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Effective Learning of Probabilistic Models for Clinical Predictions from Longitudinal Data

arXiv.org Machine Learning

Such information includes: the database in modern hospital systems, usually known as Electronic Health Records (EHR), which store the patients' diagnosis, medication, laboratory test results, medical image data, etc.; information on various health behaviors tracked and stored by wearable devices, ubiquitous sensors and mobile applications, such as the smoking status, alcoholism history, exercise level, sleeping conditions, etc.; information collected by census or various surveys regarding sociodemographic factors of the target cohort; and information on people's mental health inferred from their social media activities or social networks such as Twitter, Facebook, etc. These health-related data come from heterogeneous sources, describe assorted aspects of the individual's health conditions. Such data is rich in structure and information which has great research potentials for revealing unknown medical knowledge about genomic epidemiology, disease developments and correlations, drug discoveries, medical diagnosis, mental illness prevention, health behavior adaption, etc. In real-world problems, the number of features relating to a certain health condition could grow exponentially with the development of new information techniques for collecting and measuring data. To reveal the causal influence between various factors and a certain disease or to discover the correlations among diseases from data at such a tremendous scale, requires the assistance of advanced information technology such as data mining, machine learning, text mining, etc. Machine learning technology not only provides a way for learning qualitative relationships among features and patients, but also the quantitative parameters regarding the strength of such correlations.


Towards automated symptoms assessment in mental health

arXiv.org Machine Learning

Activity and motion analysis has the potential to be used as a diagnostic tool for mental disorders. However, to-date, little work has been performed in turning stratification measures of activity into useful symptom markers. The research presented in this thesis has focused on the identification of objective activity and behaviour metrics that could be useful for the analysis of mental health symptoms in the above mentioned dimensions. Particular attention is given to the analysis of objective differences between disorders, as well as identification of clinical episodes of mania and depression in bipolar patients, and deterioration in borderline personality disorder patients. A principled framework is proposed for mHealth monitoring of psychiatric patients, based on measurable changes in behaviour, represented in physical activity time series, collected via mobile and wearable devices. The framework defines methods for direct computational analysis of symptoms in disorganisation and psychomotor dimensions, as well as measures for indirect assessment of mood, using patterns of physical activity, sleep and circadian rhythms. The approach of computational behaviour analysis, proposed in this thesis, has the potential for early identification of clinical deterioration in ambulatory patients, and allows for the specification of distinct and measurable behavioural phenotypes, thus enabling better understanding and treatment of mental disorders.


Deep Bayesian Gaussian Processes for Uncertainty Estimation in Electronic Health Records

arXiv.org Machine Learning

One major impediment to the wider use of deep learning for clinical decision making is the difficulty of assigning a level of confidence to model predictions. Currently, deep Bayesian neural networks and sparse Gaussian processes are the main two scalable uncertainty estimation methods. However, deep Bayesian neural network suffers from lack of expressiveness, and more expressive models such as deep kernel learning, which is an extension of sparse Gaussian process, captures only the uncertainty from the higher level latent space. Therefore, the deep learning model under it lacks interpretability and ignores uncertainty from the raw data. In this paper, we merge features of the deep Bayesian learning framework with deep kernel learning to leverage the strengths of both methods for more comprehensive uncertainty estimation. Through a series of experiments on predicting the first incidence of heart failure, diabetes and depression applied to large-scale electronic medical records, we demonstrate that our method is better at capturing uncertainty than both Gaussian processes and deep Bayesian neural networks in terms of indicating data insufficiency and distinguishing true positive and false positive predictions, with a comparable generalisation performance. Furthermore, by assessing the accuracy and area under the receiver operating characteristic curve over the predictive probability, we show that our method is less susceptible to making overconfident predictions, especially for the minority class in imbalanced datasets. Finally, we demonstrate how uncertainty information derived by the model can inform risk factor analysis towards model interpretability.


Automated Pain Detection from Facial Expressions using FACS: A Review

arXiv.org Machine Learning

Facial pain expression is an important modality for assessing pain, especially when the patient's verbal ability to communicate is impaired. The facial muscle-based action units (AUs), which are defined by the Facial Action Coding System (FACS), have been widely studied and are highly reliable as a method for detecting facial expressions (FE) including valid detection of pain. Unfortunately, FACS coding by humans is a very time-consuming task that makes its clinical use prohibitive. Significant progress on automated facial expression recognition (AFER) has led to its numerous successful applications in FACS-based affective computing problems. However, only a handful of studies have been reported on automated pain detection (APD), and its application in clinical settings is still far from a reality. In this paper, we review the progress in research that has contributed to automated pain detection, with focus on 1) the framework-level similarity between spontaneous AFER and APD problems; 2) the evolution of system design including the recent development of deep learning methods; 3) the strategies and considerations in developing a FACS-based pain detection framework from existing research; and 4) introduction of the most relevant databases that are available for AFER and APD studies. We attempt to present key considerations in extending a general AFER framework to an APD framework in clinical settings. In addition, the performance metrics are also highlighted in evaluating an AFER or an APD system.


AutoCogniSys: IoT Assisted Context-Aware Automatic Cognitive Health Assessment

arXiv.org Artificial Intelligence

Cognitive impairment has become epidemic in older adult population. The recent advent of tiny wearable and ambient devices, a.k.a Internet of Things (IoT) provides ample platforms for continuous functional and cognitive health assessment of older adults. In this paper, we design, implement and evaluate AutoCogniSys, a context-aware automated cognitive health assessment system, combining the sensing powers of wearable physiological (Electrodermal Activity, Photoplethysmography) and physical (Accelerometer, Object) sensors in conjunction with ambient sensors. We design appropriate signal processing and machine learning techniques, and develop an automatic cognitive health assessment system in a natural older adults living environment. We validate our approaches using two datasets: (i) a naturalistic sensor data streams related to Activities of Daily Living and mental arousal of 22 older adults recruited in a retirement community center, individually living in their own apartments using a customized inexpensive IoT system (IRB #HP-00064387) and (ii) a publicly available dataset for emotion detection. The performance of AutoCogniSys attests max. 93\% of accuracy in assessing cognitive health of older adults.