Simple and Effective Visual Models for Gene Expression Cancer Diagnostics

In the paper we show that diagnostic classes in cancer gene expression data sets, which most often include thousands of features (genes), may be effectively separated with simple two-dimensional plots such as scatterplot and radviz graph. The principal innovation proposed in the paper is a method called VizRank, which is able to score and identify the best among possibly millions of candidate projections for visualizations. Compared to recently much applied techniques in the field of cancer genomics that include neural networks, support vector machines and various ensemble-based approaches, VizRank is fast and finds visualization models that can be easily examined and interpreted by domain experts. Our experiments on a number of gene expression data sets show that VizRank was always able to find data visualizations with a small number of (two to seven) genes and excellent class separation. In addition to providing grounds for gene expression cancer diagnosis, VizRank and its visualizations also identify small sets of relevant genes, uncover interesting gene interactions and point to outliers and potential misclassifications in cancer data sets

A Cooperative Development System for an Interactive Introductory Programming Course

We present a system for a cooperative development of computer programs that was created for the lab sessions of an introductory programming course at the University of Ljubljana, Slovenia. The system relieved the students from the tedious task of retyping programs developed by the teaching assistant and enabled them to cooperate with the teaching assistant in solving programming problems. We thus made the lab sessions more efficient and interactive and brought them closer to the spirit of active learning approaches

Search versus Knowledge: An Empirical Study of Minimax on KRK

This article presents the results of an empirical experiment designed to gain insight into what is the effect of the minimax algorithm on the evaluation function. The experiment’s simulations were performed upon the KRK chess endgame. Our results show that dependencies between evaluations of sibling nodes in a game tree and an abundance of possibilities to commit blunders present in the KRK endgame are not sufficient to explain the success of the minimax principle in practical game-playing as was previously believed. The article shows that minimax in combination with a noisy evaluation function introduces a bias into the backed-up evaluations and argues that this bias is what masked the effectiveness of the minimax in previous studies

Interactive Vegetation Rendering with Slicing and Blending

Detailed and interactive 3D rendering of vegetation is one of the challenges of traditional polygon-oriented computer graphics, due to large geometric complexity even of simple plants. In this paper we introduce a simplified image-based rendering approach based solely on alpha-blended textured polygons. The simplification is based on the limitations of human perception of complex geometry. Our approach renders dozens of detailed trees in real-time with off-the-shelf hardware, while providing significantly improved image quality over existing real-time techniques. The method is based on using ordinary mesh-based rendering for the solid parts of a tree, its trunk and limbs. The sparse parts of a tree, its twigs and leaves, are instead represented with a set of slices, an image-based representation. A slice is a planar layer, represented with an ordinary alpha or color-keyed texture; a set of parallel slices is a slicing. Rendering from an arbitrary viewpoint in a 360 degree circle around the center of a tree is achieved by blending between the nearest two slicings. In our implementation, only 6 slicings with 5 slices each are sufficient to visualize a tree for a moving or stationary observer with the perceptually similar quality as the original model

An Automatic Human Face Detection Method

This article contains a proposal for an automatic human face detection method, that tries to join several theories proposed by different authors. The method is based on detection of shape features (eye pairs) and skin color. The method assumes certain circumstances and constraints, respectively. Therefore it is not applicable universally. Given the constraints, it is effective enough for applications where fast execution is required. Test results are given and at the end some directives for future work are discussed

Superquadrics for segmentation and modeling range data

We present a novel approach to reliable and efficient recovery of part-descriptions in terms of superquadric models from range data. We show that superquadrics can directly be recovered from unsegmented data, thus avoiding any presegmentation steps (e.g., in terms of surfaces). The approach is based on the recover-andselect paradigm. We present several experiments on real and synthetic range images, where we demonstrate the stability of the results with respect to viewpoint and noise

Does replication groups scoring reduce false positive rate in SNP interaction discovery?

BACKGROUNG. Computational methods that infer single nucleotide polymorphism (SNP) interactions from phenotype data may uncover new biological mechanisms in non-Mendelian diseases. However, practical aspects of such analysis face many problems. Present experimental studies typically use SNP arrays with hundreds of thousands of SNPs but record only hundreds of samples. Candidate SNP pairs inferred by interaction analysis may include a high proportion of false positives. Recently, Gayan et al. (2008) proposed to reduce the number of false positives by combining results of interaction analysis performed on subsets of data (replication groups), rather than analyzing the entire data set directly. If performing as hypothesized, replication groups scoring could improve interaction analysis and also any type of feature ranking and selection procedure in systems biology. Because Gayan et al. do not compare their approach to the standard interaction analysis techniques, we here investigate if replication groups indeed reduce the number of reported false positive interactions. RESULTS. A set of simulated and false interaction-imputed experimental SNP data sets were used to compare the inference of SNP-SNP interactions by means of replication groups to the standard approach where the entire data set was directly used to score all candidate SNP pairs. In all our experiments, the inference of interactions from the entire data set (e.g. without using the replication groups) reported fewer false positives. CONCLUSIONS. With respect to the direct scoring approach the utility of replication groups does not reduce false positive rates, and may, depending on the data set, often perform worse

Virtual Skiing as an Art Installation

The Virtual Skiing game allows the user to immerse himself into the skiing sensation without using any obvious hardware interfaces. To achieve the movement down the virtual skiing slope the skier who stands on a pair of skis attached to the floor performs the same movements as on real skis, in particular this is the case on carving skis: tilting the body to the left initiates a left turn, tilting the body to the right initiates a right turn, by lowering the body, the speed is increased. The skier observes his progress down the virtual slope projected on the wall in front of him. The skier’s movements are recorded using a video camera placed in front of him and processed on a PC in real time to drive the projected animation of the virtual slope

Capturing Panoramic Depth Images with a Single Standard Camera

In this paper we present a panoramic depth imaging system. The system is mosaic-based which means that we use a single rotating camera and assemble the captured images in a mosaic. Due to a setoff of the camera’s optical center from the rotational center of the system we are able to capture the motion parallax effect which enables the stereo reconstruction. The camera is rotating on a circular path with the step defined by an angle equivalent to one column of the captured image. The equation for depth estimation can be easily extracted from system geometry. To find the corresponding points on a stereo pair of panoramic images the epipolar geometry needs to be determined. It can be shown that the epipolar geometry is very simple if we are doing the reconstruction based on a symmetric pair of stereo panoramic images. We get a symmetric pair of stereo panoramic images when we take symmetric columns on the left and on the right side from the captured image center column. Epipolar lines of the symmetrical pair of panoramic images are image rows. We focused mainly on the system analysis. The system performs well in the reconstruction of small indoor spaces

Structural Descriptions in Human-Assisted Robot Visual Learning

The paper presents an approach to using structural descriptions, obtained through a human-robot tutoring dialogue, as labels for the visual object models a robot learns. The paper shows how structural descriptions enable relating models for different aspects of one and the same object, and how being able to relate descriptions for visual models and discourse referents enables incremental updating of model descriptions through dialogue (either robot- or human-initiated). The approach has been implemented in an integrated architecture for human-assisted robot visual learning