Variational Physiologically Informed Solution to Hemodynamic and Perfusion Response Estimation from ASL fMRI Data

International audienceFunctional Arterial Spin Labeling (fASL) MRI can provide a quantitative measurement of cerebral blood flow. A joint detection-estimation (JDE) framework has been considered to extract task-related perfusion and hemodynamic responses not restricted to canonical response function shapes. In this work, we provide a variational expectation-maximization (VEM) algorithm for hemodynamic and perfusion responses estimation. This approach provides a lower computational load compared to previous attempts, and facilitates the incorporation of prior knowledge and constraints in the estimation. Validation on simulated and real data sets has been performed

Machine learning for modeling the progression of Alzheimer disease dementia using clinical data: A systematic literature review

OBJECTIVE: Alzheimer disease (AD) is the most common cause of dementia, a syndrome characterized by cognitive impairment severe enough to interfere with activities of daily life. We aimed to conduct a systematic literature review (SLR) of studies that applied machine learning (ML) methods to clinical data derived from electronic health records in order to model risk for progression of AD dementia. MATERIALS AND METHODS: We searched for articles published between January 1, 2010, and May 31, 2020, in PubMed, Scopus, ScienceDirect, IEEE Explore Digital Library, Association for Computing Machinery Digital Library, and arXiv. We used predefined criteria to select relevant articles and summarized them according to key components of ML analysis such as data characteristics, computational algorithms, and research focus. RESULTS: There has been a considerable rise over the past 5 years in the number of research papers using ML-based analysis for AD dementia modeling. We reviewed 64 relevant articles in our SLR. The results suggest that majority of existing research has focused on predicting progression of AD dementia using publicly available datasets containing both neuroimaging and clinical data (neurobehavioral status exam scores, patient demographics, neuroimaging data, and laboratory test values). DISCUSSION: Identifying individuals at risk for progression of AD dementia could potentially help to personalize disease management to plan future care. Clinical data consisting of both structured data tables and clinical notes can be effectively used in ML-based approaches to model risk for AD dementia progression. Data sharing and reproducibility of results can enhance the impact, adaptation, and generalizability of this research

Large-scale Data Analysis and Deep Learning Using Distributed Cyberinfrastructures and High Performance Computing

Data in many research fields continues to grow in both size and complexity. For instance, recent technological advances have caused an increased throughput in data in various biological-related endeavors, such as DNA sequencing, molecular simulations, and medical imaging. In addition, the variance in the types of data (textual, signal, image, etc.) adds an additional complexity in analyzing the data. As such, there is a need for uniquely developed applications that cater towards the type of data. Several considerations must be made when attempting to create a tool for a particular dataset. First, we must consider the type of algorithm required for analyzing the data. Next, since the size and complexity of the data imposes high computation and memory requirements, it is important to select a proper hardware environment on which to build the application. By carefully both developing the algorithm and selecting the hardware, we can provide an effective environment in which to analyze huge amounts of highly complex data in a large-scale manner. In this dissertation, I go into detail regarding my applications using big data and deep learning techniques to analyze complex and large data. I investigate how big data frameworks, such as Hadoop, can be applied to problems such as large-scale molecular dynamics simulations. Following this, many popular deep learning frameworks are evaluated and compared to find those that suit certain hardware setups and deep learning models. Then, we explore an application of deep learning to a biomedical problem, namely ADHD diagnosis from fMRI data. Lastly, I demonstrate a framework for real-time and fine-grained vehicle detection and classification. With each of these works in this dissertation, a unique large-scale analysis algorithm or deep learning model is implemented that caters towards the problem and leverages specialized computing resources

Harvesting Context and Mining Emotions Related to Olfactory Cultural Heritage

UIDB/00657/2020 UIDP/00657/2020This paper presents an Artificial Intelligence approach to mining context and emotions related to olfactory cultural heritage narratives, particularly to fairy tales. We provide an overview of the role of smell and emotions in literature, as well as highlight the importance of olfactory experience and emotions from psychology and linguistic perspectives. We introduce a methodology for extracting smells and emotions from text, as well as demonstrate the context-based visualizations related to smells and emotions implemented in a novel smell tracker tool. The evaluation is performed using a collection of fairy tales from Grimm and Andersen. We find out that fairy tales often connect smell with the emotional charge of situations. The experimental results show that we can detect smells and emotions in fairy tales with an F1 score of 91.62 and 79.2, respectively.publishersversionpublishe

Assessment of the Physiological Network in Sleep Apnea

Objective: Machine Learning models, in particular Artificial Neural Networks, have shown to be applicable in clinical research for tumor detection and sleep phase classification. Applications in systems medicine and biology, for example in Physiological Networks, could benefit from the ability of these methods to recognize patterns in high-dimensional data, but decisions of an Artificial Neural Network cannot be interpreted based on the model itself. In a medical context this is an undesirable characteristic, because hidden age, gender or other data biases negatively impact the model quality. If insights are based on a biased model, the ability of an independent study to come to similar conclusions is limited and therefore an essential property of scientific experiments, known as results reproducibility, is violated. Besides results reproducibility, methods reproducibility allows others to reproduce exact outputs of computational experiments, but requires data, code and runtime environments to be available. These challenges in interpretability and reproducibility are addressed as part of an assessment of the Physiological Network in Obstructive Sleep Apnea. Approach: A research platform is developed, that connects medical data, code and environ-ments to enable methods reproducibility. The platform employs a compute cluster or cloud to accelerate the demanding model training. Artificial Neural Networks are trained on the Physiological Network data of a healthy control group for age and gender prediction to verify the influence of these biases. In a subsequent study, an Artificial Neural Network is trained to classify the Physiological Networks in Obstructive Sleep Apnea and a healthy control group. The state-of-the-art interpretation method DeepLift is applied to explain model predictions. Results: An existing collaboration platform has been extended for sleep research data and modern container technologies are used to distribute training environments in compute clusters. Artificial Neural Network models predict the age of healthy subjects in a resolution of one decade and correctly classify the gender with 91% accuracy. Due to the verified biases, a matched dataset is created for the classification of Obstructive Sleep Apnea. The classification accuracy reaches 87% and DeepLift provides biomarkers as significant indicators towards or against the disorder. Analysis of misclassified samples shows potential Obstructive Sleep Apnea phenotypes. Significance: The presented platform is extensible for future use cases and focuses on the reproducibility of computational experiments, a concern across many disciplines. Machine learning approaches solve analysis tasks on high-dimensional data and novel interpretation techniques provide the required transparency for medical applications.Ziel: Methoden des maschinellen Lernens, insbesondere künstliche neuronale Netze, finden Anwendung in der klinischen Forschung, um beispielsweise Tumorzellen oder Schlafphasen zu klassifizieren. Anwendungen in der Systemmedizin und -biologie, wie physiologische Netzwerke, könnten von der Fähigkeit dieser Methoden, Muster in großen Merkmalsräumen zu finden, profitieren. Allerdings sind Entscheidungen eines künstlichen neuronalen Netzes nicht allein anhand des Modells interpretierbar. In einem medizinischen Kontext ist dies eine unerwünschte Charakteristik, weil die Daten, mit denen ein Modell trainiert wird, versteckte Einflüsse wie Alters- und Geschlechtsabhängigkeiten beinhalten können. Erkenntnisse, die auf einem beeinflussten Modell basieren, sind nur bedingt durch unabhängige Studien nach-vollziehbar, sodass keine Ergebnisreproduzierbarkeit gegeben ist. Neben der Ergebnisreproduzier-barkeit bezeichnet Methodenreproduzierbarkeit die Möglichkeit exakte Programmausgaben zu reproduzieren, was die Verfügbarkeit von Daten, Programmcode und Ausführungsumgebungen voraussetzt. Diese Promotion untersucht Veränderungen im physiologischen Netzwerk bei obstruktivem Schlafapnoesyndrom mit Methoden des maschinellen Lernens und adressiert dabei die genannten Herausforderungen der Interpretierbarkeit und Reproduzierbarkeit. Ansatz: Es wird eine Forschungsplattform entwickelt, die medizinische Daten, Programmcode und Ausführungsumgebungen verknüpft und damit Methodenreproduzierbarkeit ermöglicht. Die Plattform bindet zur Beschleunigung des ressourcenintensiven Modelltrainings verteilte Rechenressourcen in Form eines Clusters oder einer Cloud an. Künstliche neuronale Netze werden zur Bestimmung des Alters und des Geschlechts anhand der physiologischen Daten einer gesunden Kontrollgruppe trainiert, um den Einfluss der Alters- und Geschlechtsabhängigkeiten zu untersuchen. In einer Folgestudie werden die Unterschiede im physiologischen Netzwerk einer Gruppe mit obstruktivem Schlafapnoesyndrom und einer gesunden Kontrollgruppe klassifiziert. DeepLift, eine Interpretationsmethode nach aktuellem Stand der Technik, wird zur Erklärung der Modellvorhersagen angewendet. Ergebnisse: Eine existierende Forschungsplattform wurde für die Verarbeitung schlafbezogener Forschungsdaten erweitert und Containertechnologien ermöglichen die Bereitstellung der Ausführungsumgebung eines Experiments in einem Cluster. Künstliche neuronale Netze können anhand der physiologischen Daten das Alter einer Person bis auf eine Dekade genau bestimmen und eine Geschlechtsklassifikation erreicht eine Genauigkeit von 91%. Die Ergebnisse bestätigen den Einfluss der Alters- und Geschlechtsabhängigkeiten, sodass für Schlafapnoeklassifikationen zunächst eine Datenbasis geschaffen wird, in der die Geschlechts- und Altersverteilung zwischen gesunden und kranken Gruppen ausgeglichen ist. Die resultierenden Modelle erreichen eine Klassifikationsgenauigkeit von 87%. DeepLift weist auf Biomarker und mögliche physiologische Schlafapnoe-Phänotypen im Tiefschlaf hin. Signifikanz: Die vorgestellte Plattform ist für zukünftige Anwendungsfälle erweiterbar und ermöglicht Methodenreproduzierbarkeit, was über den Einsatz in der Medizin hinaus auch in anderen Disziplinen von Bedeutung ist. Maschinelles Lernen bietet sinnvolle Ansätze für die Analyse hochdimensionaler Daten und neue Interpretationstechniken schaffen die notwendige Transparenz für medizinische Anwendungszwecke

AAAI Workshop on Artificial Intelligence with Biased or Scarce Data (AIBSD)

This book is a collection of the accepted papers presented at the Workshop on Artificial Intelligence with Biased or Scarce Data (AIBSD) in conjunction with the 36th AAAI Conference on Artificial Intelligence 2022. During AIBSD 2022, the attendees addressed the existing issues of data bias and scarcity in Artificial Intelligence and discussed potential solutions in real-world scenarios. A set of papers presented at AIBSD 2022 is selected for further publication and included in this book