conLSH: Context based Locality Sensitive Hashing for Mapping of noisy SMRT Reads

Single Molecule Real-Time (SMRT) sequencing is a recent advancement of Next Gen technology developed by Pacific Bio (PacBio). It comes with an explosion of long and noisy reads demanding cutting edge research to get most out of it. To deal with the high error probability of SMRT data, a novel contextual Locality Sensitive Hashing (conLSH) based algorithm is proposed in this article, which can effectively align the noisy SMRT reads to the reference genome. Here, sequences are hashed together based not only on their closeness, but also on similarity of context. The algorithm has $\mathcal{O}(n^{\rho+1})$ space requirement, where $n$ is the number of sequences in the corpus and $\rho$ is a constant. The indexing time and querying time are bounded by $\mathcal{O}( \frac{n^{\rho+1} \cdot \ln n}{\ln \frac{1}{P_2}})$ and $\mathcal{O}(n^\rho)$ respectively, where $P_2 > 0$, is a probability value. This algorithm is particularly useful for retrieving similar sequences, a widely used task in biology. The proposed conLSH based aligner is compared with rHAT, popularly used for aligning SMRT reads, and is found to comprehensively beat it in speed as well as in memory requirements. In particular, it takes approximately $24.2\%$ less processing time, while saving about $70.3\%$ in peak memory requirement for H.sapiens PacBio dataset.

An Improved Video Analysis using Context based Extension of LSH

Locality Sensitive Hashing (LSH) based algorithms have already shown their promise in finding approximate nearest neighbors in high dimen- sional data space. However, there are certain scenarios, as in sequential data, where the proximity of a pair of points cannot be captured without considering their surroundings or context. In videos, as for example, a particular frame is meaningful only when it is seen in the context of its preceding and following frames. LSH has no mechanism to handle the con- texts of the data points. In this article, a novel scheme of Context based Locality Sensitive Hashing (conLSH) has been introduced, in which points are hashed together not only based on their closeness, but also because of similar context. The contribution made in this article is three fold. First, conLSH is integrated with a recently proposed fast optimal sequence alignment algorithm (FOGSAA) using a layered approach. The resultant method is applied to video retrieval for extracting similar sequences. The pro- posed algorithm yields more than 80% accuracy on an average in different datasets. It has been found to save 36.3% of the total time, consumed by the exhaustive search. conLSH reduces the search space to approximately 42% of the entire dataset, when compared with an exhaustive search by the aforementioned FOGSAA, Bag of Words method and the standard LSH implementations. Secondly, the effectiveness of conLSH is demon- strated in action recognition of the video clips, which yields an average gain of 12.83% in terms of classification accuracy over the state of the art methods using STIP descriptors. The last but of great significance is that this article provides a way of automatically annotating long and composite real life videos. The source code of conLSH is made available at http://www.isical.ac.in/~bioinfo_miu/conLSH/conLSH.html