3053834
Evidence for growth of microbial genomes by short segmental duplications
Textual analysis of microbial genomes reveals footprints of their early evolution of the genomes. It is shown that distributions frequency occurrence of words less than nine letters in genomes have widths that are many times those of Poisson distributions. This phenomenon suggests a simple biologically plausible model for the growth of genomes: the genome first grows randomly to an initial length of approximately one thousand nucleotides (1 kb), or about one thousandth of its final length, thereafter mainly grows by random short segmental duplication. We show that using duplicated segments averaging around 25 b, model sequences generated in this model possess statistical properties characteristic of present day genomes. Both the initial length and the duplicated segment length support an RNA world at the time duplication began.
2484888
Search for evolution-related-oligonucleotides and conservative words in rRNA sequences
We describe a method for finding unmapped conserved words in rRNA sequences that is effective, utilizes evolutionary information and does not depend on multiple sequence alignment. Evolutionary distance (called n-distance) between a pair of 16S or 18S rRNA sequences is defined in terms of the difference in the two sets of frequencies of occurrence of oligonucleotides n bases long (n-mers) given by the sequences. These n-distances are used to reconstruct phylogenetic trees for 35 representative organisms from all three kingdoms. The quality of the tree generally improves with increasing n and reaches a plateau of best fit at n=7 or 8. Hence the 7-mer or 8-mer (oligonucleotide of 7 or 8 bases) frequencies provide a basis to describe rRNA evolution. Based on the analysis of the contribution of a particular 7-mers to 7-distances, a set of 612 7-mers (called evolution-related-oligonucleotides, EROs) that are critical to the topology of the best phylogenetic tree are identified. Expanding from this set of EROs, evolution-related conservative words longer than 7 bases in 16S rRNA sequences from an enlarged set of 98 organisms in bacteria and archaea are identified based on two criteria: 1) the word is highly conserved in nearly all species of a kingdom (or a sub-kingdom); and 2) the word is located at nearly the same site in each sequence. Three examples of words thus found are: the 13-mer ggattagataccc located at the end of a loop near H24 (in E.coli) is conservative in almost all species in archaea and bacteria. The 8-mer aacgagcg located on H35 is also conservative in archaea and bacteria. Its expansion, the 32-mer tgttgggttaagtcccgcaacgagcgcaaccc, is conservative in bacteria but not in archaea.
30584838
Shannon Information in Complete Genomes
Shannon information in the genomes of all completely sequenced prokaryotes and eukaryotes are measured in word lengths of two to ten letters. It is found that in a scale-dependent way, the Shannon information in complete genomes are much greater than that in matching random sequences - thousands of times greater in the case of short words. Furthermore, with the exception of the 14 chromosomes of Plasmodium falciparum, the Shannon information in all available complete genomes belong to a universality class given by an extremely simple formula. The data are consistent with a model for genome growth composed of two main ingredients: random segmental duplications that increase the Shannon information in a scale-independent way, and random point mutations that preferentially reduces the larger-scale Shannon information. The inference drawn from the present study is that the large-scale and coarse-grained growth of genomes was selectively neutral and this suggests an independent corroboration of Kimura's neutral theory of evolution.
19776539
Stack value file: custom microarchitecture for the stack
As processor performance increases, there is a corresponding increase in the demands on the memory system, including caches. Research papers have proposed partitioning the cache into instruction/data, temporal/non-temporal, and/or stack/non-stack regions. Each of these designs can improve performance by constructing two separate structures which can be probed in parallel while reducing contention. In this paper, we propose a new memory organization that partitions data references into stack and nonstack regions. Non-stack references are routed to a conventional cache. Stack references, on the other hand, are shown to have several characteristics that can be leveraged to improve performance using a less conventional storage organization. This paper enumerates those characteristics and proposes a new microarchitectural feature, the stack value file (SVF), which exploits them to improve instruction-level parallelism, reduce stack access latencies, reduce demand on the first-level cache, and reduce data bus traffic. Our results show that the SVF can improve execution performance by 29 to 65% while reducing overhead traffic for the stack region by many orders of magnitude over cache structures of the same size.
15518000
MediAssist: Using Content-Based Analysis and Context to Manage Personal Photo Collections
We present work which organises personal digital photo collections based on contextual information, such as time and location, combined with content-based analysis such as face detection and other feature detectors. The MediAssist demonstration system illustrates the results of our research into digital photo management, showing how a combination of automatically extracted context and content-based information, together with user annotation, facilitates efficient searching of personal photo collections.
19085830
An analysis of multiple-class vacation queues with individual thresholds
This study examines a multiple-class M/G/1 queue with multiple thresholds. Each class of customer arrives according to an independent Poisson process, and each class has its own threshold. The idle server is reactivated as soon as any one of the thresholds is reached. Both FCFS and non-preemptive priority cases are considered. The Laplace-Stieltjes transform of the waiting time distribution function and the mean waiting time for each class of customers are derived.
11497645
Spam Deobfuscation using a Hidden Markov Model
To circumvent spam filters, many spammers attempt to obfuscate their emails by deliberately misspelling words or introducing other errors into the text. For example viagra may be written vigra, or mortgage written m0rt gage. Even though humans have little difficulty reading obfuscated emails, most content-based filters are unable to recognize these obfuscated spam words. In this paper, we present a hidden Markov model for deobfuscating spam emails. We empirically demonstrate that our model is robust to many types of obfuscation including misspellings, incorrect segmentations (adding/removing spaces), and substitutions/insertions of non-alphabetic characters.
14075351
A Dynamic Bayesian Network Model for Autonomous 3D Reconstruction from a Single Indoor Image
When we look at a picture, our prior knowledge about the world allows us to resolve some of the ambiguities that are inherent to monocular vision, and thereby infer 3d information about the scene. We also recognize different objects, decide on their orientations, and identify how they are connected to their environment. Focusing on the problem of autonomous 3d reconstruction of indoor scenes, in this paper we present a dynamic Bayesian network model capable of resolving some of these ambiguities and recovering 3d information for many images. Our model assumes a "floorwall" geometry on the scene and is trained to recognize the floor-wall boundary in each column of the image. When the image is produced under perspective geometry, we show that this model can be used for 3d reconstruction from a single image. To our knowledge, this was the first monocular approach to automatically recover 3d reconstructions from single indoor images.