Stable Feature Selection for Biomarker Discovery

Feature selection techniques have been used as the workhorse in biomarker discovery applications for a long time. Surprisingly, the stability of feature selection with respect to sampling variations has long been under-considered. It is only until recently that this issue has received more and more attention. In this article, we review existing stable feature selection methods for biomarker discovery using a generic hierarchal framework. We have two objectives: (1) providing an overview on this new yet fast growing topic for a convenient reference; (2) categorizing existing methods under an expandable framework for future research and development

Conditional t-SNE: Complementary t-SNE embeddings through factoring out prior information

Dimensionality reduction and manifold learning methods such as t-Distributed Stochastic Neighbor Embedding (t-SNE) are routinely used to map high-dimensional data into a 2-dimensional space to visualize and explore the data. However, two dimensions are typically insufficient to capture all structure in the data, the salient structure is often already known, and it is not obvious how to extract the remaining information in a similarly effective manner. To fill this gap, we introduce \emph{conditional t-SNE} (ct-SNE), a generalization of t-SNE that discounts prior information from the embedding in the form of labels. To achieve this, we propose a conditioned version of the t-SNE objective, obtaining a single, integrated, and elegant method. ct-SNE has one extra parameter over t-SNE; we investigate its effects and show how to efficiently optimize the objective. Factoring out prior knowledge allows complementary structure to be captured in the embedding, providing new insights. Qualitative and quantitative empirical results on synthetic and (large) real data show ct-SNE is effective and achieves its goal

Semantic image retrieval using relevance feedback and transaction logs

Due to the recent improvements in digital photography and storage capacity, storing large amounts of images has been made possible, and efficient means to retrieve images matching a user’s query are needed. Content-based Image Retrieval (CBIR) systems automatically extract image contents based on image features, i.e. color, texture, and shape. Relevance feedback methods are applied to CBIR to integrate users’ perceptions and reduce the gap between high-level image semantics and low-level image features. The precision of a CBIR system in retrieving semantically rich (complex) images is improved in this dissertation work by making advancements in three areas of a CBIR system: input, process, and output. The input of the system includes a mechanism that provides the user with required tools to build and modify her query through feedbacks. Users behavioral in CBIR environments are studied, and a new feedback methodology is presented to efficiently capture users’ image perceptions. The process element includes image learning and retrieval algorithms. A Long-term image retrieval algorithm (LTL), which learns image semantics from prior search results available in the system’s transaction history, is developed using Factor Analysis. Another algorithm, a short-term learner (STL) that captures user’s image perceptions based on image features and user’s feedbacks in the on-going transaction, is developed based on Linear Discriminant Analysis. Then, a mechanism is introduced to integrate these two algorithms to one retrieval procedure. Finally, a retrieval strategy that includes learning and searching phases is defined for arranging images in the output of the system. The developed relevance feedback methodology proved to reduce the effect of human subjectivity in providing feedbacks for complex images. Retrieval algorithms were applied to images with different degrees of complexity. LTL is efficient in extracting the semantics of complex images that have a history in the system. STL is suitable for query and images that can be effectively represented by their image features. Therefore, the performance of the system in retrieving images with visual and conceptual complexities was improved when both algorithms were applied simultaneously. Finally, the strategy of retrieval phases demonstrated promising results when the query complexity increases

The Parallel Distributed Image Search Engine (ParaDISE)

Image retrieval is a complex task that differs according to the context and the user requirements in any specific field, for example in a medical environment. Search by text is often not possible or optimal and retrieval by the visual content does not always succeed in modelling high-level concepts that a user is looking for. Modern image retrieval techniques consists of multiple steps and aim to retrieve information from large–scale datasets and not only based on global image appearance but local features and if possible in a connection between visual features and text or semantics. This paper presents the Parallel Distributed Image Search Engine (ParaDISE), an image retrieval system that combines visual search with text–based retrieval and that is available as open source and free of charge. The main design concepts of ParaDISE are flexibility, expandability, scalability and interoperability. These concepts constitute the system, able to be used both in real–world applications and as an image retrieval research platform. Apart from the architecture and the implementation of the system, two use cases are described, an application of ParaDISE in retrieval of images from the medical literature and a visual feature evaluation for medical image retrieval. Future steps include the creation of an open source community that will contribute and expand this platform based on the existing parts