Scalable Similarity Search for Molecular Descriptors

Similarity search over chemical compound databases is a fundamental task in the discovery and design of novel drug-like molecules. Such databases often encode molecules as non-negative integer vectors, called molecular descriptors, which represent rich information on various molecular properties. While there exist efficient indexing structures for searching databases of binary vectors, solutions for more general integer vectors are in their infancy. In this paper we present a time- and space- efficient index for the problem that we call the succinct intervals-splitting tree algorithm for molecular descriptors (SITAd). Our approach extends efficient methods for binary-vector databases, and uses ideas from succinct data structures. Our experiments, on a large database of over 40 million compounds, show SITAd significantly outperforms alternative approaches in practice.Comment: To be appeared in the Proceedings of SISAP'1

Termination of Triangular Integer Loops is Decidable

We consider the problem whether termination of affine integer loops is decidable. Since Tiwari conjectured decidability in 2004, only special cases have been solved. We complement this work by proving decidability for the case that the update matrix is triangular.Comment: Full version (with proofs) of a paper published in the Proceedings of the 31st International Conference on Computer Aided Verification (CAV '19), New York, NY, USA, Lecture Notes in Computer Science, Springer-Verlag, 201

Nonmethane hydrocarbon measurements in the North Atlantic Flight Corridor during the Subsonic Assessment Ozone and Nitrogen Oxide Experiment

Mixing ratios of nonmethane hydrocarbons (NMHCs) were not enhanced in whole air samples collected within the North Atlantic Flight Corridor (NAFC) during the fall of 1997. The investigation was conducted aboard NASA's DC-8 research aircraft, as part of the Subsonic Assessment (SASS) Ozone and Nitrogen Oxide Experiment (SONEX). NMHC enhancements were not detected within the general organized tracking system of the NAFC, nor during two tail chases of the DC-8's own exhaust. Because positive evidence of aircraft emissions was demonstrated by enhancements in both nitrogen oxides and condensation nuclei during SONEX, the NMHC results suggest that the commercial air traffic fleet operating in the North Atlantic region does not contribute at all or contributes negligibly to NMHCs in the NAFC. Copyright 2000 by the American Geophysical Union

Radially restricted linear energy transfer for high-energy protons: A new analytical approach

Radially restricted linear energy transfer (LET) is a basic physical parameter relevant to radiation biology and radiation protection. In this report a convenient method is presented for the analytical computation of this quantity without the need for complicated simulation. The method uses the energy-re-stricted LETL, as recently redefined in a 1993 ICRU draft document and supplements it by a relatively simple term that represents the energy of fast rays lost within distancer from the track core. The method provides a better fit than other models and is valid over the entire range of radial distance from track center to the maximum radial distance traveled by the most energetic secondary electrons.L r computed by this approach differs only a few percent from the values Contribution to the international symposium on heavy ions research: space, radiation protection and therapy, 21–24 March 1994, Sophia-Antipolis, Franc

Partial Homology Relations - Satisfiability in terms of Di-Cographs

Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons can be used to infer such homology relations (e.g.\ orthology, paralogy, xenology). They are \emph{satisfiable} if the relations can be explained by an event-labeled gene tree, i.e., they can simultaneously co-exist in an evolutionary history of the underlying genes. Every gene tree is equivalently interpreted as a so-called cotree that entirely encodes the structure of a di-cograph. Thus, satisfiable homology relations must necessarily form a di-cograph. The inferred homology relations might not cover each pair of genes and thus, provide only partial knowledge on the full set of homology relations. Moreover, for particular pairs of genes, it might be known with a high degree of certainty that they are not orthologs (resp.\ paralogs, xenologs) which yields forbidden pairs of genes. Motivated by this observation, we characterize (partial) satisfiable homology relations with or without forbidden gene pairs, provide a quadratic-time algorithm for their recognition and for the computation of a cotree that explains the given relations

Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network

BACKGROUND It is widely accepted that genetic regulatory systems are 'modular', in that the whole system is made up of smaller 'subsystems' corresponding to specific biological functions. Most attempts to identify modules in genetic regulatory systems have relied on the topology of the underlying network. However, it is the temporal activity (dynamics) of genes and proteins that corresponds to biological functions, and hence it is dynamics that we focus on here for identifying subsystems. RESULTS Using Boolean network models as an exemplar, we present a new technique to identify subsystems, based on their dynamical properties. The main part of the method depends only on the stable dynamics (attractors) of the system, thus requiring no prior knowledge of the underlying network. However, knowledge of the logical relationships between the network components can be used to describe how each subsystem is regulated. To demonstrate its applicability to genetic regulatory systems, we apply the method to a model of the Drosophila segment polarity network, providing a detailed breakdown of the system. CONCLUSION We have designed a technique for decomposing any set of discrete-state, discrete-time attractors into subsystems. Having a suitable mathematical model also allows us to describe how each subsystem is regulated and how robust each subsystem is against perturbations. However, since the subsystems are found directly from the attractors, a mathematical model or underlying network topology is not necessarily required to identify them, potentially allowing the method to be applied directly to experimental expression data

On Multiphase-Linear Ranking Functions

Multiphase ranking functions ($\mathit{M{\Phi}RFs}$) were proposed as a means to prove the termination of a loop in which the computation progresses through a number of "phases", and the progress of each phase is described by a different linear ranking function. Our work provides new insights regarding such functions for loops described by a conjunction of linear constraints (single-path loops). We provide a complete polynomial-time solution to the problem of existence and of synthesis of $\mathit{M{\Phi}RF}$ of bounded depth (number of phases), when variables range over rational or real numbers; a complete solution for the (harder) case that variables are integer, with a matching lower-bound proof, showing that the problem is coNP-complete; and a new theorem which bounds the number of iterations for loops with $\mathit{M{\Phi}RFs}$. Surprisingly, the bound is linear, even when the variables involved change in non-linear way. We also consider a type of lexicographic ranking functions, $\mathit{LLRFs}$, more expressive than types of lexicographic functions for which complete solutions have been given so far. We prove that for the above type of loops, lexicographic functions can be reduced to $\mathit{M{\Phi}RFs}$, and thus the questions of complexity of detection and synthesis, and of resulting iteration bounds, are also answered for this class.Comment: typos correcte

BPS States on M5-brane in Large C-field Background

We extensively study BPS solutions of the low energy effective theory of M5-brane in large C-field background. This provides us an opportunity to explore the interactions turned on by C-field background through the Nambu-Poisson structure. The BPS states considered in this paper include the M-waves, the self-dual string (M2 ending on M5), tilted M5-brane, holomorphic embedding of M5-brane and the intersection of two M5-branes along a 3-brane.Comment: 25 pages, reference adde

Hidden conformal symmetry of extreme and non-extreme Einstein-Maxwell-Dilaton-Axion black holes

The hidden conformal symmetry of extreme and non-extreme Einstein-Maxwell-Dilaton-Axion (EMDA) black holes is addressed in this paper. For the non-extreme one, employing the wave equation of massless scalars, the conformal symmetry with left temperature $T_{L}=\frac{M}{2\pi a}$ and right temperature $T_{R}=\frac{\sqrt{M^{2}-a^{2}}}{2\pi a}$ in the near region is found. The conformal symmetry is spontaneously broken due to the periodicity of the azimuthal angle. The microscopic entropy is derived by the Cardy formula and is fully in consistence with the Bekenstein-Hawking area-entropy law. The absorption cross section in the near region is calculated and exactly equals that in a 2D CFT. For the extreme case, by redefining the conformal coordinates, the duality between the solution space and CFT is studied. The microscopic entropy is found to exactly agree with the area-entropy law.Comment: V3, typos corrected, version to appear in JHE

New Near Horizon Limit in Kerr/CFT

The extremal Kerr black hole with the angular momentum J is conjectured to be dual to CFT with central charges c_L=c_R=12J. However, the central charge in the right sector remains to be explicitly derived so far. In order to investigate this issue, we introduce new near horizon limits of (near) extremal Kerr and five-dimensional Myers-Perry black holes. We obtain Virasoro algebras as asymptotic symmetries and calculate the central charges associated with them. One of them is equivalent to that of the previous studies, and the other is non-zero, but still the order of near extremal parameter. Redefining the algebras to take the standard form, we obtain a finite value as expected by the Kerr/CFT correspondence.Comment: 25 pages, minor changes, references adde