine learning models is their vulnerability to small adversarial perturbations to the input, which incurs a security risk when they are applied to critical areas.In this thesis, we develop systematic and efficient tools for interpreting machine learning models and evaluating their adversarial robustness. Part I focuses on model interpretation. We derive an efficient feature scoring method by exploiting the graph structure in data. We also develop a learning-based method under an information-based framework. As an attempt to leverage prior knowledge about what constitutes a satisfying interpretation in a given domain, we propose a systematic approach to exploiting syntactic constituency structure by leveraging a parse tree for interpretation of models in the setting of linguistic data. Part II focuses on the evaluation of adversarial robustness. We first propose a probabilistic framework for generating adversarial examples on discrete data, and develop two algorithms to implement it. We also introduce a novel attack method in the setting where the attacker has access to model decisions alone. We investigate the robustness of various machine learning models and existing defense mechanisms under the proposed attack method. In Part III, we build a connection between the two fields by developing a method for detecting adversarial examples via tools in model interpretation

Towards Improving Generalization of Multi-Task Learning

Multi-task Learning (MTL), which involves the simultaneous learning of multiple tasks, can achieve better performance than learning each task independently. It has achieved great success in various applications, ranging from computer vision to bioinformatics. However, involving multiple tasks in a single learning process is complicated, for both cooperation and competition exist across the including tasks; furthermore, the cooperation boosts the generalization of MTL while the competition degenerates it. There lacks of a systematic study on how to improve MTL's generalization by handling the cooperation and competition. This thesis systematically studies this problem and proposed four novel MTL methods to enhance the between-task cooperation or reduce the between-task competition. Specifically, for the between-task cooperation, adversarial multi-task representation learning (AMTRL) and semi-supervised multi-task learning (Semi-MTL) are studied; furthermore, a novel adaptive AMTRL method and a novel representation consistency regularization-based Semi-MTL method are proposed respectively. As to the between-task competition, this thesis analyzes the task variance and task imbalance; furthermore, a novel task variance regularization-based MTL method and a novel task-imbalance-aware MTL method are proposed respectively. The above proposed methods can improve the generalization of MTL and achieve state-of-the-art performance in real-word MTL applications

Trusted Artificial Intelligence in Manufacturing; Trusted Artificial Intelligence in Manufacturing

The successful deployment of AI solutions in manufacturing environments hinges on their security, safety and reliability which becomes more challenging in settings where multiple AI systems (e.g., industrial robots, robotic cells, Deep Neural Networks (DNNs)) interact as atomic systems and with humans. To guarantee the safe and reliable operation of AI systems in the shopfloor, there is a need to address many challenges in the scope of complex, heterogeneous, dynamic and unpredictable environments. Specifically, data reliability, human machine interaction, security, transparency and explainability challenges need to be addressed at the same time. Recent advances in AI research (e.g., in deep neural networks security and explainable AI (XAI) systems), coupled with novel research outcomes in the formal specification and verification of AI systems provide a sound basis for safe and reliable AI deployments in production lines. Moreover, the legal and regulatory dimension of safe and reliable AI solutions in production lines must be considered as well. To address some of the above listed challenges, fifteen European Organizations collaborate in the scope of the STAR project, a research initiative funded by the European Commission in the scope of its H2020 program (Grant Agreement Number: 956573). STAR researches, develops, and validates novel technologies that enable AI systems to acquire knowledge in order to take timely and safe decisions in dynamic and unpredictable environments. Moreover, the project researches and delivers approaches that enable AI systems to confront sophisticated adversaries and to remain robust against security attacks. This book is co-authored by the STAR consortium members and provides a review of technologies, techniques and systems for trusted, ethical, and secure AI in manufacturing. The different chapters of the book cover systems and technologies for industrial data reliability, responsible and transparent artificial intelligence systems, human centered manufacturing systems such as human-centred digital twins, cyber-defence in AI systems, simulated reality systems, human robot collaboration systems, as well as automated mobile robots for manufacturing environments. A variety of cutting-edge AI technologies are employed by these systems including deep neural networks, reinforcement learning systems, and explainable artificial intelligence systems. Furthermore, relevant standards and applicable regulations are discussed. Beyond reviewing state of the art standards and technologies, the book illustrates how the STAR research goes beyond the state of the art, towards enabling and showcasing human-centred technologies in production lines. Emphasis is put on dynamic human in the loop scenarios, where ethical, transparent, and trusted AI systems co-exist with human workers. The book is made available as an open access publication, which could make it broadly and freely available to the AI and smart manufacturing communities