IMPROVING MOLECULAR FINGERPRINT SIMILARITY VIA ENHANCED FOLDING

Drug discovery depends on scientists finding similarity in molecular fingerprints to the drug target. A new way to improve the accuracy of molecular fingerprint folding is presented. The goal is to alleviate a growing challenge due to excessively long fingerprints. This improved method generates a new shorter fingerprint that is more accurate than the basic folded fingerprint. Information gathered during preprocessing is used to determine an optimal attribute order. The most commonly used blocks of bits can then be organized and used to generate a new improved fingerprint for more optimal folding. We thenapply the widely usedTanimoto similarity search algorithm to benchmark our results. We show an improvement in the final results using this method to generate an improved fingerprint when compared against other traditional folding methods

Beyond Hypertree Width: Decomposition Methods Without Decompositions

The general intractability of the constraint satisfaction problem has motivated the study of restrictions on this problem that permit polynomial-time solvability. One major line of work has focused on structural restrictions, which arise from restricting the interaction among constraint scopes. In this paper, we engage in a mathematical investigation of generalized hypertree width, a structural measure that has up to recently eluded study. We obtain a number of computational results, including a simple proof of the tractability of CSP instances having bounded generalized hypertree width

Property Testing via Set-Theoretic Operations

Given two testable properties $\mathcal{P}_{1}$ and $\mathcal{P}_{2}$, under what conditions are the union, intersection or set-difference of these two properties also testable? We initiate a systematic study of these basic set-theoretic operations in the context of property testing. As an application, we give a conceptually different proof that linearity is testable, albeit with much worse query complexity. Furthermore, for the problem of testing disjunction of linear functions, which was previously known to be one-sided testable with a super-polynomial query complexity, we give an improved analysis and show it has query complexity O(1/\eps^2), where \eps is the distance parameter.Comment: Appears in ICS 201

Efficient and Error-Correcting Data Structures for Membership and Polynomial Evaluation

We construct efficient data structures that are resilient against a constant fraction of adversarial noise. Our model requires that the decoder answers most queries correctly with high probability and for the remaining queries, the decoder with high probability either answers correctly or declares "don't know." Furthermore, if there is no noise on the data structure, it answers all queries correctly with high probability. Our model is the common generalization of a model proposed recently by de Wolf and the notion of "relaxed locally decodable codes" developed in the PCP literature. We measure the efficiency of a data structure in terms of its length, measured by the number of bits in its representation, and query-answering time, measured by the number of bit-probes to the (possibly corrupted) representation. In this work, we study two data structure problems: membership and polynomial evaluation. We show that these two problems have constructions that are simultaneously efficient and error-correcting.Comment: An abridged version of this paper appears in STACS 201

Bijections behind the Ramanujan Polynomials

The Ramanujan polynomials were introduced by Ramanujan in his study of power series inversions. In an approach to the Cayley formula on the number of trees, Shor discovers a refined recurrence relation in terms of the number of improper edges, without realizing the connection to the Ramanujan polynomials. On the other hand, Dumont and Ramamonjisoa independently take the grammatical approach to a sequence associated with the Ramanujan polynomials and have reached the same conclusion as Shor's. It was a coincidence for Zeng to realize that the Shor polynomials turn out to be the Ramanujan polynomials through an explicit substitution of parameters. Shor also discovers a recursion of Ramanujan polynomials which is equivalent to the Berndt-Evans-Wilson recursion under the substitution of Zeng, and asks for a combinatorial interpretation. The objective of this paper is to present a bijection for the Shor recursion, or and Berndt-Evans-Wilson recursion, answering the question of Shor. Such a bijection also leads to a combinatorial interpretation of the recurrence relation originally given by Ramanujan.Comment: 18 pages, 7 figure