Joint co-clustering: co-clustering of genomic and clinical bioimaging data

AbstractFor better understanding the genetic mechanisms underlying clinical observations, and better defining a group of potential candidates for protein-family-inhibiting therapy, it is interesting to determine the correlations between genomic, clinical data and data coming from high resolution and fluorescent microscopy. We introduce a computational method, called joint co-clustering, that can find co-clusters or groups of genes, bioimaging parameters and clinical traits that are believed to be closely related to each other based on the given empirical information. As bioimaging parameters, we quantify the expression of growth factor receptor EGFR/erb-B family in non-small cell lung carcinoma (NSCLC) through a fully-automated computer-aided analysis approach. This immunohistochemical analysis is usually performed by pathologists via visual inspection of tissue samples images. Our fully-automated techniques streamlines this error-prone and time-consuming process, thereby facilitating analysis and diagnosis. Experimental results for several real-life datasets demonstrate the high quantitative precision of our approach. The joint co-clustering method was tested with the receptor EGFR/erb-B family data on non-small cell lung carcinoma (NSCLC) tissue and identified statistically significant co-clusters of genes, receptor protein expression and clinical traits. The validation of our results with the literature suggest that the proposed method can provide biologically meaningful co-clusters of genes and traits and that it is a very promising approach to analyse large-scale biological data and to study multi-factorial genetic pathologies through their genetic alterations

Comparison of Deep Learning and the Classical Machine Learning Algorithm for the Malware Detection

Recently, Deep Learning has been showing promising results in various Artificial Intelligence applications like image recognition, natural language processing, language modeling, neural machine translation, etc. Although, in general, it is computationally more expensive as compared to classical machine learning techniques, their results are found to be more effective in some cases. Therefore, in this paper, we investigated and compared one of the Deep Learning Architecture called Deep Neural Network (DNN) with the classical Random Forest (RF) machine learning algorithm for the malware classification. We studied the performance of the classical RF and DNN with 2, 4 & 7 layers architectures with the four different feature sets, and found that irrespective of the features inputs, the classical RF accuracy outperforms the DNN.Comment: 11 Pages, 1 figur

Topology polymorphism graph for lung tumor segmentation in PET-CT images

Accurate lung tumor segmentation is problematic when the tumor boundary or edge, which reflects the advancing edge of the tumor, is difficult to discern on chest CT or PET. We propose a ‘topo-poly’ graph model to improve identification of the tumor extent. Our model incorporates an intensity graph and a topology graph. The intensity graph provides the joint PET-CT foreground similarity to differentiate the tumor from surrounding tissues. The topology graph is defined on the basis of contour tree to reflect the inclusion and exclusion relationship of regions. By taking into account different topology relations, the edges in our model exhibit topological polymorphism. These polymorphic edges in turn affect the energy cost when crossing different topology regions under a random walk framework, and hence contribute to appropriate tumor delineation. We validated our method on 40 patients with non-small cell lung cancer where the tumors were manually delineated by a clinical expert. The studies were separated into an ‘isolated’ group (n = 20) where the lung tumor was located in the lung parenchyma and away from associated structures / tissues in the thorax and a ‘complex’ group (n = 20) where the tumor abutted / involved a variety of adjacent structures and had heterogeneous FDG uptake. The methods were validated using Dice’s similarity coefficient (DSC) to measure the spatial volume overlap and Hausdorff distance (HD) to compare shape similarity calculated as the maximum surface distance between the segmentation results and the manual delineations. Our method achieved an average DSC of 0.881  ±  0.046 and HD of 5.311  ±  3.022 mm for the isolated cases and DSC of 0.870  ±  0.038 and HD of 9.370  ±  3.169 mm for the complex cases. Student’s t-test showed that our model outperformed the other methods (p-values <0.05)

Recognizing overlapped particles during a crystallization process from in situ video images for measuring their size distributions

International audienceThis paper presents a method to recognize polygonal-shaped particles (i.e. rectangles, regular/irregular prisms) among agglomerated crystals from in-situ images during a crystallization process. The aim is to measure the particle size distributions (PSD); a key measurement needed for monitoring and controlling industrial crystallization operations . The method is first based on detecting the geometric features of the particles identified by their salient corners. A clustering technique is then applied by grouping three correspondent salient corners belonging to the same polygon. The efficiency of the method is tested on particles of Ammonium Oxalate (AO) monitored during batch crystallization in pure water. Particle size distributions are calculated, and a quantitative comparison between automatic and manual sizing is performed

Attribute Equilibrium Dominance Reduction Accelerator (DCCAEDR) Based on Distributed Coevolutionary Cloud and Its Application in Medical Records

© 2013 IEEE. Aimed at the tremendous challenge of attribute reduction for big data mining and knowledge discovery, we propose a new attribute equilibrium dominance reduction accelerator (DCCAEDR) based on the distributed coevolutionary cloud model. First, the framework of N-populations distributed coevolutionary MapReduce model is designed to divide the entire population into N subpopulations, sharing the reward of different subpopulations' solutions under a MapReduce cloud mechanism. Because the adaptive balancing between exploration and exploitation can be achieved in a better way, the reduction performance is guaranteed to be the same as those using the whole independent data set. Second, a novel Nash equilibrium dominance strategy of elitists under the N bounded rationality regions is adopted to assist the subpopulations necessary to attain the stable status of Nash equilibrium dominance. This further enhances the accelerator's robustness against complex noise on big data. Third, the approximation parallelism mechanism based on MapReduce is constructed to implement rule reduction by accelerating the computation of attribute equivalence classes. Consequently, the entire attribute reduction set with the equilibrium dominance solution can be achieved. Extensive simulation results have been used to illustrate the effectiveness and robustness of the proposed DCCAEDR accelerator for attribute reduction on big data. Furthermore, the DCCAEDR is applied to solve attribute reduction for traditional Chinese medical records and to segment cortical surfaces of the neonatal brain 3-D-MRI records, and the DCCAEDR shows the superior competitive results, when compared with the representative algorithms

Manipulation of Polymorphic Objects Using Two Robotic Arms through CNN Networks

This article presents an interaction system for two 5 DOF (Degrees of Freedom) manipulators with 3-finger grippers, which will be used to grab and displace up to 10 polymorphic objects shaped as pentominoes, inside a VRML (Virtual Reality Modeling Language) environment, by performing element detection and classification using an R-CNN (Region Proposal Convolutional Neural Network), and point detection and gripping orientation using a DAG-CNN (Directed Acyclic Graph-Convolutional Neural Network). It was analyzed the feasibility or not of a grasp is determined depending on how the geometry of an element fits the free space between the gripper fingers. A database was created to be used as training data with each of the grasp positions for the polyshapes, so the network training can be focused on finding the desired grasp positions, enabling any other grasp found to be considered a feasible grasp, and eliminating the need to find additional better grasp points, changing the shape, inclination and angle of rotation. Under varying test conditions, the test successfully achieved gripping of each object with one manipulator and passing it to the second manipulator as part of the grouping process, in the opposite end of the work area, using an R-CNN and a DAG-CNN, with an accuracy of 95.5% and 98.8%, respectively, and performing a geometric analysis of the objects to determine the displacement and rotation required by the gripper for each individual grip

Detection of retinal hemorrhages in the presence of blood vessels

Segmentation of hemorrhages helps in improving the efficiency of computer assisted image analysis of diseases like diabetic retinopathy and hypertensive retinopathy. Hemorrhages are blood leakages lying in close proximity to blood vessels, which makes their delineation from blood vessels challenging. We use multiresolution morphological processing with a view of achieving perceptual grouping of the hemorrhagic candidates occurring in variable shapes, sizes and textures. We propose a novel method of suppression of candidates lying on blood vessels while attaining a good segmentation of true hemorrhages including the ones attached to the vessels. Evaluated on 191 images having different degrees of pathological severity, our method achieved > 82% sensitivity at < 7 false positives per image (FPPI). We further observe that the sensitivity is higher for candidates with bigger sizes

Combined nanometric and phylogenetic analysis of unique endocytic compartments in Giardia lamblia sheds light on the evolution of endocytosis in Metamonada

BACKGROUND: Giardia lamblia, a parasitic protist of the Metamonada supergroup, has evolved one of the most diverged endocytic compartment systems investigated so far. Peripheral endocytic compartments, currently known as peripheral vesicles or vacuoles (PVs), perform bulk uptake of fluid phase material which is then digested and sorted either to the cell cytosol or back to the extracellular space. RESULTS: Here, we present a quantitative morphological characterization of these organelles using volumetric electron microscopy and super-resolution microscopy (SRM). We defined a morphological classification for the heterogenous population of PVs and performed a comparative analysis of PVs and endosome-like organelles in representatives of phylogenetically related taxa, Spironucleus spp. and Tritrichomonas foetus. To investigate the as-yet insufficiently understood connection between PVs and clathrin assemblies in G. lamblia, we further performed an in-depth search for two key elements of the endocytic machinery, clathrin heavy chain (CHC) and clathrin light chain (CLC), across different lineages in Metamonada. Our data point to the loss of a bona fide CLC in the last Fornicata common ancestor (LFCA) with the emergence of a protein analogous to CLC (GlACLC) in the Giardia genus. Finally, the location of clathrin in the various compartments was quantified. CONCLUSIONS: Taken together, this provides the first comprehensive nanometric view of Giardia's endocytic system architecture and sheds light on the evolution of GlACLC analogues in the Fornicata supergroup and, specific to Giardia, as a possible adaptation to the formation and maintenance of stable clathrin assemblies at PVs

A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER USING SNP ARRAYS

Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that permits the detection of segmental changes in DNA copy number that span thousands of basepairs across the genome. Genome-wide association studies (GWAS) may simultaneously screen for copy number-phenotype and SNP-phenotype associations as part of the analytic strategy. However, genome-wide array analyses are particularly susceptible to batch effects as the logistics of preparing DNA and processing thousands of arrays often involves multiple laboratories and technicians, or changes over calendar time to the reagents and laboratory equipment. Failure to adjust for batch effects can lead to incorrect inference and requires inefficient post-hoc quality control procedures that exclude regions that are associated with batch. Our work extends previous model-based approaches for copy number estimation by explicitly modeling batch effects and using shrinkage to improve locus-specific estimates of copy number uncertainty. Key features of this approach include the use of diallelic genotype calls from experimental data to estimate batch- and locus-specific parameters of background and signal without the requirement of training data. We illustrate these ideas using a study of bipolar disease and a study of chromosome 21 trisomy. The former has batch effects that dominate much of the observed variation in quantile-normalized intensities, while the latter illustrates the robustness of our approach to datasets where as many as 25% of the samples have altered copy number. Locus-specific estimates of copy number can be plotted on the copy-number scale to investigate mosaicism and guide the choice of appropriate downstream approaches for smoothing the copy number as a function of physical position. The software is open source and implemented in the R package CRLMM available at Bioconductor (http:www.bioconductor.org)