Mining Predictive Patterns and Extension to Multivariate Temporal Data

An important goal of knowledge discovery is the search for patterns in the data that can help explaining its underlying structure. To be practically useful, the discovered patterns should be novel (unexpected) and easy to understand by humans. In this thesis, we study the problem of mining patterns (defining subpopulations of data instances) that are important for predicting and explaining a specific outcome variable. An example is the task of identifying groups of patients that respond better to a certain treatment than the rest of the patients. We propose and present efficient methods for mining predictive patterns for both atemporal and temporal (time series) data. Our first method relies on frequent pattern mining to explore the search space. It applies a novel evaluation technique for extracting a small set of frequent patterns that are highly predictive and have low redundancy. We show the benefits of this method on several synthetic and public datasets. Our temporal pattern mining method works on complex multivariate temporal data, such as electronic health records, for the event detection task. It first converts time series into time-interval sequences of temporal abstractions and then mines temporal patterns backwards in time, starting from patterns related to the most recent observations. We show the benefits of our temporal pattern mining method on two real-world clinical tasks

Graph analysis of functional brain networks: practical issues in translational neuroscience

The brain can be regarded as a network: a connected system where nodes, or units, represent different specialized regions and links, or connections, represent communication pathways. From a functional perspective communication is coded by temporal dependence between the activities of different brain areas. In the last decade, the abstract representation of the brain as a graph has allowed to visualize functional brain networks and describe their non-trivial topological properties in a compact and objective way. Nowadays, the use of graph analysis in translational neuroscience has become essential to quantify brain dysfunctions in terms of aberrant reconfiguration of functional brain networks. Despite its evident impact, graph analysis of functional brain networks is not a simple toolbox that can be blindly applied to brain signals. On the one hand, it requires a know-how of all the methodological steps of the processing pipeline that manipulates the input brain signals and extract the functional network properties. On the other hand, a knowledge of the neural phenomenon under study is required to perform physiological-relevant analysis. The aim of this review is to provide practical indications to make sense of brain network analysis and contrast counterproductive attitudes

Leveraging Time Series Data in Similarity Based Healthcare Predictive Models: The Case of Early ICU Mortality Prediction

Patient time series classification faces challenges in high degrees of dimensionality and missingness. In light of patient similarity theory, this study explores effective temporal feature engineering and reduction, missing value imputation, and change point detection methods that can afford similarity-based classification models with desirable accuracy enhancement. We select a piecewise aggregation approximation method to extract fine-grain temporal features and propose a minimalist method to impute missing values in temporal features. For dimensionality reduction, we adopt a gradient descent search method for feature weight assignment. We propose new patient status and directional change definitions based on medical knowledge or clinical guidelines about the value ranges for different patient status levels, and develop a method to detect change points indicating positive or negative patient status changes. We evaluate the effectiveness of the proposed methods in the context of early Intensive Care Unit mortality prediction. The evaluation results show that the k-Nearest Neighbor algorithm that incorporates methods we select and propose significantly outperform the relevant benchmarks for early ICU mortality prediction. This study makes contributions to time series classification and early ICU mortality prediction via identifying and enhancing temporal feature engineering and reduction methods for similarity-based time series classification. Keywords: time-series classification, similarity-based classification, mortality prediction, directional change poin

Abnormal Infant Movements Classification With Deep Learning on Pose-Based Features

The pursuit of early diagnosis of cerebral palsy has been an active research area with some very promising results using tools such as the General Movements Assessment (GMA). In our previous work, we explored the feasibility of extracting pose-based features from video sequences to automatically classify infant body movement into two categories, normal and abnormal. The classification was based upon the GMA, which was carried out on the video data by an independent expert reviewer. In this paper we extend our previous work by extracting the normalised pose-based feature sets, Histograms of Joint Orientation 2D (HOJO2D) and Histograms of Joint Displacement 2D (HOJD2D), for use in new deep learning architectures. We explore the viability of using these pose-based feature sets for automated classification within a deep learning framework by carrying out extensive experiments on five new deep learning architectures. Experimental results show that the proposed fully connected neural network FCNet performed robustly across different feature sets. Furthermore, the proposed convolutional neural network architectures demonstrated excellent performance in handling features in higher dimensionality. We make the code, extracted features and associated GMA labels publicly available

Progression Modeling of Cognitive Disease Using Temporal Data Mining: Research Landscape, Gaps and Solution Design

Dementia is a cognitive disorder whose diagnosis and progression monitoring is very difficult due to a very slow onset and progression. It is difficult to detect whether cognitive decline is due to ageing process or due to some form of dementia as MRI scans of the brain cannot reliably differentiate between ageing related volume loss and pathological changes. Laboratory tests on blood or CSF samples have also not proved very useful. Alzheimer�s disease (AD) is recognized as the most common cause of dementia. Development of sensitive and reliable tool for evaluation in terms of early diagnosis and progression monitoring of AD is required. Since there is an absence of specific markers for predicting AD progression, there is a need to learn more about specific attributes and their temporal relationships that lead to this disease and determine progression from mild cognitive impairment to full blown AD. Various stages of disease and transitions from one stage to the have be modelled based on longitudinal patient data. This paper provides a critical review of the methods to understand disease progression modelling and determine factors leading to progression of AD from initial to final stages. Then the design of a machine learning based solution is proposed to handle the gaps in current research

Short-segment heart sound classification using an ensemble of deep convolutional neural networks

This paper proposes a framework based on deep convolutional neural networks (CNNs) for automatic heart sound classification using short-segments of individual heart beats. We design a 1D-CNN that directly learns features from raw heart-sound signals, and a 2D-CNN that takes inputs of two- dimensional time-frequency feature maps based on Mel-frequency cepstral coefficients (MFCC). We further develop a time-frequency CNN ensemble (TF-ECNN) combining the 1D-CNN and 2D-CNN based on score-level fusion of the class probabilities. On the large PhysioNet CinC challenge 2016 database, the proposed CNN models outperformed traditional classifiers based on support vector machine and hidden Markov models with various hand-crafted time- and frequency-domain features. Best classification scores with 89.22% accuracy and 89.94% sensitivity were achieved by the ECNN, and 91.55% specificity and 88.82% modified accuracy by the 2D-CNN alone on the test set.Comment: 8 pages, 1 figure, conferenc