Objective: Modern medicine needs to shift from a wait and react, curative discipline to a preventative, interdisciplinary science aiming at providing personalised, systemic and precise treatment plans to patients. The aim of this work is to present how the integration of machine learning approaches with mechanistic computational modelling could yield a reliable infrastructure to run probabilistic simulations where the entire organism is considered as a whole. Methods: We propose a general framework that composes advanced AI approaches and integrates mathematical modelling in order to provide a panoramic view over current and future physiological conditions. The proposed architecture is based on a graph neural network (GNNs) forecasting clinically relevant endpoints (such as blood pressure) and a generative adversarial network (GANs) providing a proof of concept of transcriptomic integrability. Results: We show the results of the investigation of pathological effects of overexpression of ACE2 across different signalling pathways in multiple tissues on cardiovascular functions. We provide a proof of concept of integrating a large set of composable clinical models using molecular data to drive local and global clinical parameters and derive future trajectories representing the evolution of the physiological state of the patient. Significance: We argue that the graph representation of a computational patient has potential to solve important technological challenges in integrating multiscale computational modelling with AI. We believe that this work represents a step forward towards a healthcare digital twin.

This thesis focuses on the research and development of the Hemodynamic Tissue Signature (HTS) method: an unsupervised machine learning approach to describe the vascular heterogeneity of glioblastomas by means of perfusion MRI analysis. The HTS builds on the concept of habitats. An habitat is defined as a sub-region of the lesion with a particular MRI profile describing a specific physiological behavior. The HTS method delineates four habitats within the glioblastoma: the High Angiogenic Tumor (HAT) habitat, as the most perfused region of the enhancing tumor; the Low Angiogenic Tumor (LAT) habitat, as the region of the enhancing tumor with a lower angiogenic profile; the potentially Infiltrated Peripheral Edema (IPE) habitat, as the non-enhancing region adjacent to the tumor with elevated perfusion indexes; and the Vasogenic Peripheral Edema (VPE) habitat, as the remaining edema of the lesion with the lowest perfusion profile. The results of this thesis have been published in ten scientific contributions, including top-ranked journals and conferences in the areas of Medical Informatics, Statistics and Probability, Radiology & Nuclear Medicine, Machine Learning and Data Mining and Biomedical Engineering. An industrial patent registered in Spain (ES201431289A), Europe (EP3190542A1) and EEUU (US20170287133A1) was also issued, summarizing the efforts of the thesis to generate tangible assets besides the academic revenue obtained from research publications. Finally, the methods, technologies and original ideas conceived in this thesis led to the foundation of ONCOANALYTICS CDX, a company framed into the business model of companion diagnostics for pharmaceutical compounds, thought as a vehicle to facilitate the industrialization of the ONCOhabitats technology.

Deep learning is a group of exciting new technologies for neural networks. Through a combination of advanced training techniques and neural network architectural components, it is now possible to create neural networks that can handle tabular data, images, text, and audio as both input and output. Deep learning allows a neural network to learn hierarchies of information in a way that is like the function of the human brain. This course will introduce the student to classic neural network structures, Convolution Neural Networks (CNN), Long Short-Term Memory (LSTM), Gated Recurrent Neural Networks (GRU), General Adversarial Networks (GAN), and reinforcement learning. Application of these architectures to computer vision, time series, security, natural language processing (NLP), and data generation will be covered. High-Performance Computing (HPC) aspects will demonstrate how deep learning can be leveraged both on graphical processing units (GPUs), as well as grids. Focus is primarily upon the application of deep learning to problems, with some introduction to mathematical foundations. Readers will use the Python programming language to implement deep learning using Google TensorFlow and Keras. It is not necessary to know Python prior to this book; however, familiarity with at least one programming language is assumed.

This thesis develops a conceptual framework considering social data as representing the surface layer of a hierarchy of human social behaviours, needs and cognition which is employed to transform social data into representations that preserve social behaviours and their causalities. Based on this framework two platforms were built to capture insights from fast-paced and slow-paced social data. For fast-paced, a self-structuring and incremental learning technique was developed to automatically capture salient topics and corresponding dynamics over time. An event detection technique was developed to automatically monitor those identified topic pathways for significant fluctuations in social behaviours using multiple indicators such as volume and sentiment. This platform is demonstrated using two large datasets with over 1 million tweets. The separated topic pathways were representative of the key topics of each entity and coherent against topic coherence measures. Identified events were validated against contemporary events reported in news. Secondly for the slow-paced social data, a suite of new machine learning and natural language processing techniques were developed to automatically capture self-disclosed information of the individuals such as demographics, emotions and timeline of personal events. This platform was trialled on a large text corpus of over 4 million posts collected from online support groups. This was further extended to transform prostate cancer related online support group discussions into a multidimensional representation and investigated the self-disclosed quality of life of patients (and partners) against time, demographics and clinical factors. The capabilities of this extended platform have been demonstrated using a text corpus collected from 10 prostate cancer online support groups comprising of 609,960 prostate cancer discussions and 22,233 patients.

Machine behavior that is based on learning algorithms can be significantly influenced by the exposure to data of different qualities. Up to now, those qualities are solely measured in technical terms, but not in ethical ones, despite the significant role of training and annotation data in supervised machine learning. This is the first study to fill this gap by describing new dimensions of data quality for supervised machine learning applications. Based on the rationale that different social and psychological backgrounds of individuals correlate in practice with different modes of human-computer-interaction, the paper describes from an ethical perspective how varying qualities of behavioral data that individuals leave behind while using digital technologies have socially relevant ramification for the development of machine learning applications. The specific objective of this study is to describe how training data can be selected according to ethical assessments of the behavior it originates from, establishing an innovative filter regime to transition from the big data rationale n = all to a more selective way of processing data for training sets in machine learning. The overarching aim of this research is to promote methods for achieving beneficial machine learning applications that could be widely useful for industry as well as academia.

Artificial intelligence (AI) has become prevalent in our everyday technologies and impacts both individuals and communities. The explainable AI (XAI) scholarship has explored the philosophical nature of explanation and technical explanations, which are usually driven by experts in lab settings and can be challenging for laypersons to understand. In addition, existing XAI research tends to focus on the individual level. Little is known about how people understand and explain AI-led decisions in the community context. Drawing from XAI and activity theory, a foundational HCI theory, we theorize how explanation is situated in a community's shared values, norms, knowledge, and practices, and how situated explanation mediates community-AI interaction. We then present a case study of AI-led moderation, where community members collectively develop explanations of AI-led decisions, most of which are automated punishments. Lastly, we discuss the implications of this framework at the intersection of CSCW, HCI, and XAI.

In poultry farming, the systematic choice, update, and implementation of periodic (t) action plans define the feed conversion rate (FCR[t]), which is an acceptable measure for successful production. Appropriate action plans provide tailored resources for broilers, allowing them to grow within the so-called thermal comfort zone, without wast or lack of resources. Although the implementation of an action plan is automatic, its configuration depends on the knowledge of the specialist, tending to be inefficient and error-prone, besides to result in different FCR[t] for each poultry house. In this article, we claim that the specialist's perception can be reproduced, to some extent, by computational intelligence. By combining deep learning and genetic algorithm techniques, we show how action plans can adapt their performance over the time, based on previous well succeeded plans. We also implement a distributed network infrastructure that allows to replicate our method over distributed poultry houses, for their smart, interconnected, and adaptive control. A supervision system is provided as interface to users. Experiments conducted over real data show that our method improves 5% on the performance of the most productive specialist, staying very close to the optimal FCR[t].

The SARS-CoV-2 (Covid-19) pandemic has caused significant strain on public health institutions around the world. Contact tracing is an essential tool to change the course of the Covid-19 pandemic. Manual contact tracing of Covid-19 cases has significant challenges that limit the ability of public health authorities to minimize community infections. Personalized peer-to-peer contact tracing through the use of mobile apps has the potential to shift the paradigm. Some countries have deployed centralized tracking systems, but more privacy-protecting decentralized systems offer much of the same benefit without concentrating data in the hands of a state authority or for-profit corporations. Machine learning methods can circumvent some of the limitations of standard digital tracing by incorporating many clues and their uncertainty into a more graded and precise estimation of infection risk. The estimated risk can provide early risk awareness, personalized recommendations and relevant information to the user. Finally, non-identifying risk data can inform epidemiological models trained jointly with the machine learning predictor. These models can provide statistical evidence for the importance of factors involved in disease transmission. They can also be used to monitor, evaluate and optimize health policy and (de)confinement scenarios according to medical and economic productivity indicators. However, such a strategy based on mobile apps and machine learning should proactively mitigate potential ethical and privacy risks, which could have substantial impacts on society (not only impacts on health but also impacts such as stigmatization and abuse of personal data). Here, we present an overview of the rationale, design, ethical considerations and privacy strategy of `COVI,' a Covid-19 public peer-to-peer contact tracing and risk awareness mobile application developed in Canada.

What if I told a story here, how would that story start?" Thus, the summarization prompt: "My second grader asked me what this passage means: …" When a given prompt isn't working and GPT-3 keeps pivoting into other modes of completion, that may mean that one hasn't constrained it enough by imitating a correct output, and one needs to go further; writing the first few words or sentence of the target output may be necessary.

Citizen Science Salon is a partnership between Discover and SciStarter.org. In 2016, a team of Alzheimer's disease researchers at Cornell University hit a dead end. The scientists were studying mice, looking for links between Alzheimer's and blood flow changes in the brain. For years, scientists have known that reduced blood flow in the brain is a symptom of Alzheimer's disease. More recent research has also shown that this reduced blood flow can be caused by clogged blood vessels -- or "stalls." And by reversing these stalls in mice, scientists were able to restore their memory.