A resource-frugal probabilistic dictionary and applications in (meta)genomics

Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing techniques, one must rely on extremely scalable methods and solutions. Indexing billions of objects is a task considered too expensive while being a fundamental need in this field. In this paper we propose a straightforward indexing structure that scales to billions of element and we propose two direct applications in genomics and metagenomics. We show that our proposal solves problem instances for which no other known solution scales-up. We believe that many tools and applications could benefit from either the fundamental data structure we provide or from the applications developed from this structure.Comment: Submitted to PSC 201

Efficient seeding techniques for protein similarity search

We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We propose several different design methods and use them to construct several alphabets.We then perform an analysis of seeds built over those alphabet and compare them with the standard Blastp seeding method [2,3], as well as with the family of vector seeds proposed in [4]. While the formalism of subset seed is less expressive (but less costly to implement) than the accumulative principle used in Blastp and vector seeds, our seeds show a similar or even better performance than Blastp on Bernoulli models of proteins compatible with the common BLOSUM62 matrix

Efficient seeding techniques for protein similarity search

We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We propose several different design methods and use them to construct several alphabets.We then perform an analysis of seeds built over those alphabet and compare them with the standard Blastp seeding method [2,3], as well as with the family of vector seeds proposed in [4]. While the formalism of subset seed is less expressive (but less costly to implement) than the accumulative principle used in Blastp and vector seeds, our seeds show a similar or even better performance than Blastp on Bernoulli models of proteins compatible with the common BLOSUM62 matrix

Reference face graph for face recognition

Face recognition has been studied extensively; however, real-world face recognition still remains a challenging task. The demand for unconstrained practical face recognition is rising with the explosion of online multimedia such as social networks, and video surveillance footage where face analysis is of significant importance. In this paper, we approach face recognition in the context of graph theory. We recognize an unknown face using an external reference face graph (RFG). An RFG is generated and recognition of a given face is achieved by comparing it to the faces in the constructed RFG. Centrality measures are utilized to identify distinctive faces in the reference face graph. The proposed RFG-based face recognition algorithm is robust to the changes in pose and it is also alignment free. The RFG recognition is used in conjunction with DCT locality sensitive hashing for efficient retrieval to ensure scalability. Experiments are conducted on several publicly available databases and the results show that the proposed approach outperforms the state-of-the-art methods without any preprocessing necessities such as face alignment. Due to the richness in the reference set construction, the proposed method can also handle illumination and expression variation

Automatic Synchronization of Multi-User Photo Galleries

In this paper we address the issue of photo galleries synchronization, where pictures related to the same event are collected by different users. Existing solutions to address the problem are usually based on unrealistic assumptions, like time consistency across photo galleries, and often heavily rely on heuristics, limiting therefore the applicability to real-world scenarios. We propose a solution that achieves better generalization performance for the synchronization task compared to the available literature. The method is characterized by three stages: at first, deep convolutional neural network features are used to assess the visual similarity among the photos; then, pairs of similar photos are detected across different galleries and used to construct a graph; eventually, a probabilistic graphical model is used to estimate the temporal offset of each pair of galleries, by traversing the minimum spanning tree extracted from this graph. The experimental evaluation is conducted on four publicly available datasets covering different types of events, demonstrating the strength of our proposed method. A thorough discussion of the obtained results is provided for a critical assessment of the quality in synchronization.Comment: ACCEPTED to IEEE Transactions on Multimedi