ALBERT

Beschreibung: Survival analysis is a statistical technique widely used in many fields of science, in particular in the medical area, and which studies the time until an event of interest occurs. Outlier detection in this co...

Beschreibung: Matrix factorization is a well established pattern discovery tool that has seen numerous applications in biomedical data analytics, such as gene expression co-clustering, patient stratification, and gene-disea...

Beschreibung: Evolutionary computation (EC) has been widely applied to biological and biomedical data. The practice of EC involves the tuning of many parameters, such as population size, generation count, selection size, an...

Beschreibung: In the nervous system, the neurons communicate through synapses. The size, morphology, and connectivity of these synapses are significant in determining the functional properties of the neural network. Therefo...

Beschreibung: Detecting differentially expressed (DE) genes between disease and normal control group is one of the most common analyses in genome-wide transcriptomic data. Since most studies don’t have a lot of samples, res...

Beschreibung: Presents the front cover for this issue of the publication.

Beschreibung: Six senior computer science educators answer questions about the current state of computer science education, software engineering, and licensing software engineers.

Beschreibung: Provides a listing of current staff, committee members and society officers.

Beschreibung: The Internet of Things is a new department with the mission of presenting fresh ideas and applications from a practitioner point of view. The authors are interested in showcasing articles about real, implemented Internet of Things (IoT) systems.

Beschreibung: Commemorating the 20th anniversary of IT Professional, the advisory board chair and four past editors in chief reflect on the first two decades of the magazine.

Beschreibung: In a case study where a Dutch small-to-medium enterprise (SME) implemented test-driven development and continuous integration, researchers observed that the SME discovered a higher number of defects compared to a baseline case study, and that there was an increase in the focus on quality and test applications.

Beschreibung: By providing access to data from numerous systems in one database and supporting the systems that can produce an appropriate customer experience, a customer data platform overcomes the limitations imposed by fragmented point solutions and presents a holistic approach to customer interactions.

Beschreibung: An introduction to the new Life in the C-Suite column, which will help C-level executives understand the vast digital world in which they live, and how they should leverage digital technology into their business processes and business models.

Beschreibung: Student Forum is a new column that intends to connect IT students with industry, government, and academia.

Beschreibung: The new IT Economics department seeks to advance the understanding of various microeconomic and macroeconomic issues that IT managers need to examine in their decisions to adopt and implement information and communications technology-related systems, services, processes, and practices.

Beschreibung: Provides a listing of current committee members and society officers.

Beschreibung: Prospective authors are requested to submit new, unpublished manuscripts for inclusion in the upcoming event described in this call for papers.

Beschreibung: The use of synthetic sequences is one of the most promising tools for advanced in silico evaluation of the quantification of cardiac deformation and strain through 3-D ultrasound (US) and magnetic resonance (MR) imaging. In this paper, we propose the first simulation framework which allows the generation of realistic 3-D synthetic cardiac US and MR (both cine and tagging) image sequences from the same virtual patient. A state-of-the-art electromechanical (E/M) model was exploited for simulating groundtruth cardiac motion fields ranging from healthy to various pathological cases, including both ventricular dyssynchrony and myocardial ischemia. The E/M groundtruth along with template MR/US images and physical simulators were combined in a unified framework for generating synthetic data. We efficiently merged several warping strategies to keep the full control of myocardial deformations while preserving realistic image texture. In total, we generated 18 virtual patients, each with synthetic 3-D US, cine MR, and tagged MR sequences. The simulated images were evaluated both qualitatively by showing realistic textures and quantitatively by observing myocardial intensity distributions similar to real data. In particular, the US simulation showed a smoother myocardium/background interface than the state-of-the-art. We also assessed the mechanical properties. The pathological subjects were discriminated from the healthy ones by both global indexes (ejection fraction and the global circumferential strain) and regional strain curves. The synthetic database is comprehensive in terms of both pathology and modality, and has a level of realism sufficient for validation purposes. All the 90 sequences are made publicly available to the research community via an open-access database.

Beschreibung: Collecting large databases of annotated medical images is crucial for the validation and testing of feature extraction, statistical analysis, and machine learning algorithms. Recent advances in cardiac electromechanical modeling and image synthesis provided a framework to generate synthetic images based on realistic mesh simulations. Nonetheless, their potential to augment an existing database with large amounts of synthetic cases requires further investigation. We build upon these works and propose a revised scheme for synthesizing pathological cardiac sequences from real healthy sequences. Our new pipeline notably involves a much easier registration problem to reduce potential artifacts, and takes advantage of mesh correspondences to generate new data from a given case without additional registration. The output sequences are thoroughly examined in terms of quality and usability on a given application: the assessment of myocardial viability, via the generation of 465 synthetic cine MR sequences (15 healthy and 450 with pathological tissue viability [random location, extent, and grade, up to myocardial infarct]). We demonstrate that: 1) our methodology improves the state-of-the-art algorithms in terms of realism and accuracy of the simulated images and 2) our methodology is well-suited for the generation of large databases at small computational cost.

Beschreibung: It is generally recognized that color information is central to the automatic and visual analysis of histopathology tissue slides. In practice, pathologists rely on color, which reflects the presence of specific tissue components, to establish a diagnosis. Similarly, automatic histopathology image analysis algorithms rely on color or intensity measures to extract tissue features. With the increasing access to digitized histopathology images, color variation and its implications have become a critical issue. These variations are the result of not only a variety of factors involved in the preparation of tissue slides but also in the digitization process itself. Consequently, different strategies have been proposed to alleviate stain-related tissue inconsistencies in automatic image analysis systems. Such techniques generally rely on collecting color statistics to perform color matching across images. In this work, we propose a different approach for stain normalization that we refer to as stain transfer. We design a discriminative image analysis model equipped with a stain normalization component that transfers stains across datasets. Our model comprises a generative network that learns data set-specific staining properties and image-specific color transformations as well as a task-specific network (e.g., classifier or segmentation network). The model is trained end-to-end using a multi-objective cost function. We evaluate the proposed approach in the context of automatic histopathology image analysis on three data sets and two different analysis tasks: tissue segmentation and classification. The proposed method achieves superior results in terms of accuracy and quality of normalized images compared to various baselines.

Beschreibung: In medical image analysis applications, the availability of the large amounts of annotated data is becoming increasingly critical. However, annotated medical data is often scarce and costly to obtain. In this paper, we address the problem of synthesizing retinal color images by applying recent techniques based on adversarial learning. In this setting, a generative model is trained to maximize a loss function provided by a second model attempting to classify its output into real or synthetic. In particular, we propose to implement an adversarial autoencoder for the task of retinal vessel network synthesis. We use the generated vessel trees as an intermediate stage for the generation of color retinal images, which is accomplished with a generative adversarial network. Both models require the optimization of almost everywhere differentiable loss functions, which allows us to train them jointly. The resulting model offers an end-to-end retinal image synthesis system capable of generating as many retinal images as the user requires, with their corresponding vessel networks, by sampling from a simple probability distribution that we impose to the associated latent space. We show that the learned latent space contains a well-defined semantic structure, implying that we can perform calculations in the space of retinal images, e.g., smoothly interpolating new data points between two retinal images. Visual and quantitative results demonstrate that the synthesized images are substantially different from those in the training set, while being also anatomically consistent and displaying a reasonable visual quality.

Beschreibung: Multi-modality medical imaging is increasingly used for comprehensive assessment of complex diseases in either diagnostic examinations or as part of medical research trials. Different imaging modalities provide complementary information about living tissues. However, multi-modal examinations are not always possible due to adversary factors, such as patient discomfort, increased cost, prolonged scanning time, and scanner unavailability. In additionally, in large imaging studies, incomplete records are not uncommon owing to image artifacts, data corruption or data loss, which compromise the potential of multi-modal acquisitions. In this paper, we propose a weakly coupled and geometry co-regularized joint dictionary learning method to address the problem of cross-modality synthesis while considering the fact that collecting the large amounts of training data is often impractical. Our learning stage requires only a few registered multi-modality image pairs as training data. To employ both paired images and a large set of unpaired data, a cross-modality image matching criterion is proposed. Then, we propose a unified model by integrating such a criterion into the joint dictionary learning and the observed common feature space for associating cross-modality data for the purpose of synthesis. Furthermore, two regularization terms are added to construct robust sparse representations. Our experimental results demonstrate superior performance of the proposed model over state-of-the-art methods.

Beschreibung: Encouraged by the recent progress in pedestrian detection, we investigate the gap between current state-of-the-art methods and the “perfect single frame detector”. We enable our analysis by creating a human baseline for pedestrian detection (over the Caltech pedestrian dataset). After manually clustering the frequent errors of a top detector, we characterise both localisation and background-versus-foreground errors. To address localisation errors we study the impact of training annotation noise on the detector performance, and show that we can improve results even with a small portion of sanitised training data. To address background/foreground discrimination, we study convnets for pedestrian detection, and discuss which factors affect their performance. Other than our in-depth analysis, we report top performance on the Caltech pedestrian dataset, and provide a new sanitised set of training and test annotations.

Beschreibung: This paper addresses the problem of robust and efficient relative rotation averaging in the context of large-scale Structure from Motion. Relative rotation averaging finds global or absolute rotations for a set of cameras from a set of observed relative rotations between pairs of cameras. We propose a generalized framework of relative rotation averaging that can use different robust loss functions and jointly optimizes for all the unknown camera rotations. Our method uses a quasi-Newton optimization which results in an efficient iteratively reweighted least squares (IRLS) formulation that works in the Lie algebra of the 3D rotation group. We demonstrate the performance of our approach on a number of large-scale data sets. We show that our method outperforms existing methods in the literature both in terms of speed and accuracy.

Beschreibung: The simultaneous removal of noise and preservation of the integrity of 3-D magnetic resonance (MR) images is a difficult and important task. In this paper, we consider characterizing MR images with 3-D operators, and present a novel 4-D transform-domain method termed ‘modified nonlocal tensor-SVD (MNL-tSVD)’ for MR image denoising. The proposed method is based on the grouping, hard-thresholding and aggregation paradigms, and can be viewed as a generalized nonlocal extension of tensor-SVD (t-SVD). By keeping MR images in its natural three-dimensional form, and collaboratively filtering similar patches, MNL-tSVD utilizes both the self-similarity property and 3-D structure of MR images to preserve more actual details and minimize the introduction of new artifacts. We show the adaptability of MNL-tSVD by incorporating it into a two-stage denoising strategy with a few adjustments. In addition, analysis of the relationship between MNL-tSVD and current the state-of-the-art 4-D transforms is given. Experimental comparisons over simulated and real brain data sets at different Rician noise levels show that MNL-tSVD can produce competitive performance compared with related approaches.

Beschreibung: Speaker diarization consists of assigning speech signals to people engaged in a dialogue. An audio-visual spatiotemporal diarization model is proposed. The model is well suited for challenging scenarios that consist of several participants engaged in multi-party interaction while they move around and turn their heads towards the other participants rather than facing the cameras and the microphones. Multiple-person visual tracking is combined with multiple speech-source localization in order to tackle the speech-to-person association problem. The latter is solved within a novel audio-visual fusion method on the following grounds: binaural spectral features are first extracted from a microphone pair, then a supervised audio-visual alignment technique maps these features onto an image, and finally a semi-supervised clustering method assigns binaural spectral features to visible persons. The main advantage of this method over previous work is that it processes in a principled way speech signals uttered simultaneously by multiple persons. The diarization itself is cast into a latent-variable temporal graphical model that infers speaker identities and speech turns, based on the output of an audio-visual association process, executed at each time slice, and on the dynamics of the diarization variable itself. The proposed formulation yields an efficient exact inference procedure. A novel dataset, that contains audio-visual training data as well as a number of scenarios involving several participants engaged in formal and informal dialogue, is introduced. The proposed method is thoroughly tested and benchmarked with respect to several state-of-the art diarization algorithms.

Beschreibung: The capabilities of (I) learning transferable knowledge across domains; and (II) fine-tuning the pre-learned base knowledge towards tasks with considerably smaller data scale are extremely important. Many of the existing transfer learning techniques are supervised approaches, among which deep learning has the demonstrated power of learning domain transferrable knowledge with large scale network trained on massive amounts of labeled data. However, in many biomedical tasks, both the data and the corresponding label can be very limited, where the unsupervised transfer learning capability is urgently needed. In this paper, we proposed a novel multi-scale convolutional sparse coding (MSCSC) method, that (I) automatically learns filter banks at different scales in a joint fashion with enforced scale-specificity of learned patterns; and (II) provides an unsupervised solution for learning transferable base knowledge and fine-tuning it towards target tasks. Extensive experimental evaluation of MSCSC demonstrates the effectiveness of the proposed MSCSC in both regular and transfer learning tasks in various biomedical domains.

Beschreibung: Learning visual representations from web data has recently attracted attention for object recognition. Previous studies have mainly focused on overcoming label noise and data bias and have shown promising results by learning directly from web data. However, we argue that it might be better to transfer knowledge from existing human labeling resources to improve performance at nearly no additional cost. In this paper, we propose a new semi-supervised method for learning via web data. Our method has the unique design of exploiting strong supervision, i.e., in addition to standard image-level labels, our method also utilizes detailed annotations including object bounding boxes and part landmarks. By transferring as much knowledge as possible from existing strongly supervised datasets to weakly supervised web images, our method can benefit from sophisticated object recognition algorithms and overcome several typical problems found in webly-supervised learning. We consider the problem of fine-grained visual categorization, in which existing training resources are scarce, as our main research objective. Comprehensive experimentation and extensive analysis demonstrate encouraging performance of the proposed approach, which, at the same time, delivers a new pipeline for fine-grained visual categorization that is likely to be highly effective for real-world applications.

Beschreibung: We are motivated by the need for a generic object proposal generation algorithm which achieves good balance between object detection recall, proposal localization quality and computational efficiency. We propose a novel object proposal algorithm, BING++ , which inherits the virtue of good computational efficiency of BING [1] but significantly improves its proposal localization quality. At high level we formulate the problem of object proposal generation from a novel probabilistic perspective, based on which our BING++ manages to improve the localization quality by employing edges and segments to estimate object boundaries and update the proposals sequentially. We propose learning the parameters efficiently by searching for approximate solutions in a quantized parameter space for complexity reduction. We demonstrate the generalization of BING++ with the same fixed parameters across different object classes and datasets. Empirically our BING++ can run at half speed of BING on CPU, but significantly improve the localization quality by 18.5 and 16.7 percent on both VOC2007 and Microhsoft COCO datasets, respectively. Compared with other state-of-the-art approaches, BING++ can achieve comparable performance, but run significantly faster.

Beschreibung: Recent years have witnessed the success of deep neural networks in dealing with a plenty of practical problems. Dropout has played an essential role in many successful deep neural networks, by inducing regularization in the model training. In this paper, we present a new regularized training approach: Shakeout. Instead of randomly discarding units as Dropout does at the training stage, Shakeout randomly chooses to enhance or reverse each unit's contribution to the next layer. This minor modification of Dropout has the statistical trait: the regularizer induced by Shakeout adaptively combines $L_{0}$ , $L_{1}$ and $L_{2}$ regularization terms. Our classification experiments with representative deep architectures on image datasets MNIST, CIFAR-10 and ImageNet show that Shakeout deals with over-fitting effectively and outperforms Dropout. We empirically demonstrate that Shakeout leads to sparser weights under both unsupervised and supervised settings. Shakeout also leads to the grouping effect of the input units in a layer. Considering the weights in reflecting the importance of connections, Shakeout is superior to Dropout, which is valuable for the deep model compression. Moreover, we demonstrate that Shakeout can effectively reduce the instability of the training process of the deep architecture.

Beschreibung: The goal of this paper is to perform 3D object detection in the context of autonomous driving. Our method aims at generating a set of high-quality 3D object proposals by exploiting stereo imagery. We formulate the problem as minimizing an energy function that encodes object size priors, placement of objects on the ground plane as well as several depth informed features that reason about free space, point cloud densities and distance to the ground. We then exploit a CNN on top of these proposals to perform object detection. In particular, we employ a convolutional neural net (CNN) that exploits context and depth information to jointly regress to 3D bounding box coordinates and object pose. Our experiments show significant performance gains over existing RGB and RGB-D object proposal methods on the challenging KITTI benchmark. When combined with the CNN, our approach outperforms all existing results in object detection and orientation estimation tasks for all three KITTI object classes. Furthermore, we experiment also with the setting where LIDAR information is available, and show that using both LIDAR and stereo leads to the best result.

Beschreibung: Phylogenetic tree reconciliation is an important technique for reconstructing the evolutionary histories of species and genes and other dependent entities. Reconciliation is typically performed in a maximum parsimony framework and the number of optimal reconciliations can grow exponentially with the size of the trees, making it difficult to understand the solution space. This paper demonstrates how a small number of reconciliations can be found that collectively contain the most highly supported events in the solution space. While we show that the formal problem is NP-complete, we give a $1-frac{1}{e}$ approximation algorithm, experimental results that indicate its effectiveness, and the new DTL-RnB software tool that uses our algorithms to summarize the space of optimal reconciliations ( www.cs.hmc.edu/dtlrnb ).

Beschreibung: We propose a methodology for model-based fault detection and diagnosis for stochastic Boolean dynamical systems indirectly observed through a single time series of transcriptomic measurements using Next Generation Sequencing (NGS) data. The fault detection consists of an innovations filter followed by a fault certification step, and requires no knowledge about the possible system faults. The innovations filter uses the optimal Boolean state estimator, called the Boolean Kalman Filter (BKF). In the presence of knowledge about the possible system faults, we propose an additional step of fault diagnosis based on a multiple model adaptive estimation (MMAE) method consisting of a bank of BKFs running in parallel. Performance is assessed by means of false detection and misdiagnosis rates, as well as average times until correct detection and diagnosis. The efficacy of the proposed methodology is demonstrated via numerical experiments using a p53-MDM2 negative feedback loop Boolean network with stuck-at faults that model molecular events commonly found in cancer.

Beschreibung: New de novo transcriptome assembly and annotation methods provide an incredible opportunity to study the transcriptome of organisms that lack an assembled and annotated genome. There are currently a number of de novo transcriptome assembly methods, but it has been difficult to evaluate the quality of these assemblies. In order to assess the quality of the transcriptome assemblies, we composed a workflow of multiple quality check measurements that in combination provide a clear evaluation of the assembly performance. We presented novel transcriptome assemblies and functional annotations for Pacific Whiteleg Shrimp ( Litopenaeus vannamei ), a mariculture species with great national and international interest, and no solid transcriptome/genome reference. We examined Pacific Whiteleg transcriptome assemblies via multiple metrics, and provide an improved gene annotation. Our investigations show that assessing the quality of an assembly purely based on the assembler's statistical measurements can be misleading; we propose a hybrid approach that consists of statistical quality checks and further biological-based evaluations.

Beschreibung: Hi-C technology, a chromosome conformation capture (3C) based method, has been developed to capture genome-wide interactions at a given resolution. The next challenge is to reconstruct 3D structure of genome from the 3C-derived data computationally. Several existing methods have been proposed to obtain a consensus structure or ensemble structures. These methods can be categorized as probabilistic models or restraint-based models. In this paper, we propose a method, named ShRec3D+, to infer a consensus 3D structure of a genome from Hi-C data. The method is a two-step algorithm which is based on ChromSDE and ShRec3D methods. First, correct the conversion factor by golden section search for converting interaction frequency data to a distance weighted graph. Second, apply shortest-path algorithm and multi-dimensional scaling (MDS) algorithm to compute the 3D coordinates of a set of genomic loci from the distance graph. We validate ShRec3D+ accuracy on both simulation data and publicly Hi-C data. Our test results indicate that our method successfully corrects the parameter with a given resolution, is more accurate than ShRec3D, and is more efficient and robust than ChromSDE.

Beschreibung: Determining gender by examining the human brain is not a simple task because the spatial structure of the human brain is complex, and no obvious differences can be seen by the naked eyes. In this paper, we propose a novel three-dimensional feature descriptor, the three-dimensional weighted histogram of gradient orientation (3D WHGO) to describe this complex spatial structure. The descriptor combines local information for signal intensity and global three-dimensional spatial information for the whole brain. We also improve a framework to address the classification of three-dimensional images based on MRI. This framework, three-dimensional spatial pyramid, uses additional information regarding the spatial relationship between features. The proposed method can be used to distinguish gender at the individual level. We examine our method by using the gender identification of individual magnetic resonance imaging (MRI) scans of a large sample of healthy adults across four research sites, resulting in up to individual-level accuracies under the optimized parameters for distinguishing between females and males. Compared with previous methods, the proposed method obtains higher accuracy, which suggests that this technology has higher discriminative power. With its improved performance in gender identification, the proposed method may have the potential to inform clinical practice and aid in research on neurological and psychiatric disorders.

Beschreibung: Ultra-high dimensional variable selection has become increasingly important in analysis of neuroimaging data. For example, in the Autism Brain Imaging Data Exchange (ABIDE) study, neuroscientists are interested in identifying important biomarkers for early detection of the autism spectrum disorder (ASD) using high resolution brain images that include hundreds of thousands voxels. However, most existing methods are not feasible for solving this problem due to their extensive computational costs. In this work, we propose a novel multiresolution variable selection procedure under a Bayesian probit regression framework. It recursively uses posterior samples for coarser-scale variable selection to guide the posterior inference on finer-scale variable selection, leading to very efficient Markov chain Monte Carlo (MCMC) algorithms. The proposed algorithms are computationally feasible for ultra-high dimensional data. Also, our model incorporates two levels of structural information into variable selection using Ising priors: the spatial dependence between voxels and the functional connectivity between anatomical brain regions. Applied to the resting state functional magnetic resonance imaging (R-fMRI) data in the ABIDE study, our methods identify voxel-level imaging biomarkers highly predictive of the ASD, which are biologically meaningful and interpretable. Extensive simulations also show that our methods achieve better performance in variable selection compared to existing methods.

Beschreibung: In systems neuroscience, it is becoming increasingly common to record the activity of hundreds of neurons simultaneously via electrode arrays. The ability to accurately measure the causal interactions among multiple neurons in the brain is crucial to understanding how neurons work in concert to generate specific brain functions. The development of new statistical methods for assessing causal influence between spike trains is still an active field of neuroscience research. Here, we suggest a copula-based Granger causality measure for the analysis of neural spike train data. This method is built upon our recent work on copula Granger causality for the analysis of continuous-valued time series by extending it to point-process neural spike train data. The proposed method is therefore able to reveal nonlinear and high-order causality in the spike trains while retaining all the computational advantages such as model-free, efficient estimation, and variability assessment of Granger causality. The performance of our algorithm can be further boosted with time-reversed data. Our method performed well on extensive simulations, and was then demonstrated on neural activity simultaneously recorded from primary visual cortex of a monkey performing a contour detection task.

Beschreibung: The focus of this paper is the frequent gene team problem. Given a quorum parameter μ and a set of m genomes, the problem is to find gene teams that occur in at least μ of the given genomes. In this paper, a new algorithm is presented. Previous solutions are efficient only when μ is small. Unlike previous solutions, the presented algorithm does not rely on examining every combination of μ genomes. Its time complexity is independent of μ. Under some realistic assumptions, the practical running time is estimated to be $O(m^{2}n^{2}; {mathrm{lg}};n)$ , where n is the maximum length of the input genomes. Experiments showed that the presented algorithm is extremely efficient. For any μ, it takes less than 1 second to process 100 bacterial genomes and takes only 10 minutes to process 2,000 genomes. The presented algorithm can be used as an effective tool for large scale genome analyses.

Beschreibung: In this era of genome-wide association studies (GWAS), the quest for understanding the genetic architecture of complex diseases is rapidly increasing more than ever before. The development of high throughput genotyping and next generation sequencing technologies enables genetic epidemiological analysis of large scale data. These advances have led to the identification of a number of single nucleotide polymorphisms (SNPs) responsible for disease susceptibility. The interactions between SNPs associated with complex diseases are increasingly being explored in the current literature. These interaction studies are mathematically challenging and computationally complex. These challenges have been addressed by a number of data mining and machine learning approaches. This paper reviews the current methods and the related software packages to detect the SNP interactions that contribute to diseases. The issues that need to be considered when developing these models are addressed in this review. The paper also reviews the achievements in data simulation to evaluate the performance of these models. Further, it discusses the future of SNP interaction analysis.

Beschreibung: Motifs in complex biological, technological, and social networks, or in other types of networks are connected to patterns that occur at significantly higher frequency compared to similar random networks. Finding motifs helps scientists to know more about networks’ structure and function, and this goal cannot be achieved without efficient algorithms. Existing methods for counting network motifs are extremely costly in CPU time and memory consumption. In addition, they restrict to the larger motifs. In this paper, a new algorithm called FraMo is presented based on ‘fractal theory’. This method consists of three phases: at first, a complex network is converted to a multifractal network. Then, using maximum likelihood estimation, distribution parameters is estimated for the multifractal network, and at last the approximate number of network motifs is calculated. Experimental results on several benchmark datasets show that our algorithm can efficiently approximate the number of motifs in any size in undirected networks and compare its performance favorably with similar existing algorithms in terms of CPU time and memory usage.

Beschreibung: Regions of interest (ROIs) based classification has been widely investigated for analysis of brain magnetic resonance imaging (MRI) images to assist the diagnosis of Alzheimer's disease (AD) including its early warning and developing stages, e.g., mild cognitive impairment (MCI) including MCI converted to AD (MCIc) and MCI not converted to AD (MCInc). Since an ROI representation of brain structures is obtained either by pre-definition or by adaptive parcellation, the corresponding ROI in different brains can be measured. However, due to noise and small sample size of MRI images, representations generated from single or multiple ROIs may not be sufficient to reveal the underlying anatomical differences between the groups of disease-affected patients and health controls (HC). In this paper, we employ a whole brain hierarchical network (WBHN) to represent each subject. The whole brain of each subject is divided into 90, 54, 14, and 1 regions based on Automated Anatomical Labeling (AAL) atlas. The connectivity between each pair of regions is computed in terms of Pearson's correlation coefficient and used as classification feature. Then, to reduce the dimensionality of features, we select the features with higher $F-$ scores. Finally, we use multiple kernel boosting (MKBoost) algorithm to perform the classification. Our proposed method is evaluated on MRI images of 710 subjects (200 AD, 120 MCIc, 160 MCInc, and 230 HC) from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. The experimental results show that our proposed method achieves an accuracy of 94.65 percent and an area under the receiver operating characteristic (ROC) curve (AUC) of 0.954 for AD/HC classification, an accuracy of 89.63 percent and an AUC of 0.907 for AD/MCI classification, an- accuracy of 85.79 percent and an AUC of 0.826 for MCI/HC classification, and an accuracy of 72.08 percent and an AUC of 0.716 for MCIc/MCInc classification, respectively. Our results demonstrate that our proposed method is efficient and promising for clinical applications for the diagnosis of AD via MRI images.

Beschreibung: Enumeration of chemical structures is useful for drug design, which is one of the main targets of computational biology and bioinformatics. A chemical graph $G$ with no other cycles than benzene rings is called tree-like , and becomes a tree $T$ possibly with multiple edges if we contract each benzene ring into a single virtual atom of valence 6. All tree-like chemical graphs with a given tree representation $T$ are called the substituted benzene isomers of $T$ . When we replace each virtual atom in $T$ with a benzene ring to obtain a substituted benzene isomer, distinct isomers of $T$ are caused by the difference in arrangements of atom groups around a benzene ring. In this paper, we propose an efficient algorithm that enumerates all substituted benzene isomers of a given tree representation $T$ . Our algorithm first counts the number

Beschreibung: Determining the dynamics of pathways associated with cancer progression is critical for understanding the etiology of diseases. Advances in biological technology have facilitated the simultaneous genomic profiling of multiple patients at different clinical stages, thus generating the dynamic genomic data for cancers. Such data provide enable investigation of the dynamics of related pathways. However, methods for integrative analysis of dynamic genomic data are inadequate. In this study, we develop a novel nonnegative matrix factorization algorithm for dynamic modules ( NMF-DM ), which simultaneously analyzes multiple networks for the identification of stage-specific and dynamic modules. NMF-DM applies the temporal smoothness framework by balancing the networks at the current stage and the previous stage. Experimental results indicate that the NMF-DM algorithm is more accurate than the state-of-the-art methods in artificial dynamic networks. In breast cancer networks, NMF-DM reveals the dynamic modules that are important for cancer stage transitions. Furthermore, the stage-specific and dynamic modules have distinct topological and biochemical properties. Finally, we demonstrate that the stage-specific modules significantly improve the accuracy of cancer stage prediction. The proposed algorithm provides an effective way to explore the time-dependent cancer genomic data.

Beschreibung: MicroRNAs (miRNAs) are known as an important indicator of cancers. The presence of cancer can be detected by identifying the responsible miRNAs. A fuzzy-rough entropy measure (FREM) is developed which can rank the miRNAs and thereby identify the relevant ones. FREM is used to determine the relevance of a miRNA in terms of separability between normal and cancer classes. While computing the FREM for a miRNA, fuzziness takes care of the overlapping between normal and cancer expressions, whereas rough lower approximation determines their class sizes. MiRNAs are sorted according to the highest relevance (i.e., the capability of class separation) and a percentage among them is selected from the top ranked ones. FREM is also used to determine the redundancy between two miRNAs and the redundant ones are removed from the selected set, as per the necessity. A histogram based patient selection method is also developed which can help to reduce the number of patients to be dealt during the computation of FREM, while compromising very little with the performance of the selected miRNAs for most of the data sets. The superiority of the FREM as compared to some existing methods is demonstrated extensively on six data sets in terms of sensitivity, specificity, and $F$ score. While for these data sets the $F$ score of the miRNAs selected by our method varies from 0.70 to 0.91 using SVM, those results vary from 0.37 to 0.90 for some other methods. Moreover, all the selected miRNAs corroborate with the findings of biological investigations or pathway analysis tools. The source code of FREM is available at http://www.jayanta.droppages.com/FREM.html .

Beschreibung: Identification of combinatorial markers from multiple data sources is a challenging task in bioinformatics. Here, we propose a novel computational framework for identifying significant combinatorial markers ( $SCM$ s) using both gene expression and methylation data. The gene expression and methylation data are integrated into a single continuous data as well as a (post-discretized) boolean data based on their intrinsic (i.e., inverse) relationship. A novel combined score of methylation and expression data (viz., $CoMEx$ ) is introduced which is computed on the integrated continuous data for identifying initial non-redundant set of genes. Thereafter, (maximal) frequent closed homogeneous genesets are identified using a well-known biclustering algorithm applied on the integrated boolean data of the determined non-redundant set of genes. A novel sample-based weighted support ( $WS$ ) is then proposed that is consecutively calculated on the integrated boolean data of the determined non-redundant set of genes in order to identify the non-redundant significant genesets. The top few resulting genesets are identified as potential $SCM$ s. Since our proposed method generates a smaller number of significant non-redundant genesets than those by other popular methods, the method is much faster than the others. Application of the proposed techniq- e on an expression and a methylation data for Uterine tumor or Prostate Carcinoma produces a set of significant combination of markers. We expect that such a combination of markers will produce lower false positives than individual markers.

Beschreibung: The challenges of assessing alcohol consumption can be greater in Indigenous communities where there may be culturally distinct approaches to communication, sharing of drinking containers and episodic patterns...

Beschreibung: In this paper, we seek to improve deep neural networks by generalizing the pooling operations that play a central role in the current architectures. We pursue a careful exploration of approaches to allow pooling to learn and to adapt to complex and variable patterns. The two primary directions lie in: (1) learning a pooling function via (two strategies of) combining of max and average pooling, and (2) learning a pooling function in the form of a tree-structured fusion of pooling filters that are themselves learned. In our experiments every generalized pooling operation we explore improves performance when used in place of average or max pooling. We experimentally demonstrate that the proposed pooling operations provide a boost in invariance properties relative to conventional pooling and set the state of the art on several widely adopted benchmark datasets. These benefits come with only a light increase in computational overhead during training (ranging from additional 5 to 15 percent in time complexity) and a very modest increase in the number of model parameters (e.g., additional 1, 9, and 27 parameters for mixed, gated, and 2-level tree pooling operators, respectively). To gain more insights about our proposed pooling methods, we also visualize the learned pooling masks and the embeddings of the internal feature responses for different pooling operations. Our proposed pooling operations are easy to implement and can be applied within various deep neural network architectures.

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Beschreibung: Prospective authors are requested to submit new, unpublished manuscripts for inclusion in the upcoming event described in this call for papers.

Beschreibung: The Lombardy Aerospace Industry Cluster [1] was founded in Italy in 2014 as the final step in constructing a representative institution for the regional system of aerospace industries. The process was initiated in 2009 with the first formal contacts between the local industry federation and the regional government of Lombardy, which led to the foundation of a provisional body (Distretto Aerospaziale Lombardo) in preparation for a more formalized industry cluster to come and in light of a mandate to represent the local aerospace industry politically.

Beschreibung: Hyperspectral imagery contains hundreds of contiguous bands with a wealth of spectral signatures, making it possible to distinguish materials through subtle spectral discrepancies. Because these spectral bands are highly correlated, dimensionality reduction, as the name suggests, seeks to reduce data dimensionality without losing desirable information. This article reviews discriminant analysisbased dimensionality-reduction approaches for hyperspectral imagery, including typical linear discriminant analysis (LDA), state-of-the-art sparse graph-based discriminant analysis (SGDA), and their extensions.

Beschreibung: Presents the introductory editorial for this issue of the publication.

Beschreibung: Describes the above-named upcoming conference event. May include topics to be covered or calls for papers.

Beschreibung: Graph algorithm is pervasive in many applications ranging from targeted advertising to natural language processing. Recently, Asynchronous Graph Processing (AGP) is becoming a promising model to support graph algorithm on large-scale distributed computing platforms because it enables faster convergence speed and lower synchronization cost than the synchronous model for no barrier between iterations. However, existing AGP methods still suffer from poor performance for inefficient vertex state propagation. In this paper, we propose an effective and low-cost forward and backward sweeping execution method to accelerate state propagation for AGP, based on a key observation that states in AGP can be propagated between vertices much faster when the vertices are processed sequentially along the graph path within each round. Through dividing graph into paths and asynchronously processing vertices on each path in an alternative forward and backward way according to their order on this path, vertex states in our approach can be quickly propagated to other vertices and converge in a faster way with only little additional overhead. In order to efficiently support it over distributed platforms, we also propose a scheme to reduce the communication overhead along with a static priority ordering scheme to further improve the convergence speed. Experimental results on a cluster with 1,024 cores show that our approach achieves excellent scalability for large-scale graph algorithms and the overall execution time is reduced by at least 39.8 percent, in comparison with the most cutting-edge methods.

Beschreibung: Deal selection on Groupon is a typical social learning and decision making process, where the quality of a deal is usually unknown to the customers. The customers must acquire this knowledge through social learning from other social medias such as reviews on Yelp. Additionally, the quality of a deal depends on both the state of the vendor and decisions of other customers on Groupon. How social learning and network externality affect the decisions of customers in deal selection on Groupon is our main interest. We develop a data-driven game-theoretic framework to understand the rational deal selection behaviors cross social medias. The sufficient condition of the Nash equilibrium is identified. A value-iteration algorithm is proposed to find the optimal deal selection strategy. We conduct a year-long experiment to trace the competitions among deals on Groupon and the corresponding Yelp ratings. We utilize the dataset to analyze the deal selection game with realistic settings. Finally, the performance of the proposed social learning framework is evaluated with real data. The results suggest that customers do make decisions in a rational way instead of following naive strategies, and there is still room to improve their decisions with assistance from the proposed framework.

Beschreibung: Recent advances in imaging genetics produce large amounts of data including functional MRI images, single nucleotide polymorphisms (SNPs), and cognitive assessments. Understanding the complex interactions among these heterogeneous and complementary data has the potential to help with diagnosis and prevention of mental disorders. However, limited efforts have been made due to the high dimensionality, group structure, and mixed type of these data. In this paper, we present a novel method to detect conditional associations between imaging genetics data. We use projected distance correlation to build a conditional dependency graph among high-dimensional mixed data, and then use multiple testing to detect significant group level associations (e.g., regions of interest-gene). In addition, we introduce a scalable algorithm based on orthogonal greedy algorithm, yielding the greedy projected distance correlation (G-PDC). This can reduce the computational cost, which is critical for analyzing large volume of imaging genomics data. The results from our simulations demonstrate a higher degree of accuracy with G-PDC than distance correlation, Pearson’s correlation, and partial correlation, especially when the correlation is nonlinear. Finally, we apply our method to the Philadelphia Neurodevelopmental data cohort with 866 samples including fMRI images and SNP profiles. The results uncover several statistically significant and biologically interesting interactions, which are further validated with many existing studies. The MATLAB code is available at https://sites.google.com/site/jianfang86/gPDC .

Beschreibung: We present a multi-scale approach of tumor modeling in order to predict its evolution during radiotherapy. Within this context we focus on three different scales of tumor modeling: microscopic (individual cells in a voxel), mesoscopic (population of cells in a voxel) and macroscopic (whole tumor), with transition interfaces between these three scales. At the cellular level, the description is based on phase transfer probabilities in the cellular cycle. At the mesoscopic scale we represent populations of cells according to different stages in a cell cycle. Finally, at the macroscopic scale, the tumor description is based on the use of FDG PET image voxels. These three scales exist naturally: biological data are collected at the macroscopic scale, but the pathological behavior of the tumor is based on an abnormal cell-cycle at the microscopic scale. On the other hand, the introduction of a mesoscopic scale is essential in order to reduce the gap between the two extreme, in terms of resolution, description levels. It also reduces the computational burden of simulating a large number of individual cells. As an application of the proposed multi-scale model, we simulate the effect of oxygen on tumor evolution during radiotherapy. Two consecutive FDG PET images of 17 rectal cancer patients undergoing radiotherapy are used to simulate the tumor evolution during treatment. The simulated results are compared with those obtained on a third FDG PET image acquired two weeks after the beginning of the treatment.

Beschreibung: In this paper, we investigate the estimation of the maximum target registration error (TRE) magnitude of the target location while using point-based rigid registration in the image guided system. Under the uniform restriction of fiducial localization error (FLE) magnitude, we explicitly formulate the estimation as an optimization problem. Through analyzing the approximated problem which assumes the rigidity of the fiducial set holds with the perturbation of FLE, we present a strict lower bound for the maximum TRE magnitude. The simulations show that the lower bound is close to the actual maximum TRE magnitude for the target locations lying far away from the fiducial points. Unlike the expected TRE magnitude in which all fiducial points contribute, the lower bound is only related to the fiducial points serving as the vertices of the convex hull of the fiducial set. Our analysis provides a new perspective of investigating the problem of TRE estimation and is helpful for the surgeons to learn about the worst situation during using the image guided system.

Beschreibung: Brain tumors are the most common malignant neurologic tumors with the highest mortality and disability rate. Because of the delicate structure of the brain, the clinical use of several commonly used biopsy diagnosis is limited for brain tumors. Radiomics is an emerging technique for noninvasive diagnosis based on quantitative medical image analyses. However, current radiomics techniques are not standardized regarding feature extraction, feature selection, and decision making. In this paper, we propose a sparse representation-based radiomics (SRR) system for the diagnosis of brain tumors. First, we developed a dictionary learning- and sparse representation-based feature extraction method that exploits the statistical characteristics of the lesion area, leading to fine and more effective feature extraction compared with the traditional explicitly calculation-based methods. Then, we set up an iterative sparse representation method to solve the redundancy problem of the extracted features. Finally, we proposed a novel multi-feature collaborative sparse representation classification framework that introduces a new coefficient of regularization term to combine features from multi-modal images at the sparse representation coefficient level. Two clinical problems were used to validate the performance and usefulness of the proposed SRR system. One was the differential diagnosis between primary central nervous system lymphoma (PCNSL) and glioblastoma (GBM), and the other was isocitrate dehydrogenase 1 estimation for gliomas. The SRR system had superior PCNSL and GBM differentiation performance compared with some advanced imaging techniques and yielded 11% better performance for estimating IDH1 compared with the traditional radiomics methods.

Beschreibung: We present the first in vivo images of anisotropic conductivity distribution in the human head, measured at a frequency of approximately 10 Hz. We used magnetic resonance electrical impedance tomography techniques to encode phase changes caused by current flow within the head via two independent electrode pairs. These results were then combined with diffusion tensor imaging data to reconstruct full anisotropic conductivity distributions in 5-mm-thick slices of the brains of two participants. Conductivity values recovered in this paper were broadly consistent with literature values. We anticipate that this technique will be of use in many areas of neuroscience, most importantly in functional imaging via inverse electroencephalogram. Future studies will involve pulse sequence acceleration to maximize brain coverage and resolution.

Beschreibung: The most commonly used evaluation metrics for quality assessment of retinal vessel segmentation are sensitivity, specificity, and accuracy, which are based on pixel-to-pixel matching. However, due to the inter-observer problem that vessels annotated by different observers vary in both thickness and location, pixel-to-pixel matching is too restrictive to fairly evaluate the results of vessel segmentation. In this paper, the proposed skeletal similarity metric is constructed by comparing the skeleton maps generated from the reference and the source vessel segmentation maps. To address the inter-observer problem, instead of using a pixel-to-pixel matching strategy, each skeleton segment in the reference skeleton map is adaptively assigned with a searching range whose radius is determined based on its vessel thickness. Pixels in the source skeleton map located within the searching range are then selected for similarity calculation. The skeletal similarity consists of a curve similarity, which measures the structural similarity between the reference and the source skeleton maps and a thickness similarity, which measures the thickness consistency between the reference and the source vessel segmentation maps. In contrast to other metrics that provide a global score for the overall performance, we modify the definitions of true positive, false negative, true negative, and false positive based on the skeletal similarity, based on which sensitivity, specificity, accuracy, and other objective measurements can be constructed. More importantly, the skeletal similarity metric has better potential to be used as a pixelwise loss function for training deep learning models for retinal vessel segmentation. Through comparison of a set of examples, we demonstrate that the redefined metrics based on the skeletal similarity are more effective for quality evaluation, especially with greater tolerance to the inter-observer problem.

Beschreibung: We are developing a 1-mm 3 resolution, high-sensitivity positron emission tomography (PET) system for loco-regional cancer imaging. The completed system will comprise two $16.5times 10$ cm detector panels and contain 4 608 position sensitive avalanche photodiodes (PSAPDs) coupled to arrays of $0.9times 0.9times 1$ mm 3 LYSO crystal elements for a total of 294 912 crystal elements. For the first time, this paper summarizes the design and reports the performance of a significant portion of the final clinical PET system, comprising 1 536 PSAPDs, 98 304 crystal elements, and an active field-of-view (FOV) of $16.5times3.3$ cm. The sub-system performance parameters, such as energy, time, and spatial resolutions are predictive of the performance of the final system due to the modular design. Analysis of the multiplexed crystal flood histograms shows 84% of the crystal elements have〉99% crystal identification accuracy. The 511 keV photopeak energy resolution was 11.34±0.06% full-width half maximum (FWHM), and coincidence timing resolution was 13.92 ± 0.01 ns FWHM at 511 keV. The spatial resolution was measured using maximum likelihood expectation maximization reconstruction of a grid of point sources suspended in warm background. The averaged resolution over the central 6 cm of the FOV is 1.01 ± 0.13 mm in the X-direction, 1.84 ± 0.20 mm in the Y-direction, and 0.84 ± 0.11 mm in the Z-direction. Quantitative analysis of acquired micro-Derenzo phantom images shows better than 1.2 mm resolution at the center of the FOV, with subsequent resolution degradation in the y-direction toward the edge of the FOV caused by limited angle tomography effec- s.

Beschreibung: We consider the challenges in estimating the state-related changes in brain connectivity networks with a large number of nodes. Existing studies use the sliding-window analysis or time-varying coefficient models, which are unable to capture both smooth and abrupt changes simultaneously, and rely on ad-hoc approaches to the high-dimensional estimation. To overcome these limitations, we propose a Markov-switching dynamic factor model, which allows the dynamic connectivity states in functional magnetic resonance imaging (fMRI) data to be driven by lower-dimensional latent factors. We specify a regime-switching vector autoregressive (SVAR) factor process to quantity the time-varying directed connectivity. The model enables a reliable, data-adaptive estimation of change-points of connectivity regimes and the massive dependencies associated with each regime. We develop a three-step estimation procedure: 1) extracting the factors using principal component analysis, 2) identifying connectivity regimes in a low-dimensional subspace based on the factor-based SVAR model, and 3) constructing high-dimensional state connectivity metrics based on the subspace estimates. Simulation results show that our estimator outperforms $K$ -means clustering of time-windowed coefficients, providing more accurate estimate of time-evolving connectivity. It achieves percentage of reduction in mean squared error by 60% when the network dimension is comparable to the sample size. When applied to the resting-state fMRI data, our method successfully identifies modular organization in the resting-statenetworksin consistencywith other studies. It further reveals changes in brain states with variations across subjects and distinct large-scale directed connectivity patterns across states.

Beschreibung: This paper reports on the feasibility of using a quasi-Newton optimization algorithm, limited-memory Broyden-Fletcher-Goldfarb-Shanno with boundary constraints (L-BFGS-B), for penalized image reconstruction problems in emission tomography (ET). For further acceleration, an additional preconditioning technique based on a diagonal approximation of the Hessian was introduced. The convergence rate of L-BFGS-B and the proposed preconditioned algorithm (L-BFGS-B-PC) was evaluated with simulated data with various factors, such as the noise level, penalty type, penalty strength and background level. Data of three 18 F-FDG patient acquisitions were also reconstructed. Results showed that the proposed L-BFGS-B-PC outperforms L-BFGS-B in convergence rate for all simulated conditions and the patient data. Based on these results, L-BFGS-B-PC shows promise for clinical application.

Beschreibung: Attenuation correction for positron-emission tomography (PET)/magnetic resonance (MR) hybrid imaging systems and dose planning for MR-based radiation therapy remain challenging due to insufficient high-energy photon attenuation information. We present a novel approach that uses the learned nonlinear local descriptors and feature matching to predict pseudo computed tomography (pCT) images from T1-weighted and T2-weighted magnetic resonance imaging (MRI) data. The nonlinear local descriptors are obtained by projecting the linear descriptors into the nonlinear high-dimensional space using an explicit feature map and low-rank approximation with supervised manifold regularization. The nearest neighbors of each local descriptor in the input MR images are searched in a constrained spatial range of the MR images among the training dataset. Then the pCT patches are estimated through k-nearest neighbor regression. The proposed method for pCT prediction is quantitatively analyzed on a dataset consisting of paired brain MRI and CT images from 13 subjects. Our method generates pCT images with a mean absolute error (MAE) of 75.25 ± 18.05 Hounsfield units, a peak signal-to-noise ratio of 30.87 ± 1.15 dB, a relative MAE of 1.56 ± 0.5% in PET attenuation correction, and a dose relative structure volume difference of 0.055 ± 0.107% in ${D}_{98%}$ , as compared with true CT. The experimental results also show that our method outperforms four state-of-the-art methods.

Beschreibung: Various perceptual domains have underlying compositional semantics that are rarely captured in current models. We suspect this is because directly learning the compositional structure has evaded these models. Yet, the compositional structure of a given domain can be grounded in a separate domain thereby simplifying its learning. To that end, we propose a new approach to modeling bimodal perceptual domains that explicitly relates distinct projections across each modality and then jointly learns a bimodal sparse representation. The resulting model enables compositionality across these distinct projections and hence can generalize to unobserved percepts spanned by this compositional basis. For example, our model can be trained on red triangles and blue squares ; yet, implicitly will also have learned red squares and blue triangles . The structure of the projections and hence the compositional basis is learned automatically; no assumption is made on the ordering of the compositional elements in either modality. Although our modeling paradigm is general, we explicitly focus on a tabletop building-blocks setting. To test our model, we have acquired a new bimodal dataset comprising images and spoken utterances of colored shapes (blocks) in the tabletop setting. Our experiments demonstrate the benefits of explicitly leveraging compositionality in both quantitative and human evaluation studies.

Beschreibung: Robust and effective shape prior modeling from a set of training data remains a challenging task, since the shape variation is complicated, and shape models should preserve local details as well as handle shape noises. To address these challenges, a novel robust projective dictionary learning (RPDL) scheme is proposed in this paper. Specifically, the RPDL method integrates the dimension reduction and dictionary learning into a unified framework for shape prior modeling, which can not only learn a robust and representative dictionary with the energy preservation of the training data, but also reduce the dimensionality and computational cost via the subspace learning. In addition, the proposed RPDL algorithm is regularized by using the $ell _{1}$ norm to handle the outliers and noises, and is embedded in an online framework so that of memory and time efficiency. The proposed method is employed to model prostate shape prior for the application of magnetic resonance transrectal ultrasound registration. The experimental results demonstrate that our method provides more accurate and robust shape modeling than the state-of-the-art methods do. The proposed RPDL method is applicable for modeling other organs, and hence, a general solution for the problem of shape prior modeling.

Beschreibung: Building upon recent Deep Neural Network architectures, current approaches lying in the intersection of Computer Vision and Natural Language Processing have achieved unprecedented breakthroughs in tasks like automatic captioning or image retrieval. Most of these learning methods, though, rely on large training sets of images associated with human annotations that specifically describe the visual content. In this paper we propose to go a step further and explore the more complex cases where textual descriptions are loosely related to the images. We focus on the particular domain of news articles in which the textual content often expresses connotative and ambiguous relations that are only suggested but not directly inferred from images. We introduce an adaptive CNN architecture that shares most of the structure for multiple tasks including source detection, article illustration and geolocation of articles. Deep Canonical Correlation Analysis is deployed for article illustration, and a new loss function based on Great Circle Distance is proposed for geolocation. Furthermore, we present BreakingNews, a novel dataset with approximately 100K news articles including images, text and captions, and enriched with heterogeneous meta-data (such as GPS coordinates and user comments). We show this dataset to be appropriate to explore all aforementioned problems, for which we provide a baseline performance using various Deep Learning architectures, and different representations of the textual and visual features. We report very promising results and bring to light several limitations of current state-of-the-art in this kind of domain, which we hope will help spur progress in the field.

Beschreibung: Machine learning algorithms for the analysis of time-series often depend on the assumption that utilised data are temporally aligned. Any temporal discrepancies arising in the data is certain to lead to ill-generalisable models, which in turn fail to correctly capture properties of the task at hand. The temporal alignment of time-series is thus a crucial challenge manifesting in a multitude of applications. Nevertheless, the vast majority of algorithms oriented towards temporal alignment are either applied directly on the observation space or simply utilise linear projections-thus failing to capture complex, hierarchical non-linear representations that may prove beneficial, especially when dealing with multi-modal data (e.g., visual and acoustic information). To this end, we present Deep Canonical Time Warping (DCTW), a method that automatically learns non-linear representations of multiple time-series that are (i) maximally correlated in a shared subspace, and (ii) temporally aligned. Furthermore, we extend DCTW to a supervised setting, where during training, available labels can be utilised towards enhancing the alignment process. By means of experiments on four datasets, we show that the representations learnt significantly outperform state-of-the-art methods in temporal alignment, elegantly handling scenarios with heterogeneous feature sets, such as the temporal alignment of acoustic and visual information.

Beschreibung: Domain adaptation between diverse source and target domains is challenging, especially in the real-world visual recognition tasks where the images and videos consist of significant variations in viewpoints, illuminations, qualities, etc. In this paper, we propose a new approach for domain generalization and domain adaptation based on exemplar SVMs. Specifically, we decompose the source domain into many subdomains, each of which contains only one positive training sample and all negative samples. Each subdomain is relatively less diverse, and is expected to have a simpler distribution. By training one exemplar SVM for each subdomain, we obtain a set of exemplar SVMs. To further exploit the inherent structure of source domain, we introduce a nuclear-norm based regularizer into the objective function in order to enforce the exemplar SVMs to produce a low-rank output on training samples. In the prediction process, the confident exemplar SVM classifiers are selected and reweigted according to the distribution mismatch between each subdomain and the test sample in the target domain. We formulate our approach based on the logistic regression and least square SVM algorithms, which are referred to as low rank exemplar SVMs (LRE-SVMs) and low rank exemplar least square SVMs (LRE-LSSVMs), respectively. A fast algorithm is also developed for accelerating the training of LRE-LSSVMs. We further extend Domain Adaptation Machine (DAM) to learn an optimal target classifier for domain adaptation, and show that our approach can also be applied to domain adaptation with evolving target domain, where the target data distribution is gradually changing. The comprehensive experiments for object recognition and action recognition demonstrate the effectiveness of our approach for domain generalization and domain adaptation with fixed and evolving target domains.

Beschreibung: In content-based image retrieval, SIFT feature and the feature from deep convolutional neural network (CNN) have demonstrated promising performance. To fully explore both visual features in a unified framework for effective and efficient retrieval, we propose a collaborative index embedding method to implicitly integrate the index matrices of them. We formulate the index embedding as an optimization problem from the perspective of neighborhood sharing and solve it with an alternating index update scheme. After the iterative embedding, only the embedded CNN index is kept for on-line query, which demonstrates significant gain in retrieval accuracy, with very economical memory cost. Extensive experiments have been conducted on the public datasets with million-scale distractor images. The experimental results reveal that, compared with the recent state-of-the-art retrieval algorithms, our approach achieves competitive accuracy performance with less memory overhead and efficient query computation.

Beschreibung: In this paper, we propose a context-aware local binary feature learning (CA-LBFL) method for face recognition. Unlike existing learning-based local face descriptors such as discriminant face descriptor (DFD) and compact binary face descriptor (CBFD) which learn each feature code individually, our CA-LBFL exploits the contextual information of adjacent bits by constraining the number of shifts from different binary bits, so that more robust information can be exploited for face representation. Given a face image, we first extract pixel difference vectors (PDV) in local patches, and learn a discriminative mapping in an unsupervised manner to project each pixel difference vector into a context-aware binary vector. Then, we perform clustering on the learned binary codes to construct a codebook, and extract a histogram feature for each face image with the learned codebook as the final representation. In order to exploit local information from different scales, we propose a context-aware local binary multi-scale feature learning (CA-LBMFL) method to jointly learn multiple projection matrices for face representation. To make the proposed methods applicable for heterogeneous face recognition, we present a coupled CA-LBFL (C-CA-LBFL) method and a coupled CA-LBMFL (C-CA-LBMFL) method to reduce the modality gap of corresponding heterogeneous faces in the feature level, respectively. Extensive experimental results on four widely used face datasets clearly show that our methods outperform most state-of-the-art face descriptors.

Beschreibung: Single modality action recognition on RGB or depth sequences has been extensively explored recently. It is generally accepted that each of these two modalities has different strengths and limitations for the task of action recognition. Therefore, analysis of the RGB+D videos can help us to better study the complementary properties of these two types of modalities and achieve higher levels of performance. In this paper, we propose a new deep autoencoder based shared-specific feature factorization network to separate input multimodal signals into a hierarchy of components. Further, based on the structure of the features, a structured sparsity learning machine is proposed which utilizes mixed norms to apply regularization within components and group selection between them for better classification performance. Our experimental results show the effectiveness of our cross-modality feature analysis framework by achieving state-of-the-art accuracy for action classification on five challenging benchmark datasets.

Beschreibung: Recently, cross-modal search has attracted considerable attention but remains a very challenging task because of the integration complexity and heterogeneity of the multi-modal data. To address both challenges, in this paper, we propose a novel method termed hetero-manifold regularisation (HMR) to supervise the learning of hash functions for efficient cross-modal search. A hetero-manifold integrates multiple sub-manifolds defined by homogeneous data with the help of cross-modal supervision information. Taking advantages of the hetero-manifold, the similarity between each pair of heterogeneous data could be naturally measured by three order random walks on this hetero-manifold. Furthermore, a novel cumulative distance inequality defined on the hetero-manifold is introduced to avoid the computational difficulty induced by the discreteness of hash codes. By using the inequality, cross-modal hashing is transformed into a problem of hetero-manifold regularised support vector learning. Therefore, the performance of cross-modal search can be significantly improved by seamlessly combining the integrated information of the hetero-manifold and the strong generalisation of the support vector machine. Comprehensive experiments show that the proposed HMR achieve advantageous results over the state-of-the-art methods in several challenging cross-modal tasks.

Beschreibung: We propose Multi-Task Learning with Low Rank Attribute Embedding (MTL-LORAE) to address the problem of person re-identification on multi-cameras. Re-identifications on different cameras are considered as related tasks, which allows the shared information among different tasks to be explored to improve the re-identification accuracy. The MTL-LORAE framework integrates low-level features with mid-level attributes as the descriptions for persons. To improve the accuracy of such description, we introduce the low-rank attribute embedding, which maps original binary attributes into a continuous space utilizing the correlative relationship between each pair of attributes. In this way, inaccurate attributes are rectified and missing attributes are recovered. The resulting objective function is constructed with an attribute embedding error and a quadratic loss concerning class labels. It is solved by an alternating optimization strategy. The proposed MTL-LORAE is tested on four datasets and is validated to outperform the existing methods with significant margins.

Beschreibung: In the early days, content-based image retrieval (CBIR) was studied with global features. Since 2003, image retrieval based on local descriptors ( de facto SIFT) has been extensively studied for over a decade due to the advantage of SIFT in dealing with image transformations. Recently, image representations based on the convolutional neural network (CNN) have attracted increasing interest in the community and demonstrated impressive performance. Given this time of rapid evolution, this article provides a comprehensive survey of instance retrieval over the last decade. Two broad categories, SIFT-based and CNN-based methods, are presented. For the former, according to the codebook size, we organize the literature into using large/medium-sized/small codebooks. For the latter, we discuss three lines of methods, i.e., using pre-trained or fine-tuned CNN models, and hybrid methods. The first two perform a single-pass of an image to the network, while the last category employs a patch-based feature extraction scheme. This survey presents milestones in modern instance retrieval, reviews a broad selection of previous works in different categories, and provides insights on the connection between SIFT and CNN-based methods. After analyzing and comparing retrieval performance of different categories on several datasets, we discuss promising directions towards generic and specialized instance retrieval.

Beschreibung: This paper proposes a method for line segment detection in digital images. We propose a novel linelet-based representation to model intrinsic properties of line segments in rasterized image space. Based on this, line segment detection, validation, and aggregation frameworks are constructed. For a numerical evaluation on real images, we propose a new benchmark dataset of real images with annotated lines called YorkUrban-LineSegment. The results show that the proposed method outperforms state-of-the-art methods numerically and visually. To our best knowledge, this is the first report of numerical evaluation of line segment detection on real images.

Beschreibung: This paper introduces a fast and efficient segmentation technique for 2D images and 3D point clouds of building facades. Facades of buildings are highly structured and consequently most methods that have been proposed for this problem aim to make use of this strong prior information. Contrary to most prior work, we are describing a system that is almost domain independent and consists of standard segmentation methods. We train a sequence of boosted decision trees using auto-context features. This is learned using stacked generalization. We find that this technique performs better, or comparable with all previous published methods and present empirical results on all available 2D and 3D facade benchmark datasets. The proposed method is simple to implement, easy to extend, and very efficient at test-time inference.

Beschreibung: A minimum hybridization network is a rooted phylogenetic network that displays two given rooted phylogenetic trees using a minimum number of reticulations. Previous mathematical work on their calculation has usually assumed the input trees to be bifurcating, correctly rooted, or that they both contain the same taxa. These assumptions do not hold in biological studies and “realistic” trees have multifurcations, are difficult to root, and rarely contain the same taxa. We present a new algorithm for computing minimum hybridization networks for a given pair of “realistic” rooted phylogenetic trees. We also describe how the algorithm might be used to improve the rooting of the input trees. We introduce the concept of “autumn trees”, a nice framework for the formulation of algorithms based on the mathematics of “maximum acyclic agreement forests”. While the main computational problem is hard, the run-time depends mainly on how different the given input trees are. In biological studies, where the trees are reasonably similar, our parallel implementation performs well in practice. The algorithm is available in our open source program Dendroscope 3, providing a platform for biologists to explore rooted phylogenetic networks. We demonstrate the utility of the algorithm using several previously studied data sets.

Beschreibung: The human colorectal carcinoma cell line (Caco-2) is a commonly used in-vitro test that predicts the absorption potential of orally administered drugs. In-silico prediction methods, based on the Caco-2 assay data, may increase the effectiveness of the high-throughput screening of new drug candidates. However, previously developed in-silico models that predict the Caco-2 cellular permeability of chemical compounds use handcrafted features that may be dataset-specific and induce over-fitting problems. Deep Neural Network (DNN) generates high-level features based on non-linear transformations for raw features, which provides high discriminant power and, therefore, creates a good generalized model. We present a DNN-based binary Caco-2 permeability classifier. Our model was constructed based on 663 chemical compounds with in-vitro Caco-2 apparent permeability data. Two hundred nine molecular descriptors are used for generating the high-level features during DNN model generation. Dropout regularization is applied to solve the over-fitting problem and the non-linear activation. The Rectified Linear Unit (ReLU) is adopted to reduce the vanishing gradient problem. The results demonstrate that the high-level features generated by the DNN are more robust than handcrafted features for predicting the cellular permeability of structurally diverse chemical compounds in Caco-2 cell lines.

Beschreibung: Read trimming is a fundamental first step of the analysis of next generation sequencing (NGS) data. Traditionally, it is performed heuristically, and algorithmic work in this area has been neglected. Here, we address this topic and formulate three optimization problems for block-based trimming (truncating the same low-quality positions at both ends for all reads and removing low-quality truncated reads). We find that all problems are NP-hard. Hence, we investigate the approximability of the problems. Two of them are NP-hard to approximate. However, the non-random distribution of quality scores in NGS data sets makes it tempting to speculate that quality constraints for read positions are typically satisfied by fulfilling quality constraints for reads. Thus, we propose three relaxed problems and develop efficient polynomial-time algorithms for them including heuristic speed-up techniques and parallelizations. We apply these optimized block trimming algorithms to 12 data sets from three species, four sequencers, and read lengths ranging from 36 to 101 bp and find that (i) the omitted constraints are indeed almost always satisfied, (ii) the optimized read trimming algorithms typically yield a higher number of untrimmed bases than traditional heuristics, and (iii) these results can be generalized to alternative objective functions beyond counting the number of untrimmed bases.

Beschreibung: Advances in de novo synthesis of DNA and computational gene design methods make possible the customization of genes by direct manipulation of features such as codon bias and mRNA secondary structure. Codon context is another feature significantly affecting mRNA translational efficiency, but existing methods and tools for evaluating and designing novel optimized protein coding sequences utilize untested heuristics and do not provide quantifiable guarantees on design quality. In this study we examine statistical properties of codon context measures in an effort to better understand the phenomenon. We analyze the computational complexity of codon context optimization and design exact and efficient heuristic gene recoding algorithms under reasonable constraint models. We also present a web-based tool for evaluating codon context bias in the appropriate context.

Beschreibung: To assess the genetic diversity of an environmental sample in metagenomics studies, the amplicon sequences of 16s rRNA genes need to be clustered into operational taxonomic units (OTUs). Many existing tools for OTU clustering trade off between accuracy and computational efficiency. We propose a novel OTU clustering algorithm, hc-OTU, which achieves high accuracy and fast runtime by exploiting homopolymer compaction and k-mer profiling to significantly reduce the computing time for pairwise distances of amplicon sequences. We compare the proposed method with other widely used methods, including UCLUST, CD-HIT, MOTHUR, ESPRIT, ESPRIT-TREE, and CLUSTOM, comprehensively, using nine different experimental datasets and many evaluation metrics, such as normalized mutual information, adjusted Rand index, measure of concordance, and F-score. Our evaluation reveals that the proposed method achieves a level of accuracy comparable to the respective accuracy levels of MOTHUR and ESPRIT-TREE, two widely used OTU clustering methods, while delivering orders-of-magnitude speedups.

Beschreibung: Recent studies have suggested abnormal brain network organization in subjects with Autism Spectrum Disorders (ASD). Here we applied spectral clustering algorithm, diverse centrality measures (betweenness (BC), clustering (CC), eigenvector (EC), and degree (DC)), and also the network entropy (NE) to identify brain sub-systems associated with ASD. We have found that BC increases in the following ASD clusters: in the somatomotor, default-mode, cerebellar, and fronto-parietal. On the other hand, CC, EC, and DC decrease in the somatomotor, default-mode, and cerebellar clusters. Additionally, NE decreases in ASD in the cerebellar cluster. These findings reinforce the hypothesis of under-connectivity in ASD and suggest that the difference in the network organization is more prominent in the cerebellar system. The cerebellar cluster presents reduced NE in ASD, which relates to a more regular organization of the networks. These results might be important to improve current understanding about the etiological processes and the development of potential tools supporting diagnosis and therapeutic interventions.