The role of earth observation in an integrated deprived area mapping “system” for low-to-middle income countries

Urbanization in the global South has been accompanied by the proliferation of vast informal and marginalized urban areas that lack access to essential services and infrastructure. UN-Habitat estimates that close to a billion people currently live in these deprived and informal urban settlements, generally grouped under the term of urban slums. Two major knowledge gaps undermine the efforts to monitor progress towards the corresponding sustainable development goal (i.e., SDG 11—Sustainable Cities and Communities). First, the data available for cities worldwide is patchy and insufficient to differentiate between the diversity of urban areas with respect to their access to essential services and their specific infrastructure needs. Second, existing approaches used to map deprived areas (i.e., aggregated household data, Earth observation (EO), and community-driven data collection) are mostly siloed, and, individually, they often lack transferability and scalability and fail to include the opinions of different interest groups. In particular, EO-based-deprived area mapping approaches are mostly top-down, with very little attention given to ground information and interaction with urban communities and stakeholders. Existing top-down methods should be complemented with bottom-up approaches to produce routinely updated, accurate, and timely deprived area maps. In this review, we first assess the strengths and limitations of existing deprived area mapping methods. We then propose an Integrated Deprived Area Mapping System (IDeAMapS) framework that leverages the strengths of EO- and community-based approaches. The proposed framework offers a way forward to map deprived areas globally, routinely, and with maximum accuracy to support SDG 11 monitoring and the needs of different interest groups

Automation Process for Morphometric Analysis of Volumetric CT Data from Pulmonary Vasculature in Rats

With advances in medical imaging scanners, it has become commonplace to generate large multidimensional datasets. These datasets require tools for a rapid, thorough analysis. To address this need, we have developed an automated algorithm for morphometric analysis incorporating A Visualization Workshop computational and image processing libraries for three-dimensional segmentation, vascular tree generation and structural hierarchical ordering with a two-stage numeric optimization procedure for estimating vessel diameters. We combine this new technique with our mathematical models of pulmonary vascular morphology to quantify structural and functional attributes of lung arterial trees. Our physiological studies require repeated measurements of vascular structure to determine differences in vessel biomechanical properties between animal models of pulmonary disease. Automation provides many advantages including significantly improved speed and minimized operator interaction and biasing. The results are validated by comparison with previously published rat pulmonary arterial micro-CT data analysis techniques, in which vessels were manually mapped and measured using intense operator intervention

Probabilistic Models of Motor Production

N. Bernstein defined the ability of the central neural system (CNS) to control many degrees of freedom of a physical body with all its redundancy and flexibility as the main problem in motor control. He pointed at that man-made mechanisms usually have one, sometimes two degrees of freedom (DOF); when the number of DOF increases further, it becomes prohibitively hard to control them. The brain, however, seems to perform such control effortlessly. He suggested the way the brain might deal with it: when a motor skill is being acquired, the brain artificially limits the degrees of freedoms, leaving only one or two. As the skill level increases, the brain gradually "frees" the previously fixed DOF, applying control when needed and in directions which have to be corrected, eventually arriving to the control scheme where all the DOF are "free". This approach of reducing the dimensionality of motor control remains relevant even today. One the possibles solutions of the Bernstetin's problem is the hypothesis of motor primitives (MPs) - small building blocks that constitute complex movements and facilitite motor learnirng and task completion. Just like in the visual system, having a homogenious hierarchical architecture built of similar computational elements may be beneficial. Studying such a complicated object as brain, it is important to define at which level of details one works and which questions one aims to answer. David Marr suggested three levels of analysis: 1. computational, analysing which problem the system solves; 2. algorithmic, questioning which representation the system uses and which computations it performs; 3. implementational, finding how such computations are performed by neurons in the brain. In this thesis we stay at the first two levels, seeking for the basic representation of motor output. In this work we present a new model of motor primitives that comprises multiple interacting latent dynamical systems, and give it a full Bayesian treatment. Modelling within the Bayesian framework, in my opinion, must become the new standard in hypothesis testing in neuroscience. Only the Bayesian framework gives us guarantees when dealing with the inevitable plethora of hidden variables and uncertainty. The special type of coupling of dynamical systems we proposed, based on the Product of Experts, has many natural interpretations in the Bayesian framework. If the dynamical systems run in parallel, it yields Bayesian cue integration. If they are organized hierarchically due to serial coupling, we get hierarchical priors over the dynamics. If one of the dynamical systems represents sensory state, we arrive to the sensory-motor primitives. The compact representation that follows from the variational treatment allows learning of a motor primitives library. Learned separately, combined motion can be represented as a matrix of coupling values. We performed a set of experiments to compare different models of motor primitives. In a series of 2-alternative forced choice (2AFC) experiments participants were discriminating natural and synthesised movements, thus running a graphics Turing test. When available, Bayesian model score predicted the naturalness of the perceived movements. For simple movements, like walking, Bayesian model comparison and psychophysics tests indicate that one dynamical system is sufficient to describe the data. For more complex movements, like walking and waving, motion can be better represented as a set of coupled dynamical systems. We also experimentally confirmed that Bayesian treatment of model learning on motion data is superior to the simple point estimate of latent parameters. Experiments with non-periodic movements show that they do not benefit from more complex latent dynamics, despite having high kinematic complexity. By having a fully Bayesian models, we could quantitatively disentangle the influence of motion dynamics and pose on the perception of naturalness. We confirmed that rich and correct dynamics is more important than the kinematic representation. There are numerous further directions of research. In the models we devised, for multiple parts, even though the latent dynamics was factorized on a set of interacting systems, the kinematic parts were completely independent. Thus, interaction between the kinematic parts could be mediated only by the latent dynamics interactions. A more flexible model would allow a dense interaction on the kinematic level too. Another important problem relates to the representation of time in Markov chains. Discrete time Markov chains form an approximation to continuous dynamics. As time step is assumed to be fixed, we face with the problem of time step selection. Time is also not a explicit parameter in Markov chains. This also prohibits explicit optimization of time as parameter and reasoning (inference) about it. For example, in optimal control boundary conditions are usually set at exact time points, which is not an ecological scenario, where time is usually a parameter of optimization. Making time an explicit parameter in dynamics may alleviate this

Topic supervised non-negative matrix factorization

Topic models have been extensively used to organize and interpret the contents of large, unstructured corpora of text documents. Although topic models often perform well on traditional training vs. test set evaluations, it is often the case that the results of a topic model do not align with human interpretation. This interpretability fallacy is largely due to the unsupervised nature of topic models, which prohibits any user guidance on the results of a model. In this paper, we introduce a semi-supervised method called topic supervised non-negative matrix factorization (TS-NMF) that enables the user to provide labeled example documents to promote the discovery of more meaningful semantic structure of a corpus. In this way, the results of TS-NMF better match the intuition and desired labeling of the user. The core of TS-NMF relies on solving a non-convex optimization problem for which we derive an iterative algorithm that is shown to be monotonic and convergent to a local optimum. We demonstrate the practical utility of TS-NMF on the Reuters and PubMed corpora, and find that TS-NMF is especially useful for conceptual or broad topics, where topic key terms are not well understood. Although identifying an optimal latent structure for the data is not a primary objective of the proposed approach, we find that TS-NMF achieves higher weighted Jaccard similarity scores than the contemporary methods, (unsupervised) NMF and latent Dirichlet allocation, at supervision rates as low as 10% to 20%

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Detection of atrial fibrillation episodes in long-term heart rhythm signals using a support vector machine

Atrial fibrillation (AF) is a serious heart arrhythmia leading to a significant increase of the risk for occurrence of ischemic stroke. Clinically, the AF episode is recognized in an electrocardiogram. However, detection of asymptomatic AF, which requires a long-term monitoring, is more efficient when based on irregularity of beat-to-beat intervals estimated by the heart rate (HR) features. Automated classification of heartbeats into AF and non-AF by means of the Lagrangian Support Vector Machine has been proposed. The classifier input vector consisted of sixteen features, including four coefficients very sensitive to beat-to-beat heart changes, taken from the fetal heart rate analysis in perinatal medicine. Effectiveness of the proposed classifier has been verified on the MIT-BIH Atrial Fibrillation Database. Designing of the LSVM classifier using very large number of feature vectors requires extreme computational efforts. Therefore, an original approach has been proposed to determine a training set of the smallest possible size that still would guarantee a high quality of AF detection. It enables to obtain satisfactory results using only 1.39% of all heartbeats as the training data. Post-processing stage based on aggregation of classified heartbeats into AF episodes has been applied to provide more reliable information on patient risk. Results obtained during the testing phase showed the sensitivity of 98.94%, positive predictive value of 98.39%, and classification accuracy of 98.86%.Web of Science203art. no. 76

Fast quantitative susceptibility mapping with L1-regularization and automatic parameter selection

Purpose To enable fast reconstruction of quantitative susceptibility maps with total variation penalty and automatic regularization parameter selection. Methods ℓ[subscript 1]-Regularized susceptibility mapping is accelerated by variable splitting, which allows closed-form evaluation of each iteration of the algorithm by soft thresholding and fast Fourier transforms. This fast algorithm also renders automatic regularization parameter estimation practical. A weighting mask derived from the magnitude signal can be incorporated to allow edge-aware regularization. Results Compared with the nonlinear conjugate gradient (CG) solver, the proposed method is 20 times faster. A complete pipeline including Laplacian phase unwrapping, background phase removal with SHARP filtering, and ℓ[subscript 1]-regularized dipole inversion at 0.6 mm isotropic resolution is completed in 1.2 min using MATLAB on a standard workstation compared with 22 min using the CG solver. This fast reconstruction allows estimation of regularization parameters with the L-curve method in 13 min, which would have taken 4 h with the CG algorithm. The proposed method also permits magnitude-weighted regularization, which prevents smoothing across edges identified on the magnitude signal. This more complicated optimization problem is solved 5 times faster than the nonlinear CG approach. Utility of the proposed method is also demonstrated in functional blood oxygen level–dependent susceptibility mapping, where processing of the massive time series dataset would otherwise be prohibitive with the CG solver. Conclusion Online reconstruction of regularized susceptibility maps may become feasible with the proposed dipole inversion

The Hierarchic treatment of marine ecological information from spatial networks of benthic platforms

Measuring biodiversity simultaneously in different locations, at different temporal scales, and over wide spatial scales is of strategic importance for the improvement of our understanding of the functioning of marine ecosystems and for the conservation of their biodiversity. Monitoring networks of cabled observatories, along with other docked autonomous systems (e.g., Remotely Operated Vehicles [ROVs], Autonomous Underwater Vehicles [AUVs], and crawlers), are being conceived and established at a spatial scale capable of tracking energy fluxes across benthic and pelagic compartments, as well as across geographic ecotones. At the same time, optoacoustic imaging is sustaining an unprecedented expansion in marine ecological monitoring, enabling the acquisition of new biological and environmental data at an appropriate spatiotemporal scale. At this stage, one of the main problems for an effective application of these technologies is the processing, storage, and treatment of the acquired complex ecological information. Here, we provide a conceptual overview on the technological developments in the multiparametric generation, storage, and automated hierarchic treatment of biological and environmental information required to capture the spatiotemporal complexity of a marine ecosystem. In doing so, we present a pipeline of ecological data acquisition and processing in different steps and prone to automation. We also give an example of population biomass, community richness and biodiversity data computation (as indicators for ecosystem functionality) with an Internet Operated Vehicle (a mobile crawler). Finally, we discuss the software requirements for that automated data processing at the level of cyber-infrastructures with sensor calibration and control, data banking, and ingestion into large data portals.Peer ReviewedPostprint (published version

Knowledge-based best of breed approach for automated detection of clinical events based on German free text digital hospital discharge letters

OBJECTIVES: The secondary use of medical data contained in electronic medical records, such as hospital discharge letters, is a valuable resource for the improvement of clinical care (e.g. in terms of medication safety) or for research purposes. However, the automated processing and analysis of medical free text still poses a huge challenge to available natural language processing (NLP) systems. The aim of this study was to implement a knowledge-based best of breed approach, combining a terminology server with integrated ontology, a NLP pipeline and a rules engine. METHODS: We tested the performance of this approach in a use case. The clinical event of interest was the particular drug-disease interaction "proton-pump inhibitor [PPI] use and osteoporosis". Cases were to be identified based on free text digital discharge letters as source of information. Automated detection was validated against a gold standard. RESULTS: Precision of recognition of osteoporosis was 94.19%, and recall was 97.45%. PPIs were detected with 100% precision and 97.97% recall. The F-score for the detection of the given drug-disease-interaction was 96,13%. CONCLUSION: We could show that our approach of combining a NLP pipeline, a terminology server, and a rules engine for the purpose of automated detection of clinical events such as drug-disease interactions from free text digital hospital discharge letters was effective. There is huge potential for the implementation in clinical and research contexts, as this approach enables analyses of very high numbers of medical free text documents within a short time period

Biomedical ontology alignment: An approach based on representation learning

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results