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

When Hashing Met Matching: Efficient Spatio-Temporal Search for Ridesharing

Carpooling, or sharing a ride with other passengers, holds immense potential for urban transportation. Ridesharing platforms enable such sharing of rides using real-time data. Finding ride matches in real-time at urban scale is a difficult combinatorial optimization task and mostly heuristic approaches are applied. In this work, we mathematically model the problem as that of finding near-neighbors and devise a novel efficient spatio-temporal search algorithm based on the theory of locality sensitive hashing for Maximum Inner Product Search (MIPS). The proposed algorithm can find $k$ near-optimal potential matches for every ride from a pool of $n$ rides in time $O(n^{1 + \rho} (k + \log n) \log k)$ and space $O(n^{1 + \rho} \log k)$ for a small $\rho < 1$. Our algorithm can be extended in several useful and interesting ways increasing its practical appeal. Experiments with large NY yellow taxi trip datasets show that our algorithm consistently outperforms state-of-the-art heuristic methods thereby proving its practical applicability