A Comprehensive Survey on Cross-modal Retrieval

In recent years, cross-modal retrieval has drawn much attention due to the rapid growth of multimodal data. It takes one type of data as the query to retrieve relevant data of another type. For example, a user can use a text to retrieve relevant pictures or videos. Since the query and its retrieved results can be of different modalities, how to measure the content similarity between different modalities of data remains a challenge. Various methods have been proposed to deal with such a problem. In this paper, we first review a number of representative methods for cross-modal retrieval and classify them into two main groups: 1) real-valued representation learning, and 2) binary representation learning. Real-valued representation learning methods aim to learn real-valued common representations for different modalities of data. To speed up the cross-modal retrieval, a number of binary representation learning methods are proposed to map different modalities of data into a common Hamming space. Then, we introduce several multimodal datasets in the community, and show the experimental results on two commonly used multimodal datasets. The comparison reveals the characteristic of different kinds of cross-modal retrieval methods, which is expected to benefit both practical applications and future research. Finally, we discuss open problems and future research directions.Comment: 20 pages, 11 figures, 9 table

Why Can't We Predict RNA Structure At Atomic Resolution?

No existing algorithm can start with arbitrary RNA sequences and return the precise, three-dimensional structures that ensures their biological function. This chapter outlines current algorithms for automated RNA structure prediction (including our own FARNA-FARFAR), highlights their successes, and dissects their limitations, using a tetraloop and the sarcin/ricin motif as examples. The barriers to future advances are considered in light of three particular challenges: improving computational sampling, reducing reliance on experimentally solved structures, and avoiding coarse-grained representations of atomic-level interactions. To help meet these challenges and better understand the current state of the field, we propose an ongoing community-wide CASP-style experiment for evaluating the performance of current structure prediction algorithms.Comment: K. Beauchamp & P. Sripakdeevong are equally contributing authors. Submission for book: RNA 3D Structure Analysis and Prediction, editors: N. Leontis & E. Westho

L0-norm Sparse Graph-regularized SVD for Biclustering

Learning the "blocking" structure is a central challenge for high dimensional data (e.g., gene expression data). Recently, a sparse singular value decomposition (SVD) has been used as a biclustering tool to achieve this goal. However, this model ignores the structural information between variables (e.g., gene interaction graph). Although typical graph-regularized norm can incorporate such prior graph information to get accurate discovery and better interpretability, it fails to consider the opposite effect of variables with different signs. Motivated by the development of sparse coding and graph-regularized norm, we propose a novel sparse graph-regularized SVD as a powerful biclustering tool for analyzing high-dimensional data. The key of this method is to impose two penalties including a novel graph-regularized norm ($|\pmb{u}|\pmb{L}|\pmb{u}|$) and $L_0$-norm ($\|\pmb{u}\|_0$) on singular vectors to induce structural sparsity and enhance interpretability. We design an efficient Alternating Iterative Sparse Projection (AISP) algorithm to solve it. Finally, we apply our method and related ones to simulated and real data to show its efficiency in capturing natural blocking structures.Comment: 8 pages, 2 figure

DNA Steganalysis Using Deep Recurrent Neural Networks

Recent advances in next-generation sequencing technologies have facilitated the use of deoxyribonucleic acid (DNA) as a novel covert channels in steganography. There are various methods that exist in other domains to detect hidden messages in conventional covert channels. However, they have not been applied to DNA steganography. The current most common detection approaches, namely frequency analysis-based methods, often overlook important signals when directly applied to DNA steganography because those methods depend on the distribution of the number of sequence characters. To address this limitation, we propose a general sequence learning-based DNA steganalysis framework. The proposed approach learns the intrinsic distribution of coding and non-coding sequences and detects hidden messages by exploiting distribution variations after hiding these messages. Using deep recurrent neural networks (RNNs), our framework identifies the distribution variations by using the classification score to predict whether a sequence is to be a coding or non-coding sequence. We compare our proposed method to various existing methods and biological sequence analysis methods implemented on top of our framework. According to our experimental results, our approach delivers a robust detection performance compared to other tools

Kernelized Low Rank Representation on Grassmann Manifolds

Low rank representation (LRR) has recently attracted great interest due to its pleasing efficacy in exploring low-dimensional subspace structures embedded in data. One of its successful applications is subspace clustering which means data are clustered according to the subspaces they belong to. In this paper, at a higher level, we intend to cluster subspaces into classes of subspaces. This is naturally described as a clustering problem on Grassmann manifold. The novelty of this paper is to generalize LRR on Euclidean space onto an LRR model on Grassmann manifold in a uniform kernelized framework. The new methods have many applications in computer vision tasks. Several clustering experiments are conducted on handwritten digit images, dynamic textures, human face clips and traffic scene sequences. The experimental results show that the proposed methods outperform a number of state-of-the-art subspace clustering methods.Comment: 13 page

Multi-view Low-rank Sparse Subspace Clustering

Most existing approaches address multi-view subspace clustering problem by constructing the affinity matrix on each view separately and afterwards propose how to extend spectral clustering algorithm to handle multi-view data. This paper presents an approach to multi-view subspace clustering that learns a joint subspace representation by constructing affinity matrix shared among all views. Relying on the importance of both low-rank and sparsity constraints in the construction of the affinity matrix, we introduce the objective that balances between the agreement across different views, while at the same time encourages sparsity and low-rankness of the solution. Related low-rank and sparsity constrained optimization problem is for each view solved using the alternating direction method of multipliers. Furthermore, we extend our approach to cluster data drawn from nonlinear subspaces by solving the corresponding problem in a reproducing kernel Hilbert space. The proposed algorithm outperforms state-of-the-art multi-view subspace clustering algorithms on one synthetic and four real-world datasets

Video Compressive Sensing for Dynamic MRI

We present a video compressive sensing framework, termed kt-CSLDS, to accelerate the image acquisition process of dynamic magnetic resonance imaging (MRI). We are inspired by a state-of-the-art model for video compressive sensing that utilizes a linear dynamical system (LDS) to model the motion manifold. Given compressive measurements, the state sequence of an LDS can be first estimated using system identification techniques. We then reconstruct the observation matrix using a joint structured sparsity assumption. In particular, we minimize an objective function with a mixture of wavelet sparsity and joint sparsity within the observation matrix. We derive an efficient convex optimization algorithm through alternating direction method of multipliers (ADMM), and provide a theoretical guarantee for global convergence. We demonstrate the performance of our approach for video compressive sensing, in terms of reconstruction accuracy. We also investigate the impact of various sampling strategies. We apply this framework to accelerate the acquisition process of dynamic MRI and show it achieves the best reconstruction accuracy with the least computational time compared with existing algorithms in the literature.Comment: 30 pages, 9 figure

Set-Difference Range Queries

We introduce the problem of performing set-difference range queries, where answers to queries are set-theoretic symmetric differences between sets of items in two geometric ranges. We describe a general framework for answering such queries based on a novel use of data-streaming sketches we call signed symmetric-difference sketches. We show that such sketches can be realized using invertible Bloom filters (IBFs), which can be composed, differenced, and searched so as to solve set-difference range queries in a wide range of scenarios

Learning Invariant Color Features for Person Re-Identification

Matching people across multiple camera views known as person re-identification, is a challenging problem due to the change in visual appearance caused by varying lighting conditions. The perceived color of the subject appears to be different with respect to illumination. Previous works use color as it is or address these challenges by designing color spaces focusing on a specific cue. In this paper, we propose a data driven approach for learning color patterns from pixels sampled from images across two camera views. The intuition behind this work is that, even though pixel values of same color would be different across views, they should be encoded with the same values. We model color feature generation as a learning problem by jointly learning a linear transformation and a dictionary to encode pixel values. We also analyze different photometric invariant color spaces. Using color as the only cue, we compare our approach with all the photometric invariant color spaces and show superior performance over all of them. Combining with other learned low-level and high-level features, we obtain promising results in ViPER, Person Re-ID 2011 and CAVIAR4REID datasets