An Annotated Corpus for Machine Reading of Instructions in Wet Lab Protocols

We describe an effort to annotate a corpus of natural language instructions consisting of 622 wet lab protocols to facilitate automatic or semi-automatic conversion of protocols into a machine-readable format and benefit biological research. Experimental results demonstrate the utility of our corpus for developing machine learning approaches to shallow semantic parsing of instructional texts. We make our annotated Wet Lab Protocol Corpus available to the research community

iGPSe: A Visual Analytic System for Integrative Genomic Based Cancer Patient Stratification

Background: Cancers are highly heterogeneous with different subtypes. These subtypes often possess different genetic variants, present different pathological phenotypes, and most importantly, show various clinical outcomes such as varied prognosis and response to treatment and likelihood for recurrence and metastasis. Recently, integrative genomics (or panomics) approaches are often adopted with the goal of combining multiple types of omics data to identify integrative biomarkers for stratification of patients into groups with different clinical outcomes. Results: In this paper we present a visual analytic system called Interactive Genomics Patient Stratification explorer (iGPSe) which significantly reduces the computing burden for biomedical researchers in the process of exploring complicated integrative genomics data. Our system integrates unsupervised clustering with graph and parallel sets visualization and allows direct comparison of clinical outcomes via survival analysis. Using a breast cancer dataset obtained from the The Cancer Genome Atlas (TCGA) project, we are able to quickly explore different combinations of gene expression (mRNA) and microRNA features and identify potential combined markers for survival prediction. Conclusions: Visualization plays an important role in the process of stratifying given population patients. Visual tools allowed for the selection of possibly features across various datasets for the given patient population. We essentially made a case for visualization for a very important problem in translational informatics.Comment: BioVis 2014 conferenc

A Bilinear Illumination Model for Robust Face Recognition

We present a technique to generate an illumination subspace for arbitrary 3D faces based on the statistics of measured illuminations under variable lighting conditions from many subjects. A bilinear model based on the higher-order singular value decomposition is used to create a compact illumination subspace given arbitrary shape parameters from a parametric 3D face model. Using a fitting procedure based on minimizing the distance of the input image to the dynamically changing illumination subspace, we reconstruct a shape-specific illumination subspace from a single photograph. We use the reconstructed illumination subspace in various face recognition experiments with variable lighting conditions and obtain accuracies which are very competitive with previous methods that require specific training sessions or multiple images of the subject.Engineering and Applied Science

Estimation of 3D Faces and Illumination from Single Photographs Using a Bilineaur Illumination Model

3D Face modeling is still one of the biggest challenges in computer graphics. In this paper we present a novel framework that acquires the 3D shape, texture, pose and illumination of a face from a single photograph. Additionally, we show how we can recreate a face under varying illumination conditions. Or, essentially relight it. Using a custom-built face scanning system, we have collected 3D face scans and light reflection images of a large and diverse group of human subjects . We derive a morphable face model for 3D face shapes and accompanying textures by transforming the data into a linear vector sub-space. The acquired images of faces under variable illumination are then used to derive a bilinear illumination model that spans 3D face shape and illumination variations. Using both models we, in turn, propose a novel fitting framework that estimates the parameters of the morphable model given a single photograph. Our framework can deal with complex face reflectance and lighting environments in an efficient and robust manner. In the results section of our paper, we compare our methods to existing ones and demonstrate its efficacy in reconstructing 3D face models when provided with a single photograph. We also provide several examples of facial relighting (on 2D images) by performing adequate decomposition of the estimated illumination using our framework.Engineering and Applied Science

Finding Optimal Views for 3D Face Shape Modeling

A fundamental problem in multi-view 3D face modeling is the determination of the set of optimal views (poses) required for accurate 3D shape estimation of a generic face. There is no analytical solution to this problem, instead (partial) solutions require (near) exhaustive combinatorial search, hence the inherent computational difficulty of this task. We build on our previous modeling framework [Silhouette-based 3D face shape recovery, Model-based 3D face capture using shape-from-silhouettes] which uses an efficient contour-based silhouette method and extend it by aggressive pruning of the view-sphere with view clustering and various imaging constraints. A multi-view optimization search is performed using both model-based (eigenheads) and data-driven (visual hull) methods, yielding comparable best views. These constitute the first reported set of optimal views for 3D face shape capture and provide useful empirical guidelines for the design of 3D face recognition systems.Engineering and Applied Science

GRAPHIE: Graph Based Histology Image Explorer

BACKGROUND: Histology images comprise one of the important sources of knowledge for phenotyping studies in systems biology. However, the annotation and analyses of histological data have remained a manual, subjective and relatively low-throughput process. RESULTS: We introduce Graph based Histology Image Explorer (GRAPHIE)-a visual analytics tool to explore, annotate and discover potential relationships in histology image collections within a biologically relevant context. The design of GRAPHIE is guided by domain experts' requirements and well-known InfoVis mantras. By representing each image with informative features and then subsequently visualizing the image collection with a graph, GRAPHIE allows users to effectively explore the image collection. The features were designed to capture localized morphological properties in the given tissue specimen. More importantly, users can perform feature selection in an interactive way to improve the visualization of the image collection and the overall annotation process. Finally, the annotation allows for a better prospective examination of datasets as demonstrated in the users study. Thus, our design of GRAPHIE allows for the users to navigate and explore large collections of histology image datasets. CONCLUSIONS: We demonstrated the usefulness of our visual analytics approach through two case studies. Both of the cases showed efficient annotation and analysis of histology image collection

Silhouette-Based 3D Face Shape Recovery

The creation of realistic 3D face models is still a fundamental problem in computer graphics. In this paper we present a novel method to obtain the 3D shape of an arbitrary human face using a sequence of silhouette images as input. Our face model is a linear combination of eigenheads, which are obtained by a Principal Component Analysis (PCA) of laser-scanned 3D human faces. The coefficients of this linear decomposition are used as our model parameters. We introduce a near-automatic method for reconstructing a 3D face model whose silhouette images match closest to the set of input silhouettes.Engineering and Applied Science

A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data

International audienc

NON PARAMETRIC CELL NUCLEI SEGMENTATION BASED ON A TRACKING OVER DEPTH FROM 3D FLUORESCENCE CONFOCAL IMAGES

International audience3D cell nuclei segmentation from fluorescence microscopy images is a key application in many biological studies. We propose a new, fully automated and non parametric method that takes advantage of the resolution anisotropy in fluorescence microscopy. The cell nuclei are first detected in 2D at each image plane and then tracked over depth through a graph based decision to recover their 3D profiles. As the tracking fails to separate very close cell nuclei along depth, we also propose a corrective step based on an intensity projection criterion. Experimental results on real data demonstrate the efficacy of the proposed method

Improvements to Response-Surface Based Vehicle Design Using a Feature-Centric Approach

Abstract. In this paper, we present our vision for a framework to facilitate computationally-based aerospace vehicle design by improving the quality of the response surfaces that can be developed for a given cost. The response surfaces are developed using computational fluid dynamics (CFD) techniques of varying fidelity. We propose to improve the quality of a given response surface by exploiting the relationships between the response surface and the flow features that evolve in response to changes in the design parameters. The underlying technology, generalized feature mining, is employed to locate and characterize features as well as provide explanations for feature-feature and feature-vehicle interactions. We briefly describe the components of our framework and outline two different strategies to improve the quality of a response surface. We also highlight ongoing efforts