An automated bedside measure for monitoring neonatal cortical activity: a supervised deep learning-based electroencephalogram classifier with external cohort validation

Peer reviewe

Periodic pattern mining from spatio-temporal trajectory data

Rapid development in GPS tracking techniques produces a large number of spatio-temporal trajectory data. The analysis of these data provides us with a new opportunity to discover useful behavioural patterns. Spatio-temporal periodic pattern mining is employed to find temporal regularities for interesting places. Mining periodic patterns from spatio-temporal trajectories can reveal useful, important and valuable information about people's regular and recurrent movements and behaviours. Previous studies have been proposed to extract people's regular and repeating movement behavior from spatio-temporal trajectories. These previous approaches can target three following issues, (1) long individual trajectory; (2) spatial fuzziness; and (3) temporal fuzziness. First, periodic pattern mining is different to other pattern mining, such as association rule ming and sequential pattern mining, periodic pattern mining requires a very long trajectory from an individual so that the regular period can be extracted from this long single trajectory, for example, one month or one year period. Second, spatial fuzziness shows although a moving object can regularly move along the similar route, it is impossible for it to appear at the exactly same location. For instance, Bob goes to work everyday, and although he can follow a similar path from home to his workplace, the same location cannot be repeated across different days. Third, temporal fuzziness shows that periodicity is complicated including partial time span and multiple interleaving periods. In reality, the period is partial, it is highly impossible to occur through the whole movement of the object. Alternatively, the moving object has only a few periods, such as a daily period for work, or yearly period for holidays. However, it is insufficient to find effective periodic patterns considering these three issues only. This thesis aims to develop a new framework to extract more effective, understandable and meaningful periodic patterns by taking more features of spatio-temporal trajectories into account. The first feature is trajectory sequence, GPS trajectory data is temporally ordered sequences of geolocation which can be represented as consecutive trajectory segments, where each entry in each trajectory segment is closely related to the previous sampled point (trajectory node) and the latter one, rather than being isolated. Existing approaches disregard the important sequential nature of trajectory. Furthermore, they introduce both unwanted false positive reference spots and false negative reference spots. The second feature is spatial and temporal aspects. GPS trajectory data can be presented as triple data (x; y; t), x and y represent longitude and latitude respectively whilst t shows corresponding time in this location. Obviously, spatial and temporal aspects are two key factors. Existing methods do not consider these two aspects together in periodic pattern mining. Irregular time interval is the third feature of spatio-temporal trajectory. In reality, due to weather conditions, device malfunctions, or battery issues, the trajectory data are not always regularly sampled. Existing algorithms cannot deal with this issue but instead require a computationally expensive trajectory interpolation process, or it is assumed that trajectory is with regular time interval. The fourth feature is hierarchy of space. Hierarchy is an inherent property of spatial data that can be expressed in different levels, such as a country includes many states, a shopping mall is comprised of many shops. Hierarchy of space can find more hidden and valuable periodic patterns. Existing studies do not consider this inherent property of trajectory. Hidden background semantic information is the final feature. Aspatial semantic information is one of important features in spatio-temporal data, and it is embedded into the trajectory data. If the background semantic information is considered, more meaningful, understandable and useful periodic patterns can be extracted. However, existing methods do not consider the geographical information underlying trajectories. In addition, at times we are interested in finding periodic patterns among trajectory paths rather than trajectory nodes for different applications. This means periodic patterns should be identified and detected against trajectory paths rather than trajectory nodes for some applications. Existing approaches for periodic pattern mining focus on trajectories nodes rather than paths. To sum up, the aim of this thesis is to investigate solutions to these problems in periodic pattern mining in order to extract more meaningful, understandable periodic patterns. Each of three chapters addresses a different problem and then proposes adequate solutions to problems currently not addressed in existing studies. Finally, this thesis proposes a new framework to address all problems. First, we investigated a path-based solution which can target trajectory sequence and spatio-temporal aspects. We proposed an algorithm called Traclus (spatio-temporal) which can take spatial and temporal aspects into account at the same time instead of only considering spatial aspect. The result indicated our method produced more effective periodic patterns based on trajectory paths than existing node-based methods using two real-world trajectories. In order to consider hierarchy of space, we investigated existing hierarchical clustering approaches to obtain hierarchical reference spots (trajectory paths) for periodic pattern mining. HDBSCAN is an incremental version of DBSCAN which is able to handle clusters with different densities to generate a hierarchical clustering result using the single-linkage method, and then it automatically extracts clusters from a hierarchical tree. Thus, we modified traditional clustering method DBSCAN in Traclus (spatio-temporal) to HDBSCAN for extraction of hierarchical reference spots. The result is convincing, and reveals more periodic patterns than those of existing methods. Second, we introduced a stop/move method to annotate each spatio-temporal entry with a semantic label, such as restaurant, university and hospital. This method can enrich a trajectory with background semantic information so that we can easily infer people's repeating behaviors. In addition, existing methods use interpolation to make trajectory regular and then apply Fourier transform and autocorrelation to automatically detect period for each reference spot. An increasing number of trajectory nodes leads to an exponential increase of running time. Thus, we employed Lomb-Scargle periodogram to detect period for each reference spot based on raw trajectory without requiring any interpolation method. The results showed our method outperformed existing approaches on effectiveness and efficiency based on two real datasets. For hierarchical aspect, we extended previous work to find hierarchical semantic periodic patterns by applying HDBSCAN. The results were promising. Third, we apply our methodology to a case study, which reveals many interesting medical periodic patterns. These patterns can effectively explore human movement behaviors for positive medical outcomes. To sum up, this research proposed a new framework to gradually target the problems that existing methods cannot handle. These include: how to consider trajectory sequence, how to consider spatial temporal aspects together, how to deal with trajectory with irregular time interval, how to consider hierarchy of space and how to extract semantic information behind trajectory. After addressing all these problems, the experimental results demonstrate that our method can find more understandable, meaningful and effective periodic patterns than existing approaches

HealthXAI: Collaborative and explainable AI for supporting early diagnosis of cognitive decline

Our aging society claims for innovative tools to early detect symptoms of cognitive decline. Several research efforts are being made to exploit sensorized smart-homes and artificial intelligence (AI) methods to detect a decline of the cognitive functions of the elderly in order to promptly alert practitioners. Even though those tools may provide accurate predictions, they currently provide limited support to clinicians in making a diagnosis. Indeed, most AI systems do not provide any explanation of the reason why a given prediction was computed. Other systems are based on a set of rules that are easy to interpret by a human. However, those rule-based systems can cope with a limited number of abnormal situations, and are not flexible enough to adapt to different users and contextual situations. In this paper, we tackle this challenging problem by proposing a flexible AI system to recognize early symptoms of cognitive decline in smart-homes, which is able to explain the reason of predictions at a fine-grained level. Our method relies on well known clinical indicators that consider subtle and overt behavioral anomalies, as well as spatial disorientation and wandering behaviors. In order to adapt to different individuals and situations, anomalies are recognized using a collaborative approach. We experimented our approach with a large set of real world subjects, including people with MCI and people with dementia. We also implemented a dashboard to allow clinicians to inspect anomalies together with the explanations of predictions. Results show that our system's predictions are significantly correlated to the person's actual diagnosis. Moreover, a preliminary user study with clinicians suggests that the explanation capabilities of our system are useful to improve the task performance and to increase trust. To the best of our knowledge, this is the first work that explores data-driven explainable AI for supporting the diagnosis of cognitive decline

The 2019 Mathematical Oncology Roadmap.

Whether the nom de guerre is Mathematical Oncology, Computational or Systems Biology, Theoretical Biology, Evolutionary Oncology, Bioinformatics, or simply Basic Science, there is no denying that mathematics continues to play an increasingly prominent role in cancer research. Mathematical Oncology-defined here simply as the use of mathematics in cancer research-complements and overlaps with a number of other fields that rely on mathematics as a core methodology. As a result, Mathematical Oncology has a broad scope, ranging from theoretical studies to clinical trials designed with mathematical models. This Roadmap differentiates Mathematical Oncology from related fields and demonstrates specific areas of focus within this unique field of research. The dominant theme of this Roadmap is the personalization of medicine through mathematics, modelling, and simulation. This is achieved through the use of patient-specific clinical data to: develop individualized screening strategies to detect cancer earlier; make predictions of response to therapy; design adaptive, patient-specific treatment plans to overcome therapy resistance; and establish domain-specific standards to share model predictions and to make models and simulations reproducible. The cover art for this Roadmap was chosen as an apt metaphor for the beautiful, strange, and evolving relationship between Two Beasts: mathematics and cancer.NIH (R01CA16437, R01NS060752, U54CA210180, U54CA143970, U54193489, U01CA220378)James S. McDonnell FoundationBen & Catherine Ivy Foundatio

Methods and Applications for Summarising Free-Text Narratives in Electronic Health Records

As medical services move towards electronic health record (EHR) systems the breadth and depth of data stored at each patient encounter has increased. This growing wealth of data and investment in care systems has arguably put greater strain on services, as those at the forefront are pushed towards greater time spent in front of computers over their patients. To minimise the use of EHR systems clinicians often revert to using free-text data entry to circumvent the structured input fields. It has been estimated that approximately 80% of EHR data is within the free-text portion. Outside of their primary use, that is facilitating the direct care of the patient, secondary use of EHR data includes clinical research, clinical audits, service improvement research, population health analysis, disease and patient phenotyping, clinical trial recruitment to name but a few.This thesis presents a number of projects, previously published and original work in the development, assessment and application of summarisation methods for EHR free-text. Firstly, I introduce, define and motivate EHR free-text analysis and summarisation methods of open-domain text and how this compares to EHR free-text. I then introduce a subproblem in natural language processing (NLP) that is the recognition of named entities and linking of the entities to pre-existing clinical knowledge bases (NER+L). This leads to the first novel contribution the Medical Concept Annotation Toolkit (MedCAT) that provides a software library workflow for clinical NER+L problems. I frame the outputs of MedCAT as a form of summarisation by showing the tools contributing to published clinical research and the application of this to another clinical summarisation use-case ‘clinical coding’. I then consider methods for the textual summarisation of portions of clinical free-text. I show how redundancy in clinical text is empirically different to open-domain text discussing how this impacts text-to-text summarisation. I then compare methods to generate discharge summary sections from previous clinical notes using methods presented in prior chapters via a novel ‘guidance’ approach.I close the thesis by discussing my contributions in the context of state-of-the-art and how my work fits into the wider body of clinical NLP research. I briefly describe the challenges encountered throughout, offer my perspectives on the key enablers of clinical informatics research, and finally the potential future work that will go towards translating research impact to real-world benefits to healthcare systems, workers and patients alike