Gene expression reliability estimation through cluster-based analysis

Gene expression is the fundamental control of the structure and functions of the cellular versatility and adaptability of any organisms. The measurement of gene expressions is performed on images generated by optical inspection of microarray devices which allow the simultaneous analysis of thousands of genes. The images produced by these devices are used to calculate the expression levels of mRNA in order to draw diagnostic information related to human disease. The quality measures are mandatory in genes classification and in the decision-making diagnostic. However, microarrays are characterized by imperfections due to sample contaminations, scratches, precipitation or imperfect gridding and spot detection. The automatic and efficient quality measurement of microarray is needed in order to discriminate faulty gene expression levels. In this paper we present a new method for estimate the quality degree and the data's reliability of a microarray analysis. The efficiency of the proposed approach in terms of genes expression classification has been demonstrated through a clustering supervised analysis performed on a set of three different histological samples related to the Lymphoma's cancer diseas

Principal Boundary on Riemannian Manifolds

We consider the classification problem and focus on nonlinear methods for classification on manifolds. For multivariate datasets lying on an embedded nonlinear Riemannian manifold within the higher-dimensional ambient space, we aim to acquire a classification boundary for the classes with labels, using the intrinsic metric on the manifolds. Motivated by finding an optimal boundary between the two classes, we invent a novel approach -- the principal boundary. From the perspective of classification, the principal boundary is defined as an optimal curve that moves in between the principal flows traced out from two classes of data, and at any point on the boundary, it maximizes the margin between the two classes. We estimate the boundary in quality with its direction, supervised by the two principal flows. We show that the principal boundary yields the usual decision boundary found by the support vector machine in the sense that locally, the two boundaries coincide. Some optimality and convergence properties of the random principal boundary and its population counterpart are also shown. We illustrate how to find, use and interpret the principal boundary with an application in real data.Comment: 31 pages,10 figure

One-Class Classification: Taxonomy of Study and Review of Techniques

One-class classification (OCC) algorithms aim to build classification models when the negative class is either absent, poorly sampled or not well defined. This unique situation constrains the learning of efficient classifiers by defining class boundary just with the knowledge of positive class. The OCC problem has been considered and applied under many research themes, such as outlier/novelty detection and concept learning. In this paper we present a unified view of the general problem of OCC by presenting a taxonomy of study for OCC problems, which is based on the availability of training data, algorithms used and the application domains applied. We further delve into each of the categories of the proposed taxonomy and present a comprehensive literature review of the OCC algorithms, techniques and methodologies with a focus on their significance, limitations and applications. We conclude our paper by discussing some open research problems in the field of OCC and present our vision for future research.Comment: 24 pages + 11 pages of references, 8 figure

Visual and Contextual Modeling for the Detection of Repeated Mild Traumatic Brain Injury.

Currently, there is a lack of computational methods for the evaluation of mild traumatic brain injury (mTBI) from magnetic resonance imaging (MRI). Further, the development of automated analyses has been hindered by the subtle nature of mTBI abnormalities, which appear as low contrast MR regions. This paper proposes an approach that is able to detect mTBI lesions by combining both the high-level context and low-level visual information. The contextual model estimates the progression of the disease using subject information, such as the time since injury and the knowledge about the location of mTBI. The visual model utilizes texture features in MRI along with a probabilistic support vector machine to maximize the discrimination in unimodal MR images. These two models are fused to obtain a final estimate of the locations of the mTBI lesion. The models are tested using a novel rodent model of repeated mTBI dataset. The experimental results demonstrate that the fusion of both contextual and visual textural features outperforms other state-of-the-art approaches. Clinically, our approach has the potential to benefit both clinicians by speeding diagnosis and patients by improving clinical care

A Novel Framework for Highlight Reflectance Transformation Imaging

We propose a novel pipeline and related software tools for processing the multi-light image collections (MLICs) acquired in different application contexts to obtain shape and appearance information of captured surfaces, as well as to derive compact relightable representations of them. Our pipeline extends the popular Highlight Reflectance Transformation Imaging (H-RTI) framework, which is widely used in the Cultural Heritage domain. We support, in particular, perspective camera modeling, per-pixel interpolated light direction estimation, as well as light normalization correcting vignetting and uneven non-directional illumination. Furthermore, we propose two novel easy-to-use software tools to simplify all processing steps. The tools, in addition to support easy processing and encoding of pixel data, implement a variety of visualizations, as well as multiple reflectance-model-fitting options. Experimental tests on synthetic and real-world MLICs demonstrate the usefulness of the novel algorithmic framework and the potential benefits of the proposed tools for end-user applications.Terms: "European Union (EU)" & "Horizon 2020" / Action: H2020-EU.3.6.3. - Reflective societies - cultural heritage and European identity / Acronym: Scan4Reco / Grant number: 665091DSURF project (PRIN 2015) funded by the Italian Ministry of University and ResearchSardinian Regional Authorities under projects VIGEC and Vis&VideoLa