Using Artificial Neural Network to Predict a Variety of Pathogenic Microorganisms

In this study, an electronic nose is used to record breathing data from healthy patients and pneumonia patients. The electronic nose records resistance data using a micro-array of 11 sensors. The recorded data is fed to Artificial Neural Network (ANN) which is used to train a model for detection of infections. The ANN has performed accurate classification which can be further developed to an online efficient pneumonia detection system. Initially, five patients’ data are used to build up the ANN model. Then, another two patients’ data are used to test the accuracy of the model. The results show that the model predicts the same outcome that is diagnosed by Taipei Medical University Hospital where samples have to be cultured to identify whether patients have pneumonia or not. In this preliminary study, ANN has achieved good results which can be further developed to an online efficient pneumonia detection system in the near future.Taiwan Carbon Nanotube Technology Corporatio

Intermittent blood pressure prediction via multiscale entropy and ensemble artificial neural networks

This study evaluates the correlation between the intermittent blood pressure (BP) and the photoplethysmography (PPG). This study of a total of twenty-five cases is started by the partitioning of the PPG signal into a 5-minute segment. The segmented PPG is filtered by ensemble empirical mode decomposition (EEMD). The feature extraction method, multiscale entropy (MSE) is utilized for the purified signal to achieve some information. The seventy-five scale of MSE is taken into the input of the artificial neural network (ANN) modeling. The output of this system are the intermittent diastolic and systolic blood pressure. Originally, a thousand models areis created. The best model is chosen for the best single ANN model. In advanced, the ensemble artificial neural network (EANN) model is initiated to observe the testing data. The result, compared to the best single ANN model, shows that the EANN model recognizes better the testing data by producing lower mean absolute error (MAE)

Deep Gaussian processes for multiple instance learning: Application to CT intracranial hemorrhage detection

Background and objective: Intracranial hemorrhage (ICH) is a life-threatening emergency that can lead to brain damage or death, with high rates of mortality and morbidity. The fast and accurate detection of ICH is important for the patient to get an early and efficient treatment. To improve this diagnostic process, the application of Deep Learning (DL) models on head CT scans is an active area of research. Although promising results have been obtained, many of the proposed models require slice-level annotations by radiologists, which are costly and time-consuming. Methods: We formulate the ICH detection as a problem of Multiple Instance Learning (MIL) that allows training with only scan-level annotations. We develop a new probabilistic method based on Deep Gaussian Processes (DGP) that is able to train with this MIL setting and accurately predict ICH at both slice- and scan-level. The proposed DGPMIL model is able to capture complex feature relations by using multiple Gaussian Process (GP) layers, as we show experimentally. Results: To highlight the advantages of DGPMIL in a general MIL setting, we first conduct several controlled experiments on the MNIST dataset. We show that multiple GP layers outperform one-layer GP models, especially for complex feature distributions. For ICH detection experiments, we use two public brain CT datasets (RSNA and CQ500). We first train a Convolutional Neural Network (CNN) with an attention mechanism to extract the image features, which are fed into our DGPMIL model to perform the final predictions. The results show that DGPMIL model outperforms VGPMIL as well as the attention-based CNN for MIL and other state-of-the-art methods for this problem. The best performing DGPMIL model reaches an AUC-ROC of 0.957 (resp. 0.909) and an AUC-PR of 0.961 (resp. 0.889) on the RSNA (resp. CQ500) dataset. Conclusion: The competitive performance at slice- and scan-level shows that DGPMIL model provides an accurate diagnosis on slices without the need for slice-level annotations by radiologists during training. As MIL is a common problem setting, our model can be applied to a broader range of other tasks, especially in medical image classification, where it can help the diagnostic process.Project P20_00286 funded by FEDER/Junta de Andalucía-Consejería de Transformación Económica, Industria, Conocimiento y Universidadesthe European Union’s Horizon 2020 research and innovation programme under the Marie Skodowska Curie grant agreement No 860627 (CLARIFY Project).Funding for open access charge: Universidad de Granada / CBUA

Machine Learning Approaches for Automated Glaucoma Detection using Clinical Data and Optical Coherence Tomography Images

Glaucoma is a multi-factorial, progressive blinding optic-neuropathy. A variety of factors, including genetics, vasculature, anatomy, and immune factors, are involved. Worldwide more than 80 million people are affected by glaucoma, and around 300,000 in Australia, where 50% remain undiagnosed. Untreated glaucoma can lead to blindness. Early detection by Artificial intelligence (AI) is crucial to accelerate the diagnosis process and can prevent further vision loss. Many proposed AI systems have shown promising performance for automated glaucoma detection using two-dimensional (2D) data. However, only a few studies had optimistic outcomes for glaucoma detection and staging. Moreover, the automated AI system still faces challenges in diagnosing at the clinicians’ level due to the lack of interpretability of the ML algorithms and integration of multiple clinical data. AI technology would be welcomed by doctors and patients if the "black box" notion is overcome by developing an explainable, transparent AI system with similar pathological markers used by clinicians as the sign of early detection and progression of glaucomatous damage. Therefore, the thesis aimed to develop a comprehensive AI model to detect and stage glaucoma by incorporating a variety of clinical data and utilising advanced data analysis and machine learning (ML) techniques. The research first focuses on optimising glaucoma diagnostic features by combining structural, functional, demographic, risk factor, and optical coherence tomography (OCT) features. The significant features were evaluated using statistical analysis and trained in ML algorithms to observe the detection performance. Three crucial structural ONH OCT features: cross-sectional 2D radial B-scan, 3D vascular angiography and temporal-superior-nasal-inferior-temporal (TSNIT) B-scan, were analysed and trained in explainable deep learning (DL) models for automated glaucoma prediction. The explanation behind the decision making of DL models were successfully demonstrated using the feature visualisation. The structural features or distinguished affected regions of TSNIT OCT scans were precisely localised for glaucoma patients. This is consistent with the concept of explainable DL, which refers to the idea of making the decision-making processes of DL models transparent and interpretable to humans. However, artifacts and speckle noise often result in misinterpretation of the TSNIT OCT scans. This research also developed an automated DL model to remove the artifacts and noise from the OCT scans, facilitating error-free retinal layers segmentation, accurate tissue thickness estimation and image interpretation. Moreover, to monitor and grade glaucoma severity, the visual field (VF) test is commonly followed by clinicians for treatment and management. Therefore, this research uses the functional features extracted from VF images to train ML algorithms for staging glaucoma from early to advanced/severe stages. Finally, the selected significant features were used to design and develop a comprehensive AI model to detect and grade glaucoma stages based on the data quantity and availability. In the first stage, a DL model was trained with TSNIT OCT scans, and its output was combined with significant structural and functional features and trained in ML models. The best-performed ML model achieved an area under the curve (AUC): 0.98, an accuracy of 97.2%, a sensitivity of 97.9%, and a specificity of 96.4% for detecting glaucoma. The model achieved an overall accuracy of 90.7% and an F1 score of 84.0% for classifying normal, early, moderate, and advanced-stage glaucoma. In conclusion, this thesis developed and proposed a comprehensive, evidence-based AI model that will solve the screening problem for large populations and relieve experts from manually analysing a slew of patient data and associated misinterpretation problems. Moreover, this thesis demonstrated three structural OCT features that could be added as excellent diagnostic markers for precise glaucoma diagnosis

An efficient CNN-BiLSTM model for multi-class intracranial hemorrhage classification

Intracranial hemorrhage (ICH) refers to a type of bleeding that occurs within the skull. ICH may be caused by a wide range of pathology, including, trauma, hypertension, cerebral amyloid angiopa- thy, and cerebral aneurysms. Different subtypes of ICH exist based on their location in the brain, including epidural hemorrhage (EDH), subdural hemorrhage (SDH), subarachnoid hemorrhage (SAH), intraventricular hemorrhage (IVH), and intraparenchymal hemorrhage (IPH). Prompt de- tection and management of ICH are crucial as it is a life-threatening medical emergency with high morbidity and mortality rates. Despite accounting for only 10-15% of all strokes, ICH is respon- sible for over 50% of stroke-related deaths. Therefore, the presence, type, and location of an ICH must be immediately diagnosed so that the patients can receive medical intervention. However, accurately identifying ICH in CT slices can be challenging due to the brain’s complex anatomy and the variability in hemorrhage appearance. [...

An Application of Data Analytics to Outcomes of Missouri Motor Vehicle Crashes

Motor vehicle crashes are a leading cause of death in the United States, cost Americans $277 billion annually, and generate serious psychological burdens. As a result, extensive vehicle safety research focusing on the explanatory factors of crash severity is undertaken using a wide array of methodological techniques including traditional statistical models and contemporary data mining approaches. This study advances the methodological frontier of crash severity research by completing an empirical investigation that compares the performance of popular, longstanding techniques of multinomial logit and ordinal probit models with more recent methods of decision tree and artificial neural network models. To further the investigation of the benefits of data analytics, individual models are combined into model ensembles using three popular combinatory techniques. The models are estimated using 2002 to 2012 crash data from the Missouri State Highway Patrol Traffic Division - Statewide Traffic Accident Records System database, and variables examined include various driver characteristics, temporal factors, weather conditions, road characteristics, crash type, crash location, and injury severity levels. The accuracy and discriminatory power of explaining crash severity outcomes among all methods are compared using classification tables, lift charts, ROC curves, and AUC values. The CHAID decision tree model is found to have the greatest accuracy and discriminatory power relative to all evaluated modeling approaches. The modeling reveals that the presence of alcohol, driving at speeds that exceed the limit, failing to yield, driving on the wrong side of the road, violating a stop sign or signal, and driving while physically impaired lead to a large number of fatalities each year. Yet, the effect of these factors on the probability of a severe outcome is dependent upon other variables, including number of occupants involved in the crash, speed limit, lighting condition, and age of the driver. The CHAID decision tree is used in conjunction with prior literature and the current Missouri rules of the road to provide better formulated driving policies. This study concludes that policy makers should consider the interaction of conditions and driver related contributing factors when crafting future legislation or proposing modifications in driving statues

Towards Interpretable Machine Learning in Medical Image Analysis

Over the past few years, ML has demonstrated human expert level performance in many medical image analysis tasks. However, due to the black-box nature of classic deep ML models, translating these models from the bench to the bedside to support the corresponding stakeholders in the desired tasks brings substantial challenges. One solution is interpretable ML, which attempts to reveal the working mechanisms of complex models. From a human-centered design perspective, interpretability is not a property of the ML model but an affordance, i.e., a relationship between algorithm and user. Thus, prototyping and user evaluations are critical to attaining solutions that afford interpretability. Following human-centered design principles in highly specialized and high stakes domains, such as medical image analysis, is challenging due to the limited access to end users. This dilemma is further exacerbated by the high knowledge imbalance between ML designers and end users. To overcome the predicament, we first define 4 levels of clinical evidence that can be used to justify the interpretability to design ML models. We state that designing ML models with 2 levels of clinical evidence: 1) commonly used clinical evidence, such as clinical guidelines, and 2) iteratively developed clinical evidence with end users are more likely to design models that are indeed interpretable to end users. In this dissertation, we first address how to design interpretable ML in medical image analysis that affords interpretability with these two different levels of clinical evidence. We further highly recommend formative user research as the first step of the interpretable model design to understand user needs and domain requirements. We also indicate the importance of empirical user evaluation to support transparent ML design choices to facilitate the adoption of human-centered design principles. All these aspects in this dissertation increase the likelihood that the algorithms afford interpretability and enable stakeholders to capitalize on the benefits of interpretable ML. In detail, we first propose neural symbolic reasoning to implement public clinical evidence into the designed models for various routinely performed clinical tasks. We utilize the routinely applied clinical taxonomy for abnormality classification in chest x-rays. We also establish a spleen injury grading system by strictly following the clinical guidelines for symbolic reasoning with the detected and segmented salient clinical features. Then, we propose the entire interpretable pipeline for UM prognostication with cytopathology images. We first perform formative user research and found that pathologists believe cell composition is informative for UM prognostication. Thus, we build a model to analyze cell composition directly. Finally, we conduct a comprehensive user study to assess the human factors of human-machine teaming with the designed model, e.g., whether the proposed model indeed affords interpretability to pathologists. The human-centered design process is proven to be truly interpretable to pathologists for UM prognostication. All in all, this dissertation introduces a comprehensive human-centered design for interpretable ML solutions in medical image analysis that affords interpretability to end users

Machine Learning for Biomedical Application

Biomedicine is a multidisciplinary branch of medical science that consists of many scientific disciplines, e.g., biology, biotechnology, bioinformatics, and genetics; moreover, it covers various medical specialties. In recent years, this field of science has developed rapidly. This means that a large amount of data has been generated, due to (among other reasons) the processing, analysis, and recognition of a wide range of biomedical signals and images obtained through increasingly advanced medical imaging devices. The analysis of these data requires the use of advanced IT methods, which include those related to the use of artificial intelligence, and in particular machine learning. It is a summary of the Special Issue “Machine Learning for Biomedical Application”, briefly outlining selected applications of machine learning in the processing, analysis, and recognition of biomedical data, mostly regarding biosignals and medical images