Nuclei/Cell Detection in Microscopic Skeletal Muscle Fiber Images and Histopathological Brain Tumor Images Using Sparse Optimizations

Nuclei/Cell detection is usually a prerequisite procedure in many computer-aided biomedical image analysis tasks. In this thesis we propose two automatic nuclei/cell detection frameworks. One is for nuclei detection in skeletal muscle fiber images and the other is for brain tumor histopathological images. For skeletal muscle fiber images, the major challenges include: i) shape and size variations of the nuclei, ii) overlapping nuclear clumps, and iii) a series of z-stack images with out-of-focus regions. We propose a novel automatic detection algorithm consisting of the following components: 1) The original z-stack images are first converted into one all-in-focus image. 2) A sufficient number of hypothetical ellipses are then generated for each nuclei contour. 3) Next, a set of representative training samples and discriminative features are selected by a two-stage sparse model. 4) A classifier is trained using the refined training data. 5) Final nuclei detection is obtained by mean-shift clustering based on inner distance. The proposed method was tested on a set of images containing over 1500 nuclei. The results outperform the current state-of-the-art approaches. For brain tumor histopathological images, the major challenges are to handle significant variations in cell appearance and to split touching cells. The proposed novel automatic cell detection consists of: 1) Sparse reconstruction for splitting touching cells. 2) Adaptive dictionary learning for handling cell appearance variations. The proposed method was extensively tested on a data set with over 2000 cells. The result outperforms other state-of-the-art algorithms with F1 score = 0.96

Mutual information measures applied to EEG signals for sleepiness characterization

Excessive daytime sleepiness (EDS) is one of the main symptoms of several sleep related disorders with a great impact on the patient lives. While many studies have been carried out in order to assess daytime sleepiness, the automatic EDS detection still remains an open problem. In this work, a novel approach to this issue based on non-linear dynamical analysis of EEG signal was proposed. Multichannel EEG signals were recorded during five maintenance of wakefulness (MWT) and multiple sleep latency (MSLT) tests alternated throughout the day from patients suffering from sleep disordered breathing. A group of 20 patients with excessive daytime sleepiness (EDS) was compared with a group of 20 patients without daytime sleepiness (WDS), by analyzing 60-s EEG windows in waking state. Measures obtained from cross-mutual information function (CMIF) and auto-mutual-information function (AMIF) were calculated in the EEG. These functions permitted a quantification of the complexity properties of the EEG signal and the non-linear couplings between different zones of the scalp. Statistical differences between EDS and WDS groups were found in ß band during MSLT events (. p-value<0.0001). WDS group presented more complexity than EDS in the occipital zone, while a stronger nonlinear coupling between occipital and frontal zones was detected in EDS patients than in WDS. The AMIF and CMIF measures yielded sensitivity and specificity above 80% and AUC of ROC above 0.85 in classifying EDS and WDS patients.Peer ReviewedPostprint (author's final draft

Investigating the feasibility of vehicle telemetry data as a means of predicting driver workload

Driving is a safety critical task that requires a high level of attention and workload from the driver. Despite this, people often also perform secondary tasks such as eating or using a mobile phone, which increase workload levels and divert cognitive and physical attention from the primary task of driving. If a vehicle is aware that the driver is currently under high workload, the vehicle functionality can be changed in order to minimize any further demand. Traditionally, workload measurements have been performed using intrusive means such as physiological sensors. Another approach may be to use vehicle telemetry data as a performance measure for workload. In this paper, we present the Warwick-JLR Driver Monitoring Dataset (DMD) and analyse it to investigate the feasibility of using vehicle telemetry data for determining the driver workload. We perform a statistical analysis of subjective ratings, physiological data, and vehicle telemetry data collected during a track study. A data mining methodology is then presented to build predictive models using this data, for the driver workload monitoring problem

Monitoring data streams

Stream monitoring is concerned with analyzing data that is represented in the form of infinite streams. This field has gained prominence in recent years, as streaming data is generated in increasing volume and dimension in a variety of areas. It finds application in connection with monitoring industrial sensors, "smart" technology like smart houses and smart cars, wearable devices used for medical and physiological monitoring, but also in environmental surveillance or finance. However, stream monitoring is a challenging task due to the diverse and changing nature of the streaming data, its high volume and high dimensionality with thousands of sensors producing streams with millions of measurements over short time spans. Automated, scalable and efficient analysis of these streams can help to keep track of important events, highlight relevant aspects and provide better insights into the monitored system. In this thesis, we propose techniques adapted to these tasks in supervised and unsupervised settings, in particular Stream Classification and Stream Dependency Monitoring. After a motivating introduction, we introduce concepts related to streaming data and discuss technological frameworks that have emerged to deal with streaming data in the second chapter of this thesis. We introduce the notion of information theoretical entropy as a useful basis for data monitoring in the third chapter. In the second part of the thesis, we present Probabilistic Hoeffding Trees, a novel approach towards stream classification. We will show how probabilistic learning greatly improves the flexibility of decision trees and their ability to adapt to changes in data streams. The general technique is applicable to a variety of classification models and fast to compute without significantly greater memory cost compared to regular Hoeffding Trees. We show that our technique achieves better or on-par results to current state-of-the-art tree classification models on a variety of large, synthetic and real life data sets. In the third part of the thesis, we concentrate on unsupervised monitoring of data streams. We will use mutual information as entropic measure to identify the most important relationships in a monitored system. By using the powerful concept of mutual information we can, first, capture relevant aspects in a great variety of data sources with different underlying concepts and possible relationships and, second, analyze theoretical and computational complexity. We present the MID and DIMID algorithms. They perform extremely efficient on high dimensional data streams and provide accurate results, outperforming state-of-the-art algorithms for dependency monitoring. In the fourth part of this thesis, we introduce delayed relationships as a further feature in the dependency analysis. In reality, the phenomena monitored by e.g. some type of sensor might depend on another, but measurable effects can be delayed. This delay might be due to technical reasons, i.e. different stream processing speeds, or because the effects actually appear delayed over time. We present Loglag, the first algorithm that monitors dependency with respect to an optimal delay. It utilizes several approximation techniques to achieve competitive resource requirements. We demonstrate its scalability and accuracy on real world data, and also give theoretical guarantees to its accuracy

Monitoring data streams

Stream monitoring is concerned with analyzing data that is represented in the form of infinite streams. This field has gained prominence in recent years, as streaming data is generated in increasing volume and dimension in a variety of areas. It finds application in connection with monitoring industrial sensors, "smart" technology like smart houses and smart cars, wearable devices used for medical and physiological monitoring, but also in environmental surveillance or finance. However, stream monitoring is a challenging task due to the diverse and changing nature of the streaming data, its high volume and high dimensionality with thousands of sensors producing streams with millions of measurements over short time spans. Automated, scalable and efficient analysis of these streams can help to keep track of important events, highlight relevant aspects and provide better insights into the monitored system. In this thesis, we propose techniques adapted to these tasks in supervised and unsupervised settings, in particular Stream Classification and Stream Dependency Monitoring. After a motivating introduction, we introduce concepts related to streaming data and discuss technological frameworks that have emerged to deal with streaming data in the second chapter of this thesis. We introduce the notion of information theoretical entropy as a useful basis for data monitoring in the third chapter. In the second part of the thesis, we present Probabilistic Hoeffding Trees, a novel approach towards stream classification. We will show how probabilistic learning greatly improves the flexibility of decision trees and their ability to adapt to changes in data streams. The general technique is applicable to a variety of classification models and fast to compute without significantly greater memory cost compared to regular Hoeffding Trees. We show that our technique achieves better or on-par results to current state-of-the-art tree classification models on a variety of large, synthetic and real life data sets. In the third part of the thesis, we concentrate on unsupervised monitoring of data streams. We will use mutual information as entropic measure to identify the most important relationships in a monitored system. By using the powerful concept of mutual information we can, first, capture relevant aspects in a great variety of data sources with different underlying concepts and possible relationships and, second, analyze theoretical and computational complexity. We present the MID and DIMID algorithms. They perform extremely efficient on high dimensional data streams and provide accurate results, outperforming state-of-the-art algorithms for dependency monitoring. In the fourth part of this thesis, we introduce delayed relationships as a further feature in the dependency analysis. In reality, the phenomena monitored by e.g. some type of sensor might depend on another, but measurable effects can be delayed. This delay might be due to technical reasons, i.e. different stream processing speeds, or because the effects actually appear delayed over time. We present Loglag, the first algorithm that monitors dependency with respect to an optimal delay. It utilizes several approximation techniques to achieve competitive resource requirements. We demonstrate its scalability and accuracy on real world data, and also give theoretical guarantees to its accuracy

Topological Data Analyses of Time Series Using Witness Complexes

Real-time regime shift detection between chaotic dynamical systems via time series analysis demands quick and correct, theoretically guaranteed methods. Often the best implemented techniques in the field are well-motivated heuristics and even interpretable statistics are scarce. Topological data analysis can contribute to the canon of traditional methods for analyzing nonlinear time series but is not computationally cheap. We introduce a topological membership test for sliding windows of time series data that uses a sparse simplicial complex - the witness complex - to model the data and assess its performance across a range of model parameters affecting computational efficiency. We then explore how the topology of witness complexes changes across this range of model parameters. We next define a simplicial complex whose construction incorporates the temporal information available with time series data. We experimentally show that this construction results in filtrations with fewer simplices and improved topological signature. We apply our techniques to synthetic time series data including numerical solutions of classical low dimensional chaotic systems Lorenz and Rössler systems of ODEs as well as regimes of the higher dimensional Brunel neuronal network model and experimental live voltage recordings of musical instruments