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Adam Prügel-Bennett

Publications and source records attributed to Adam Prügel-Bennett.

3 recordsLinked to original sources

A Bayesian framework for extracting human gait using strong prior knowledge.

Extracting full-body motion of walking people from monocular video sequences in complex, real-world environments is an important and difficult problem, going beyond simple tracking, whose satisfactory solution demands an appropriate balance between use of prior knowledge and learning from data. We propose a consistent Bayesian framework for introducing strong prior knowledge into a system for extracting human gait. In this work, the strong prior is built from a simple articulated model having both time-invariant (static) and time-variant (dynamic) parameters. The model is easily modified to cater to situations such as walkers wearing clothing that obscures the limbs. The statistics of the parameters are learned from high-quality (indoor laboratory) data and the Bayesian framework then allows us to "bootstrap" to accurate gait extraction on the noisy images typical of cluttered, outdoor scenes. To achieve automatic fitting, we use a hidden Markov model to detect the phases of images in a walking cycle. We demonstrate our approach on silhouettes extracted from fronto-parallel ("sideways on") sequences of walkers under both high-quality indoor and noisy outdoor conditions. As well as high-quality data with synthetic noise and occlusions added, we also test walkers with rucksacks, skirts, and trench coats. Results are quantified in terms of chamfer distance and average pixel error between automatically extracted body points and corresponding hand-labeled points. No one part of the system is novel in itself, but the overall framework makes it feasible to extract gait from very much poorer quality image sequences than hitherto. This is confirmed by comparing person identification by gait using our method and a well-established baseline recognition algorithm.

Algorithms↗

An analysis of the feasibility of short read sequencing.

Several methods for ultra high-throughput DNA sequencing are currently under investigation. Many of these methods yield very short blocks of sequence information (reads). Here we report on an analysis showing the level of genome sequencing possible as a function of read length. It is shown that re-sequencing and de novo sequencing of the majority of a bacterial genome is possible with read lengths of 20-30 nt, and that reads of 50 nt can provide reconstructed contigs (a contiguous fragment of sequence data) of 1000 nt and greater that cover 80% of human chromosome 1.

Chromosomes, Human, Pair 1↗

Training HMM structure with genetic algorithm for biological sequence analysis.

SUMMARY: Hidden Markov models (HMMs) are widely used for biological sequence analysis because of their ability to incorporate biological information in their structure. An automatic means of optimizing the structure of HMMs would be highly desirable. However, this raises two important issues; first, the new HMMs should be biologically interpretable, and second, we need to control the complexity of the HMM so that it has good generalization performance on unseen sequences. In this paper, we explore the possibility of using a genetic algorithm (GA) for optimizing the HMM structure. GAs are sufficiently flexible to allow incorporation of other techniques such as Baum-Welch training within their evolutionary cycle. Furthermore, operators that alter the structure of HMMs can be designed to favour interpretable and simple structures. In this paper, a training strategy using GAs is proposed, and it is tested on finding HMM structures for the promoter and coding region of the bacterium Campylobacter jejuni. The proposed GA for hidden Markov models (GA-HMM) allows, HMMs with different numbers of states to evolve. To prevent over-fitting, a separate dataset is used for comparing the performance of the HMMs to that used for the Baum-Welch training. The GA-HMM was capable of finding an HMM comparable to a hand-coded HMM designed for the same task, which has been published previously.

Algorithms↗