Construction of embedded fMRI resting-state functional connectivity networks using manifold learning

We construct embedded functional connectivity networks (FCN) from benchmark resting-state functional magnetic resonance imaging (rsfMRI) data acquired from patients with schizophrenia and healthy controls based on linear and nonlinear manifold learning algorithms, namely, Multidimensional Scaling, Isometric Feature Mapping, Diffusion Maps, Locally Linear Embedding and kernel PCA. Furthermore, based on key global graph-theoretic properties of the embedded FCN, we compare their classification potential using machine learning. We also assess the performance of two metrics that are widely used for the construction of FCN from fMRI, namely the Euclidean distance and the cross correlation metric. We show that diffusion maps with the cross correlation metric outperform the other combinations

ISOMAP and machine learning algorithms for the construction of embedded functional connectivity networks of anatomically separated brain regions fromresting state fMRI data of patients with Schizophrenia

We construct Functional Connectivity Networks (FCN) from resting state fMRI (rsfMRI) recordings towards the classification of brain activity between healthy and schizophrenic subjects using a publicly available dataset (the COBRE dataset) of 145 subjects (74 healthy controls and 71 schizophrenic subjects). First, we match the anatomy of the brain of each individual to the Desikan- Killiany brain atlas. Then, we use the conventional approach of correlating the parcellated time series to construct FCN and ISOMAP, a nonlinear manifold learning algorithm to produce low-dimensional embeddings of the correlation matrices. For the classification analysis, we computed five key local graph-theoretic measures of the FCN and used the LASSO and Random Forest (RF) algorithms for feature selection. For the classification we used standard linear Support Vector Machines. The classification performance is tested by a double cross-validation scheme [consisting of an outer and an inner loop of “Leave one out” cross-validation (LOOCV)]. The standard cross-correlation methodology produced a classification rate of 73.1%, while ISOMAP resulted in 79.3%, thus providing a simpler model with a smaller number of features as chosen from LASSO and RF, namely the participation coefficient of the right thalamus and the strength of the right lingual gyrus

Numerical Bifurcation Analysis of PDEs From Lattice Boltzmann Model Simulations: a Parsimonious Machine Learning Approach

We address a three-tier data-driven approach for the numerical solution of the inverse problem in Partial Differential Equations (PDEs) and for their numerical bifurcation analysis from spatio-temporal data produced by Lattice Boltzmann model simulations using machine learning. In the first step, we exploit manifold learning and in particular parsimonious Diffusion Maps using leave-one-out cross-validation (LOOCV) to both identify the intrinsic dimension of the manifold where the emergent dynamics evolve and for feature selection over the parameter space. In the second step, based on the selected features, we learn the right-hand-side of the effective PDEs using two machine learning schemes, namely shallow Feedforward Neural Networks (FNNs) with two hidden layers and single-layer Random Projection Networks (RPNNs), which basis functions are constructed using an appropriate random sampling approach. Finally, based on the learned black-box PDE model, we construct the corresponding bifurcation diagram, thus exploiting the numerical bifurcation analysis toolkit. For our illustrations, we implemented the proposed method to perform numerical bifurcation analysis of the 1D FitzHugh-Nagumo PDEs from data generated by D1Q3 Lattice Boltzmann simulations. The proposed method was quite effective in terms of numerical accuracy regarding the construction of the coarse-scale bifurcation diagram. Furthermore, the proposed RPNN scheme was ∼ 20 to 30 times less costly regarding the training phase than the traditional shallow FNNs, thus arising as a promising alternative to deep learning for the data-driven numerical solution of the inverse problem for high-dimensional PDEs

Diffusion with random distribution of static traps

The random walk problem is studied in two and three dimensions in the presence of a random distribution of static traps. An efficient Monte Carlo method, based on a mapping onto a polymer model, is used to measure the survival probability P(c,t) as a function of the trap concentration c and the time t. Theoretical arguments are presented, based on earlier work of Donsker and Varadhan and of Rosenstock, why in two dimensions one expects a data collapse if -ln[P(c,t)]/ln(t) is plotted as a function of (lambda t)^{1/2}/ln(t) (with lambda=-ln(1-c)), whereas in three dimensions one expects a data collapse if -t^{-1/3}ln[P(c,t)] is plotted as a function of t^{2/3}lambda. These arguments are supported by the Monte Carlo results. Both data collapses show a clear crossover from the early-time Rosenstock behavior to Donsker-Varadhan behavior at long times.Comment: 4 pages, 6 figure

Formative research to design an implementation strategy for a postpartum hemorrhage initial response treatment bundle (E-MOTIVE): study protocol

BACKGROUND: Postpartum hemorrhage (PPH) is the leading cause of maternal death worldwide. When PPH occurs, early identification of bleeding and prompt management using evidence-based guidelines, can avert most PPH-related severe morbidities and deaths. However, adherence to the World Health Organization recommended practices remains a critical challenge. A potential solution to inefficient and inconsistent implementation of evidence-based practices is the application of a ‘clinical care bundle’ for PPH management. A clinical care bundle is a set of discrete, evidence-based interventions, administered concurrently, or in rapid succession, to every eligible person, along with teamwork, communication, and cooperation. Once triggered, all bundle components must be delivered. The E-MOTIVE project aims to improve the detection and first response management of PPH through the implementation of the “E-MOTIVE” bundle, which consists of (1) Early PPH detection using a calibrated drape, (2) uterine Massage, (3) Oxytocic drugs, (4) Tranexamic acid, (5) Intra Venous fluids, and (6) genital tract Examination and escalation when necessary. The objective of this paper is to describe the protocol for the formative phase of the E-MOTIVE project, which aims to design an implementation strategy to support the uptake of this bundle into practice. METHODS: We will use behavior change and implementation science frameworks [e.g. capability, opportunity, motivation and behavior (COM-B) and theoretical domains framework (TDF)] to guide data collection and analysis, in Kenya, Nigeria, South Africa, Sri Lanka, and Tanzania. There are four methodological components: qualitative interviews; surveys; systematic reviews; and design workshops. We will triangulate findings across data sources, participant groups, and countries to explore factors influencing current PPH detection and management, and potentially influencing E-MOTIVE bundle implementation. We will use these findings to develop potential strategies to improve implementation, which will be discussed and agreed with key stakeholders from each country in intervention design workshops. DISCUSSION: This formative protocol outlines our strategy for the systematic development of the E-MOTIVE implementation strategy. This focus on implementation considers what it would take to support roll-out and implementation of the E-MOTIVE bundle. Our approach therefore aims to maximize internal validity in the trial alongside future scalability, and implementation of the E-MOTIVE bundle in routine practice, if proven to be effective. TRIAL REGISTRATION: ClinicalTrials.gov: NCT0434166

The role of dimensionality in neuronal network dynamics

The research leading to these results has received funding from the European Union’s Seventh Framework Programme under grant agreement FP7 ICT 2011 – 284553 (Acronym: Si-CODE), the NEUROSCAFFOLDS Project n. 604263, the National Natural Science Foundation of China (Grant number: 51361130033) and the Ministry of Science and Technology of China (973 Grant number: 2014CB965003)

Ensemble approach for generalized network dismantling

Finding a set of nodes in a network, whose removal fragments the network below some target size at minimal cost is called network dismantling problem and it belongs to the NP-hard computational class. In this paper, we explore the (generalized) network dismantling problem by exploring the spectral approximation with the variant of the power-iteration method. In particular, we explore the network dismantling solution landscape by creating the ensemble of possible solutions from different initial conditions and a different number of iterations of the spectral approximation.Comment: 11 Pages, 4 Figures, 4 Table

External validation, update and development of prediction models for pre-eclampsia using an Individual Participant Data (IPD) meta-analysis: the International Prediction of Pregnancy Complication Network (IPPIC pre-eclampsia) protocol.

Background: Pre-eclampsia, a condition with raised blood pressure and proteinuria is associated with an increased risk of maternal and offspring mortality and morbidity. Early identification of mothers at risk is needed to target management. Methods/design: We aim to systematically review the existing literature to identify prediction models for pre-eclampsia. We have established the International Prediction of Pregnancy Complication Network (IPPIC), made up of 72 researchers from 21 countries who have carried out relevant primary studies or have access to existing registry databases, and collectively possess data from more than two million patients. We will use the individual participant data (IPD) from these studies to externally validate these existing prediction models and summarise model performance across studies using random-effects meta-analysis for any, late (after 34 weeks) and early (before 34 weeks) onset pre-eclampsia. If none of the models perform well, we will recalibrate (update), or develop and validate new prediction models using the IPD. We will assess the differential accuracy of the models in various settings and subgroups according to the risk status. We will also validate or develop prediction models based on clinical characteristics only; clinical and biochemical markers; clinical and ultrasound parameters; and clinical, biochemical and ultrasound tests. Discussion: Numerous systematic reviews with aggregate data meta-analysis have evaluated various risk factors separately or in combination for predicting pre-eclampsia, but these are affected by many limitations. Our large-scale collaborative IPD approach encourages consensus towards well developed, and validated prognostic models, rather than a number of competing non-validated ones. The large sample size from our IPD will also allow development and validation of multivariable prediction model for the relatively rare outcome of early onset pre-eclampsia. Trial registration: The project was registered on Prospero on the 27 November 2015 with ID: CRD42015029349

Organization of Excitable Dynamics in Hierarchical Biological Networks

This study investigates the contributions of network topology features to the dynamic behavior of hierarchically organized excitable networks. Representatives of different types of hierarchical networks as well as two biological neural networks are explored with a three-state model of node activation for systematically varying levels of random background network stimulation. The results demonstrate that two principal topological aspects of hierarchical networks, node centrality and network modularity, correlate with the network activity patterns at different levels of spontaneous network activation. The approach also shows that the dynamic behavior of the cerebral cortical systems network in the cat is dominated by the network's modular organization, while the activation behavior of the cellular neuronal network of Caenorhabditis elegans is strongly influenced by hub nodes. These findings indicate the interaction of multiple topological features and dynamic states in the function of complex biological networks