Manifold Learning in Medical Imaging

Manifold learning theory has seen a surge of interest in the modeling of large and extensive datasets in medical imaging since they capture the essence of data in a way that fundamentally outperforms linear methodologies, the purpose of which is to essentially describe things that are flat. This problematic is particularly relevant with medical imaging data, where linear techniques are frequently unsuitable for capturing variations in anatomical structures. In many cases, there is enough structure in the data (CT, MRI, ultrasound) so a lower dimensional object can describe the degrees of freedom, such as in a manifold structure. Still, complex, multivariate distributions tend to demonstrate highly variable structural topologies that are impossible to capture with a single manifold learning algorithm. This chapter will present recent techniques developed in manifold theory for medical imaging analysis, to allow for statistical organ shape modeling, image segmentation and registration from the concept of navigation of manifolds, classification, as well as disease prediction models based on discriminant manifolds. We will present the theoretical basis of these works, with illustrative results on their applications from various organs and pathologies, including neurodegenerative diseases and spinal deformities

Machine learning in orthopedics: a literature review

In this paper we present the findings of a systematic literature review covering the articles published in the last two decades in which the authors described the application of a machine learning technique and method to an orthopedic problem or purpose. By searching both in the Scopus and Medline databases, we retrieved, screened and analyzed the content of 70 journal articles, and coded these resources following an iterative method within a Grounded Theory approach. We report the survey findings by outlining the articles\u2019 content in terms of the main machine learning techniques mentioned therein, the orthopedic application domains, the source data and the quality of their predictive performance

Machine Learning in Orthopedics: A Literature Review

In this paper we present the findings of a systematic literature review covering the articles published in the last two decades in which the authors described the application of a machine learning technique and method to an orthopedic problem or purpose. By searching both in the Scopus and Medline databases, we retrieved, screened and analyzed the content of 70 journal articles, and coded these resources following an iterative method within a Grounded Theory approach. We report the survey findings by outlining the articles' content in terms of the main machine learning techniques mentioned therein, the orthopedic application domains, the source data and the quality of their predictive performance

Shape analysis for assessment of progression in spinal deformities

Adolescent idiopathic scoliosis (AIS) is a three-dimensional structural spinal deformation. It is the most common type of scoliosis. It can be visually detected as a lateral curvature in the postero-anterior plane. This condition starts in early puberty, affecting between 1-4% of the adolescent population between 10-18 years old, affecting in majority female. In severe cases (0.1% of population with AIS) the patient will require a surgical treatment. To date, the diagnosis of AIS relies on the quantification of the major curvature observed on posteroanterior and sagittal radiographs. Radiographs in standing position are the common imaging modality used in clinical settings to diagnose AIS. The assessment of the deformation is carried out using the Cobb angle method. This angle is calculated in the postero-anterior plane, and it is formed between a line drawn parallel to the superior endplate of the upper vertebra included in the scoliotic curve and a line drawn parallel to the inferior endplate of the lower vertebra of the same curve. Patients that present a Cobb angle of more than 10°, are diagnosed with AIS. The gold standard to classify curve deformations is the Lenke classification method. This paradigm is widely accepted in the clinical community. It divides spines with scoliosis into six types and provides treatment recommendations depending on the type. This method is limited to the analysis of the spine in the 2D space, since it relies on the observation of radiographs and Cobb angle measurements. On the one hand, when clinicians are treating patients with AIS, one of the main concerns is to determine whether the deformation will progress through time. Knowing beforehand of how the shape of the spine is going to evolve would aid to guide treatments strategies. On the other hand, however, patients at higher risks of progression require to be monitored more frequently, which results in constant exposure to radiation. Therefore, there is a need for an alternative radiation-free technology to reduce the use of radiographs and alleviate the perils of other health issues derived from current imaging modalities. This thesis presents a framework designed to characterize and model the variation of the shape of the spine throughout AIS. This framework includes three contributions: 1) two measurement techniques for computing 3D descriptors of the spine, and a classification method to categorize spine deformations, 2) a method to simulate the variation of the shape of the spine through time, and 3) a protocol to generate a 3D model of the spine from a volume reconstruction produced from ultrasound images. In our first contribution, we introduced two measurement techniques to characterize the shape of the spine in the 3D space, leave-n-out, and fan leave-n-out angles. In addition, a dynamic ensemble method was presented as an automated alternative to classify spinal deformations. Our measurement techniques were designed for computing the 3D descriptors and to be easy to use in a clinical setting. Also, the classification method contributes by assisting clinicians to identify patient-specific descriptors, which could help improving the classification in borderline curve deformations and, hence, suggests the proper management strategies. In order to observe how the shape of the spine progresses through time, in our second contribution, we designed a method to visualize the shape’s variation from the first visit up to 18 months, for every three months. Our method is trained with modes of variation, computed using independent component analysis from 3D model reconstructions of the spine of patients with AIS. Each of the modes of variation can be visualized for interpretation. This contribution could aid clinicians to identify which spine progression pattern might be prone to progression. Finally, our third contribution addresses the necessity of a radiation-free image modality for assessing and monitoring patients with AIS. We proposed a protocol to model a spine by identifying the spinous processes on a volume reconstruction. This reconstruction was computed from ultrasound images acquired from the external geometry of the subject. Our acquisition protocol documents a setup for image acquisition, as well as some recommendations to take into account depending on the body composition of the subjects to be scanned. We believe that this protocol could contribute to reduce the use of radiographs during the assessment and monitoring of patients with AIS

An expert system to diagnose spinal disorders

Objective: Until now, traditional invasive approaches have been the only means being leveraged to diagnose spinal disorders. Traditional manual diagnostics require a high workload, and diagnostic errors are likely to occur due to the prolonged work of physicians. In this research, we develop an expert system based on a hybrid inference algorithm and comprehensive integrated knowledge for assisting the experts in the fast and high-quality diagnosis of spinal disorders. Methods: First, for each spinal anomaly, the accurate and integrated knowledge was acquired from related experts and resources. Second, based on probability distributions and dependencies between symptoms of each anomaly, a unique numerical value known as certainty effect value was assigned to each symptom. Third, a new hybrid inference algorithm was designed to obtain excellent performance, which was an incorporation of the Backward Chaining Inference and Theory of Uncertainty. Results: The proposed expert system was evaluated in two different phases, real-world samples, and medical records evaluation. Evaluations show that in terms of real-world samples analysis, the system achieved excellent accuracy. Application of the system on the sample with anomalies revealed the degree of severity of disorders and the risk of development of abnormalities in unhealthy and healthy patients. In the case of medical records analysis, our expert system proved to have promising performance, which was very close to those of experts. Conclusion: Evaluations suggest that the proposed expert system provides promising performance, helping specialists to validate the accuracy and integrity of their diagnosis. It can also serve as an intelligent educational software for medical students to gain familiarity with spinal disorder diagnosis process, and related symptoms

Quantifying Palaeopathology Using Geometric Morphometrics

Palaeopathology is the study of disease and injury in archaeological bone. Traditional methods rely heavily on macroscopic description which can have a high degree of subjectivity and error, as well as limiting the types of research questions possible. Geometric morphometrics are a suite of shape analysis techniques and provide an opportunity to investigate possible relationships between skeletal morphological variation and disease. This thesis aims to demonstrate the potential of applying these methods in palaeopathological research and the results illustrate the benefits of using quantifiable and objective shape analysis methods in palaeopathology. The first half of the thesis discusses the use of geometric morphometrics to investigate skeletal variation to identify possible aetiological factors in the development of Schmorl's nodes and osteoarthritis. There was a strong association found between vertebral morphology and Schmorl's nodes in the lower spine. These findings have great implications for both bioarchaeological interpretation and clinical understanding of the aetiology and pathogenesis of Schmorl's nodes. Joint morphology of the proximal ulna and distal humerus was found to have no identifiable relationship with osteoarthritis, indicating that joint morphology is not a predisposing factor in elbow osteoarthritis, nor does osteoarthritis deform the joints in a systematic manner. A tentative relationship between eburnation and knee joint morphology was identified, although these results need to be verified with future research. If the association can be supported, shape analyses may provide a way for clinicians to monitor the progression of the disease. Geometric morphometrics were also shown to objectively record pathological shape deformation resulting from leprosy and residual rickets. The ability to objectively describe lesions with quantified data will greatly strengthen palaeopathology by decreasing the subjectivity and error inherent in macroscopic based methods. This thesis represents promising groundwork for the incorporation of geometric morphometrics into palaeopathological research

Gait recognition from multiple view-points

A la finalización de la tesis, la principal conclusión que se extrae es que la forma de andar permite identificar a las personas con una buena precisión (superior al 90 por ciento y llegando al 99 por ciento en determinados casos). Centrándonos en los diferentes enfoques desarrollados, el método basado en características extraídas a mano está especialmente indicado para bases de datos pequeñas en cuanto a número de muestras, ya que obtiene una buena precisión necesitando pocos datos de entrenamiento. Por otro lado, la aproximación basada en deep learning permite obtener buenos resultados para bases de datos grandes con la ventaja de que el tamaño de entrada puede ser muy pequeño, permitiendo una ejecución muy rápida. El enfoque incremental está especialmente indicado para entornos en los que se requieran añadir nuevos sujetos al sistema sin tener que entrenar el método de nuevo debido a los altos costes de tiempo y energía. Por último, el estudio de consumo nos ha permitido definir una serie de recomendaciones para poder minimizar el consumo de energía durante el entrenamiento de las redes profundas sin penalizar la precisión de las mismas. Fecha de lectura de Tesis Doctoral: 14 de diciembre 2018.Arquitectura de Computadores Resumen tesis: La identificación automática de personas está ganando mucha importancia en los últimos años ya que se puede aplicar en entornos que deben ser seguros (aeropuertos, centrales nucleares, etc) para agilizar todos los procesos de acceso. La mayoría de soluciones desarrolladas para este problema se basan en un amplio abanico de características físicas de los sujetos, como pueden ser el iris, la huella dactilar o la cara. Sin embargo, este tipo de técnicas tienen una serie de limitaciones ya que requieren la colaboración por parte del sujeto a identificar o bien son muy sensibles a cambios en la apariencia. Sin embargo, el reconocimiento del paso es una forma no invasiva de implementar estos controles de seguridad y, adicionalmente, no necesita la colaboración del sujeto. Además, es robusto frente a cambios en la apariencia del individuo ya que se centra en el movimiento. El objetivo principal de esta tesis es desarrollar un nuevo método para la identificación de personas a partir de la forma de caminar en entornos de múltiples vistas. Como entrada usamos el flujo óptico que proporciona una información muy rica sobre el movimiento del sujeto mientras camina. Para cumplir este objetivo, se han desarrollado dos técnicas diferentes: una basada en un enfoque tradicional de visión por computador donde se extraen manualmente características que definen al sujeto y, una segunda aproximación basada en aprendizaje profundo (deep learning) donde el propio método extrae sus características y las clasifica automáticamente. Además, para este último enfoque, se ha desarrollado una implementación basada en aprendizaje incremental para añadir nuevas clases sin entrenar el modelo desde cero y, un estudio energético para optimizar el consumo de energía durante el entrenamiento

An automatic wearable multi-sensor based gait analysis system for older adults.

Gait abnormalities in older adults are very common in clinical practice. They lead to serious adverse consequences such as falls and injury resulting in increased care cost. There is therefore a national imperative to address this challenge. Currently gait assessment is done using standardized clinical tools dependent on subjective evaluation. More objective gold standard methods (motion capture systems such as Qualisys and Vicon) to analyse gait rely on access to expensive complex equipment based in gait laboratories. These are not widely available for several reasons including a scarcity of equipment, need for technical staff, need for patients to attend in person, complicated time consuming procedures and overall expense. To broaden the use of accurate quantitative gait monitoring and assessment, the major goal of this thesis is to develop an affordable automatic gait analysis system that will provide comprehensive gait information and allow use in clinic or at home. It will also be able to quantify and visualize gait parameters, identify gait variables and changes, monitor abnormal gait patterns of older people in order to reduce the potential for falling and support falls risk management. A research program based on conducting experiments on volunteers is developed in collaboration with other researchers in Bournemouth University, The Royal Bournemouth Hospital and care homes. This thesis consists of five different studies toward addressing our major goal. Firstly, a study on the effects on sensor output from an Inertial Measurement Unit (IMU) attached to different anatomical foot locations. Placing an IMU over the bony prominence of the first cuboid bone is the best place as it delivers the most accurate data. Secondly, an automatic gait feature extraction method for analysing spatiotemporal gait features which shows that it is possible to extract gait features automatically outside of a gait laboratory. Thirdly, user friendly and easy to interpret visualization approaches are proposed to demonstrate real time spatiotemporal gait information. Four proposed approaches have the potential of helping professionals detect and interpret gait asymmetry. Fourthly, a validation study of spatiotemporal IMU extracted features compared with gold standard Motion Capture System and Treadmill measurements in young and older adults is conducted. The results obtained from three experimental conditions demonstrate that our IMU gait extracted features are highly valid for spatiotemporal gait variables in young and older adults. In the last study, an evaluation system using Procrustes and Euclidean distance matrix analysis is proposed to provide a comprehensive interpretation of shape and form differences between individual gaits. The results show that older gaits are distinguishable from young gaits. A pictorial and numerical system is proposed which indicates whether the assessed gait is normal or abnormal depending on their total feature values. This offers several advantages: 1) it is user friendly and is easy to set up and implement; 2) it does not require complex equipment with segmentation of body parts; 3) it is relatively inexpensive and therefore increases its affordability decreasing health inequality; and 4) its versatility increases its usability at home supporting inclusivity of patients who are home bound. A digital transformation strategy framework is proposed where stakeholders such as patients, health care professionals and industry partners can collaborate through development of new technologies, value creation, structural change, affordability and sustainability to improve the diagnosis and treatment of gait abnormalities