Biological cells classification using bio-inspired descriptor in a boosting k-NN framework

International audienceHigh-content imaging is an emerging technology for the analysis and quantification of biological phenomena. Thus, classifying a huge number of cells or quantifying markers from large sets of images by experts is a very time-consuming and poorly reproducible task. In order to overcome such limitations, we propose a supervised method for automatic cell classification. Our approach consists of two steps: the first one is an indexing stage based on specific bio-inspired features relying on the distribution of contrast information on segmented cells. The second one is a supervised learning stage that selects the prototypical samples best representing the cell categories. These prototypes are used in a leveraged k-NN framework to predict the class of unlabeled cells. In this paper we have tested our new learning algorithm on cellular images acquired for the analysis of pathologies. In order to evaluate the automatic classification performances, we tested our algorithm on the HEp2 Cells dataset of (Foggia et al, CBMS 2010). Results are very promising, showing classification precision larger than 96% on average, thus suggesting our method as a valuable decision-support tool in such cellular imaging applications

A Bio-inspired Learning and Classification Method for Subcellular Localization of a Plasma Membrane Protein

International audienceHigh-content cellular imaging is an emerging technology for studying many biological phenomena. statistical analyses on large populations (more than thousands) of cells are required. Hence classifying cells by experts is a very time-consuming task and poorly reproducible. In order to overcome such limitations, we propose an automatic supervised classification method. Our new cell classification method consists of two steps: The first one is an indexing process based on specific bio-inspired features using contrast information distributions on cell sub-regions. The second is a supervised learning process to select prototypical samples (that best represent the cells categories) which are used in a leveraged k-NN framework to predict the class of unlabeled cells. In this paper we have tested our new learning algorithm on cellular images acquired for the analysis of changes in the subcellular localization of a membrane protein (the sodium iodide symporter). In order to evaluate the automatic classification performances, we tested our algorithm on a significantly large database of cellular images annotated by experts of our group. Results in term of Mean Avarage Precision (MAP) are very promising, providing precision upper than 87% on average, thus suggesting our method as a valuable decision-support tool in such cellular imaging applications. Such supervised classification method has many other applications in cell imaging in the areas of research in basic biology and medicine but also in clinical histology

Classification of biological cells using bio-inspired descriptors

International audienceThis paper proposes a novel automated approach for the categorization of cells in fluorescence microscopy images. Our supervised classification method aims at recognizing patterns of unlabeled cells based on an annotated dataset. First, the cell images need to be indexed by encoding them in a feature space. For this purpose, we propose tailored bio-inspired features relying on the distribution of contrast information. Then, a supervised learning algorithm is proposed for classifying the cells. We carried out experiments on cellular images related to the diagnosis of autoimmune diseases, testing our classification method on the HEp-2 Cells dataset of Foggia et al (CBMS 2010). Results show classification precision larger than 96% on average, thus confirming promising application of our approach to the challenging application of cellular image classification for computer-aided diagnosis

Automatic Classification of Human Epithelial Type 2 Cell Indirect Immunofluorescence Images using Cell Pyramid Matching

This paper describes a novel system for automatic classification of images obtained from Anti-Nuclear Antibody (ANA) pathology tests on Human Epithelial type 2 (HEp-2) cells using the Indirect Immunofluorescence (IIF) protocol. The IIF protocol on HEp-2 cells has been the hallmark method to identify the presence of ANAs, due to its high sensitivity and the large range of antigens that can be detected. However, it suffers from numerous shortcomings, such as being subjective as well as time and labour intensive. Computer Aided Diagnostic (CAD) systems have been developed to address these problems, which automatically classify a HEp-2 cell image into one of its known patterns (eg. speckled, homogeneous). Most of the existing CAD systems use handpicked features to represent a HEp-2 cell image, which may only work in limited scenarios. We propose a novel automatic cell image classification method termed Cell Pyramid Matching (CPM), which is comprised of regional histograms of visual words coupled with the Multiple Kernel Learning framework. We present a study of several variations of generating histograms and show the efficacy of the system on two publicly available datasets: the ICPR HEp-2 cell classification contest dataset and the SNPHEp-2 dataset.Comment: arXiv admin note: substantial text overlap with arXiv:1304.126

Contributions on Automatic Recognition of Faces using Local Texture Features

Uno de los temas más destacados del área de visión artifical se deriva del análisis facial automático. En particular, la detección precisa de caras humanas y el análisis biométrico de las mismas son problemas que han generado especial interés debido a la gran cantidad de aplicaciones que actualmente hacen uso de estos mecnismos. En esta Tesis Doctoral se analizan por separado los problemas relacionados con detección precisa de caras basada en la localización de los ojos y el reconomcimiento facial a partir de la extracción de características locales de textura. Los algoritmos desarrollados abordan el problema de la extracción de la identidad a partir de una imagen de cara ( en vista frontal o semi-frontal), para escenarios parcialmente controlados. El objetivo es desarrollar algoritmos robustos y que puedan incorpararse fácilmente a aplicaciones reales, tales como seguridad avanzada en banca o la definición de estrategias comerciales aplicadas al sector de retail. Respecto a la extracción de texturas locales, se ha realizado un análisis exhaustivo de los descriptores más extendidos; se ha puesto especial énfasis en el estudio de los Histogramas de Grandientes Orientados (HOG features). En representaciones normalizadas de la cara, estos descriptores ofrecen información discriminativa de los elementos faciales (ojos, boca, etc.), siendo robustas a variaciones en la iluminación y pequeños desplazamientos. Se han elegido diferentes algoritmos de clasificación para realizar la detección y el reconocimiento de caras, todos basados en una estrategia de sistemas supervisados. En particular, para la localización de ojos se ha utilizado clasificadores boosting y Máquinas de Soporte Vectorial (SVM) sobre descriptores HOG. En el caso de reconocimiento de caras, se ha desarrollado un nuevo algoritmo, HOG-EBGM (HOG sobre Elastic Bunch Graph Matching). Dada la imagen de una cara, el esquema seguido por este algoritmo se puede resumir en pocos pasos: en una primera etapa se extMonzó Ferrer, D. (2012). Contributions on Automatic Recognition of Faces using Local Texture Features [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/16698Palanci

Big-Data Science in Porous Materials: Materials Genomics and Machine Learning

By combining metal nodes with organic linkers we can potentially synthesize millions of possible metal organic frameworks (MOFs). At present, we have libraries of over ten thousand synthesized materials and millions of in-silico predicted materials. The fact that we have so many materials opens many exciting avenues to tailor make a material that is optimal for a given application. However, from an experimental and computational point of view we simply have too many materials to screen using brute-force techniques. In this review, we show that having so many materials allows us to use big-data methods as a powerful technique to study these materials and to discover complex correlations. The first part of the review gives an introduction to the principles of big-data science. We emphasize the importance of data collection, methods to augment small data sets, how to select appropriate training sets. An important part of this review are the different approaches that are used to represent these materials in feature space. The review also includes a general overview of the different ML techniques, but as most applications in porous materials use supervised ML our review is focused on the different approaches for supervised ML. In particular, we review the different method to optimize the ML process and how to quantify the performance of the different methods. In the second part, we review how the different approaches of ML have been applied to porous materials. In particular, we discuss applications in the field of gas storage and separation, the stability of these materials, their electronic properties, and their synthesis. The range of topics illustrates the large variety of topics that can be studied with big-data science. Given the increasing interest of the scientific community in ML, we expect this list to rapidly expand in the coming years.Comment: Editorial changes (typos fixed, minor adjustments to figures