Non-Rigid Object Detection with LocalInterleaved Sequential Alignment (LISA).

This paper shows that the successively evaluated features used in a sliding window detection process to decide about object presence/absence also contain knowledge about object deformation. We exploit these detection features to estimate the object deformation. Estimated deformation is then immediately applied to not yet evaluated features to align them with the observed image data. In our approach, the alignment estimators are jointly learned with the detector. The joint process allows for the learning of each detection stage from less deformed training samples than in the previous stage. For the alignment estimation we propose regressors that approximate non-linear regression functions and compute the alignment parameters extremely fast.

Amino acid "little Big Bang": representing amino acid substitution matrices as dot products of Euclidian vectors.

BACKGROUND: Sequence comparisons make use of a one-letter representation for amino acids, the necessary quantitative information being supplied by the substitution matrices. This paper deals with the problem of finding a representation that provides a comprehensive description of amino acid intrinsic properties consistent with the substitution matrices. RESULTS: We present a Euclidian vector representation of the amino acids, obtained by the singular value decomposition of the substitution matrices. The substitution matrix entries correspond to the dot product of amino acid vectors. We apply this vector encoding to the study of the relative importance of various amino acid physicochemical properties upon the substitution matrices. We also characterize and compare the PAM and BLOSUM series substitution matrices. CONCLUSIONS: This vector encoding introduces a Euclidian metric in the amino acid space, consistent with substitution matrices. Such a numerical description of the amino acid is useful when intrinsic properties of amino acids are necessary, for instance, building sequence profiles or finding consensus sequences, using machine learning algorithms such as Support Vector Machine and Neural Networks algorithms.

Tracking by an optimal sequence of linear predictors.

We propose a learning approach to tracking explicitly minimizing the computational complexity of the tracking process subject to user-defined probability of failure (loss-of-lock) and precision. The tracker is formed by a Number of Sequences of Learned Linear Predictors (NoSLLiP). Robustness of NoSLLiP is achieved by modeling the object as a collection of local motion predictors--object motion is estimated by the outlier-tolerant RANSAC algorithm from local predictions. Efficiency of the NoSLLiP tracker stems from (i) the simplicity of the local predictors and (ii) from the fact that all design decisions--the number of local predictors used by the tracker, their computational complexity (i.e. the number of observations the prediction is based on), locations as well as the number of RANSAC iterations are all subject to the optimization (learning) process. All time-consuming operations are performed during the learning stage--tracking is reduced to only a few hundreds integer multiplications in each step. On PC with 1xK8 3200+, a predictor evaluation requires about 30 microseconds. The proposed approach is verified on publicly-available sequences with approximately 12000 frames with ground-truth. Experiments demonstrates, superiority in frame rates and robustness with respect to the SIFT detector, Lucas-Kanade tracker and other trackers.

FROST: a filter-based fold recognition method.

To assess the reliability of fold assignments to protein sequences, we developed a fold recognition method called FROST (Fold Recognition-Oriented Search Tool) based on a series of filters and a database specifically designed as a benchmark for this new method under realistic conditions. This benchmark database consists of proteins for which there exists, at least, another protein with an extensively similar 3D structure in a database of representative 3D structures (i.e., more than 65% of the residues in both proteins can be structurally aligned). Because the testing of our method must be carried out under conditions similar to those of real fold recognition experiments, no protein pair with sequence similarity detectable using standard sequence comparison methods such as FASTA is included in the benchmark database. While using FROST, we achieved a coverage of 60% for a rate of error of 1%. To obtain a baseline for our method, we used PSI-BLAST and 3D-PSSM. Under the same conditions, for a 1% error rate, coverages for PSI-BLAST and 3D-PSSM were 33 and 56%, respectively.