Visualizing dimensionality reduction of systems biology data

One of the challenges in analyzing high-dimensional expression data is the detection of important biological signals. A common approach is to apply a dimension reduction method, such as principal component analysis. Typically, after application of such a method the data is projected and visualized in the new coordinate system, using scatter plots or profile plots. These methods provide good results if the data have certain properties which become visible in the new coordinate system and which were hard to detect in the original coordinate system. Often however, the application of only one method does not suffice to capture all important signals. Therefore several methods addressing different aspects of the data need to be applied. We have developed a framework for linear and non-linear dimension reduction methods within our visual analytics pipeline SpRay. This includes measures that assist the interpretation of the factorization result. Different visualizations of these measures can be combined with functional annotations that support the interpretation of the results. We show an application to high-resolution time series microarray data in the antibiotic-producing organism Streptomyces coelicolor as well as to microarray data measuring expression of cells with normal karyotype and cells with trisomies of human chromosomes 13 and 21

Deep Convolutional Ranking for Multilabel Image Annotation

Multilabel image annotation is one of the most important challenges in computer vision with many real-world applications. While existing work usually use conventional visual features for multilabel annotation, features based on Deep Neural Networks have shown potential to significantly boost performance. In this work, we propose to leverage the advantage of such features and analyze key components that lead to better performances. Specifically, we show that a significant performance gain could be obtained by combining convolutional architectures with approximate top-$k$ ranking objectives, as thye naturally fit the multilabel tagging problem. Our experiments on the NUS-WIDE dataset outperforms the conventional visual features by about 10%, obtaining the best reported performance in the literature

Latent Semantic Learning with Structured Sparse Representation for Human Action Recognition

This paper proposes a novel latent semantic learning method for extracting high-level features (i.e. latent semantics) from a large vocabulary of abundant mid-level features (i.e. visual keywords) with structured sparse representation, which can help to bridge the semantic gap in the challenging task of human action recognition. To discover the manifold structure of midlevel features, we develop a spectral embedding approach to latent semantic learning based on L1-graph, without the need to tune any parameter for graph construction as a key step of manifold learning. More importantly, we construct the L1-graph with structured sparse representation, which can be obtained by structured sparse coding with its structured sparsity ensured by novel L1-norm hypergraph regularization over mid-level features. In the new embedding space, we learn latent semantics automatically from abundant mid-level features through spectral clustering. The learnt latent semantics can be readily used for human action recognition with SVM by defining a histogram intersection kernel. Different from the traditional latent semantic analysis based on topic models, our latent semantic learning method can explore the manifold structure of mid-level features in both L1-graph construction and spectral embedding, which results in compact but discriminative high-level features. The experimental results on the commonly used KTH action dataset and unconstrained YouTube action dataset show the superior performance of our method.Comment: The short version of this paper appears in ICCV 201

Towards Effective Codebookless Model for Image Classification

The bag-of-features (BoF) model for image classification has been thoroughly studied over the last decade. Different from the widely used BoF methods which modeled images with a pre-trained codebook, the alternative codebook free image modeling method, which we call Codebookless Model (CLM), attracted little attention. In this paper, we present an effective CLM that represents an image with a single Gaussian for classification. By embedding Gaussian manifold into a vector space, we show that the simple incorporation of our CLM into a linear classifier achieves very competitive accuracy compared with state-of-the-art BoF methods (e.g., Fisher Vector). Since our CLM lies in a high dimensional Riemannian manifold, we further propose a joint learning method of low-rank transformation with support vector machine (SVM) classifier on the Gaussian manifold, in order to reduce computational and storage cost. To study and alleviate the side effect of background clutter on our CLM, we also present a simple yet effective partial background removal method based on saliency detection. Experiments are extensively conducted on eight widely used databases to demonstrate the effectiveness and efficiency of our CLM method

Sparse Transfer Learning for Interactive Video Search Reranking

Visual reranking is effective to improve the performance of the text-based video search. However, existing reranking algorithms can only achieve limited improvement because of the well-known semantic gap between low level visual features and high level semantic concepts. In this paper, we adopt interactive video search reranking to bridge the semantic gap by introducing user's labeling effort. We propose a novel dimension reduction tool, termed sparse transfer learning (STL), to effectively and efficiently encode user's labeling information. STL is particularly designed for interactive video search reranking. Technically, it a) considers the pair-wise discriminative information to maximally separate labeled query relevant samples from labeled query irrelevant ones, b) achieves a sparse representation for the subspace to encodes user's intention by applying the elastic net penalty, and c) propagates user's labeling information from labeled samples to unlabeled samples by using the data distribution knowledge. We conducted extensive experiments on the TRECVID 2005, 2006 and 2007 benchmark datasets and compared STL with popular dimension reduction algorithms. We report superior performance by using the proposed STL based interactive video search reranking.Comment: 17 page