Fold Recognition via a Tree

Recently, we developed a pairwise structural alignment algorithm using realistic structural and environmental information (SAUCE). In this paper, we at first present an automatic fold hierarchical classification based on SAUCE alignments. This classification enables us to build a fold tree containing different levels of multiple structural profiles. Then a tree-based fold search algorithm is described. We applied this method to a group of structures with sequence identity less than 35% and did a series of leave one out tests. These tests are approximately comparable to fold recognition tests on superfamily level. Results show that fold recognition via a fold tree can be faster and better at detecting distant homologues than classic fold recognition methods.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/63155/1/cmb.2006.13.1565.pd

Pathogen Response Genes Mediate Caenorhabditis elegans Innate Immunity

Innate immunity is crucial in the response and defense against pathogens for invertebrates and vertebrates alike. The soil nematode Caenorhabditis elegans is a useful model to study the eukaryotic innate immune response to microbial pathogenesis. Prior research indicates that the protein receptor FSHR-1 plays an important role in the innate recognition of intestinal infection due to pathogen consumption. Determining what genes are controlled by FSHR-1 may uncover an unknown pathway that could increase not only the comprehension of the C. elegans immune system but also innate immunity generally. To characterize the function of FSHR-1, four candidate pathogen response genes that appear to be regulated by FSHR-1 were evaluated in worms infected with Pseudomonas aeruginosa. Although intestine specific RNA interference of these four genes did not show immunity phenotypes, quantitative PCR suggests that FSHR-1 regulates the basal and/or infection-induced expression of three of the four genes. To explore this FSHR-1-dependent transcriptional induction, fluorescent transgenic reporters were constructed for the three candidate FSHR-1 target genes. The spatial expression of one putative pathogen response gene was characterized in transgenic worms under both control and pathogenic conditions. RNA interference was performed to assess the FSHR-1 dependency of this expression pattern

Feature Selection via Binary Simultaneous Perturbation Stochastic Approximation

Feature selection (FS) has become an indispensable task in dealing with today's highly complex pattern recognition problems with massive number of features. In this study, we propose a new wrapper approach for FS based on binary simultaneous perturbation stochastic approximation (BSPSA). This pseudo-gradient descent stochastic algorithm starts with an initial feature vector and moves toward the optimal feature vector via successive iterations. In each iteration, the current feature vector's individual components are perturbed simultaneously by random offsets from a qualified probability distribution. We present computational experiments on datasets with numbers of features ranging from a few dozens to thousands using three widely-used classifiers as wrappers: nearest neighbor, decision tree, and linear support vector machine. We compare our methodology against the full set of features as well as a binary genetic algorithm and sequential FS methods using cross-validated classification error rate and AUC as the performance criteria. Our results indicate that features selected by BSPSA compare favorably to alternative methods in general and BSPSA can yield superior feature sets for datasets with tens of thousands of features by examining an extremely small fraction of the solution space. We are not aware of any other wrapper FS methods that are computationally feasible with good convergence properties for such large datasets.Comment: This is the Istanbul Sehir University Technical Report #SHR-ISE-2016.01. A short version of this report has been accepted for publication at Pattern Recognition Letter

Semantic Instance Annotation of Street Scenes by 3D to 2D Label Transfer

Semantic annotations are vital for training models for object recognition, semantic segmentation or scene understanding. Unfortunately, pixelwise annotation of images at very large scale is labor-intensive and only little labeled data is available, particularly at instance level and for street scenes. In this paper, we propose to tackle this problem by lifting the semantic instance labeling task from 2D into 3D. Given reconstructions from stereo or laser data, we annotate static 3D scene elements with rough bounding primitives and develop a model which transfers this information into the image domain. We leverage our method to obtain 2D labels for a novel suburban video dataset which we have collected, resulting in 400k semantic and instance image annotations. A comparison of our method to state-of-the-art label transfer baselines reveals that 3D information enables more efficient annotation while at the same time resulting in improved accuracy and time-coherent labels.Comment: 10 pages in Conference on Computer Vision and Pattern Recognition (CVPR), 201

Solving Multiclass Learning Problems via Error-Correcting Output Codes

Multiclass learning problems involve finding a definition for an unknown function f(x) whose range is a discrete set containing k &gt 2 values (i.e., k ``classes''). The definition is acquired by studying collections of training examples of the form [x_i, f (x_i)]. Existing approaches to multiclass learning problems include direct application of multiclass algorithms such as the decision-tree algorithms C4.5 and CART, application of binary concept learning algorithms to learn individual binary functions for each of the k classes, and application of binary concept learning algorithms with distributed output representations. This paper compares these three approaches to a new technique in which error-correcting codes are employed as a distributed output representation. We show that these output representations improve the generalization performance of both C4.5 and backpropagation on a wide range of multiclass learning tasks. We also demonstrate that this approach is robust with respect to changes in the size of the training sample, the assignment of distributed representations to particular classes, and the application of overfitting avoidance techniques such as decision-tree pruning. Finally, we show that---like the other methods---the error-correcting code technique can provide reliable class probability estimates. Taken together, these results demonstrate that error-correcting output codes provide a general-purpose method for improving the performance of inductive learning programs on multiclass problems.Comment: See http://www.jair.org/ for any accompanying file

A decision forest based feature selection framework for action recognition from RGB-Depth cameras

In this paper, we present an action recognition framework leveraging data mining capabilities of random decision forests trained on kinematic features. We describe human motion via a rich collection of kinematic feature time-series computed from the skeletal representation of the body in motion. We discriminatively optimize a random decision forest model over this collection to identify the most effective subset of features, localized both in time and space. Later, we train a support vector machine classifier on the selected features. This approach improves upon the baseline performance obtained using the whole feature set with a significantly less number of features (one tenth of the original). On MSRC-12 dataset (12 classes), our method achieves 94% accuracy. On the WorkoutSU-10 dataset, collected by our group (10 physical exercise classes), the accuracy is 98%. The approach can also be used to provide insights on the spatiotemporal dynamics of human actions