Multi-instance multi-label distance metric learning for genome-wide protein function prediction

Multi-instance multi-label (MIML) learning has been proven to be effective for the genome-wide protein function prediction problems where each training example is associated with not only multiple instances but also multiple class labels. To find an appropriate MIML learning method for genome-wide protein function prediction, many studies in the literature attempted to optimize objective functions in which dissimilarity between instances is measured using the Euclidean distance. But in many real applications, Euclidean distance may be unable to capture the intrinsic similarity/dissimilarity in feature space and label space. Unlike other previous approaches, in this paper, we propose to learn a multi-instance multi-label distance metric learning framework (MIMLDML) for genome-wide protein function prediction. Specifically, we learn a Mahalanobis distance to preserve and utilize the intrinsic geometric information of both feature space and label space for MIML learning. In addition, we try to deal with the sparsely labeled data by giving weight to the labeled data. Extensive experiments on seven real-world organisms covering the biological three-domain system (i.e., archaea, bacteria, and eukaryote; Woese et al., 1990) show that the MIMLDML algorithm is superior to most state-of-the-art MIML learning algorithms.     

Geometry and electronic structure of the dimethyl sulfoxide dimer. Calculation by the MNDO method

The geometric and electronic structure of the complex formed by dipole-dipole interaction between two molecules of DMSO in the "head-to-tail" orientation were calculated by the MNDO quantum-chemical method. The minimum total energy corresponds to a distance of 5.5 Å between the sulfur atoms, and the angle between the axis of the molecular dipoles is 16.4°. This agrees with calculations for liquid DMSO by molecular dynamics. The large equilibrium distance between the DMSO molecules explains its low density in the liquid phase and the high intensity of microwave absorption due to free volume sufficient for rotation of one molecule in the complex in relation to the dipole axis of the other.N. D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences, 117334 Moscow. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 6, pp. 1340–1344, June, 1992.     

Distances and volumina for graphs

It has long been realized that connected graphs have some sort of geometric structure, in that there is a natural distance function (or metric), namely, the shortest-path distance function. In fact, there are several other natural yet intrinsic distance functions, including: the resistance distance, correspondent “square-rooted” distance functions, and a so‐called “quasi‐Euclidean” distance function. Some of these distance functions are introduced here, and some are noted not only to satisfy the usual triangle inequality but also other relations such as the “tetrahedron inequality”. Granted some (intrinsic) distance function, there are different consequent graph-invariants. Here attention is directed to a sequence of graph invariants which may be interpreted as: the sum of a power of the distances between pairs of vertices of G, the sum of a power of the “areas” between triples of vertices of G, the sum of a power of the “volumes” between quartets of vertices of G, etc. The Cayley–Menger formula for n-volumes in Euclidean space is taken as the defining relation for so-called “n-volumina” in terms of graph distances, and several theorems are here established for the volumina-sum invariants (when the mentioned power is 2). This revised version was published online in July 2006 with corrections to the Cover Date.     

Large-volume wall-jet cells as electrochemical detectors for high-performance liquid chromatography

The wall-jet electrode is an attractive configuration for electrochemical detectors for high-performance liquid chromatography (h.p.l.c.) on account of its high convective mass-transfer characteristics. Another important, though less recognized, feature is its small effective cell volume, which is shown to be almost independent of the geometric cell volume. The effective volume is less than the volume of the hydrodynamic boundary layer, or only a few microlitres. The practical use of the wall-jet detector in both normal-phase and reverse-phase h.p.l.c. is discussed with particular reference to the distance between the jet and the electrode. A new cell design is proposed.     

A proof of the triangle inequality for the Tanimoto distance

A distance, or dissimilarity measure, can be defined based on the Tanimoto coefficient, a similarity measure widely applied to chemical structures. A new, simple proof that this distance satisfies the triangle inequality is presented. This revised version was published online in July 2006 with corrections to the Cover Date.     

The angular dependence of the multipole–multipole interaction for energy transfer

The interaction between multipoles is not isotropic even in cubic systems. This results in the introduction of geometric reduction factors in the calculation of energy-transfer rates in crystals. We derive these reduction factors for the cases of dipole–dipole, dipole–quadrupole, and quadrupole–quadrupole couplings and present a general procedure for their derivation in other cases. For the dipole–dipole case the geometric factor is independent of the distribution of the acceptor species, but for higher-order couplings, a significant angular dependence is found. Received: 6 November 1998 / Accepted: 15 January 1999 / Published online: 7 June 1999     

Location of charge and geometric soliton waves in dications of α,ω-substituted polyenes

A quantum-chemical investigation of the location and form of the solitons in the dications of polyenes was undertaken. It was shown that two soliton waves (both charge and geometric) in opposite phases are generated in the doubly charged conjugated systems; they coincide in form with that for the solitons in the single-charge π systems. In the dications of polyenes with a long chain both solitons are repelled from each other. In short chains a minimum distance is maintained between them, and both centers of the soliton waves can even be outside the molecule. The introduction of hydroxy or phenyl terminal groups into the dications of the polyenes leads to displacement of the centers of the charge and geometric waves without substantially distorting their form. The introduction of an amino group or tropylium residue is accompanied by displacement of the solitons to the end of the conjugation chain so that half of the soliton waves projects onto the molecule. Translated from Teoreticheskaya i éksperimental'naya Khimiya, Vol. 44, No. 5, pp. 272–278, September–October, 2008.     

Polymers,additives, surfactants and their mixtures: Computer-based search with special ftir libraries

This investigation was done with a PC of 850 MB/33 MHz, Windows 3.1 and the SPECTACLE program of LabControl/Cologne. The libraries contained standardized FTIR spectra of 3061 defined polymers, 530 industrial polymers and resins, 1969 additives (pigments, stabilizers, plasticizers etc.) 1190 surfactants and 1614 monomers, pyrolyzates and educts. For searches, the data density was reduced to 4/cm. Similarity search with standardized full spectra yields quantitative dissimilarity figures; it allows an experimental definition of identity. The derivative functions 3 and 4 of Lowry and Huppler increase the gap between identical and similar spectra. With the LH2 algorithm spectra are defined as identical if their dissimilarity values are within 10³. Since all organic matter has some spectral similarity the LH2 dissimilarity for organics will not go far beyond 10⁵. - The quality of IR preparation has a strong impact on search results. If a library contains spectra with false-light, Christiansen effect, high noise or other artefacts, peak search yields better results than similarity search with full spectra. Multicomponent systems can be searched successfully for their constituents with an algorithm combining peak and similarity searches. This algorithm is superior to all other algorithms if a library contains spectra with artefacts.     

Capillary scale light emitting diode based multi-reflection absorbance detector

We describe a light emitting diode (LED) based multi-reflection capillary scale absorbance detector based on both square and round capillaries and compare their performance with a conventional single-pass on-tube detector. The optical path length is extended by silver coating, the external surface of the capillary. The reflective geometry has been reported to be less prone to artifacts induced by refractive index changes; we do find this to be true. Although the detection volume/illuminated volume is increased some, a multi-reflection cell based on a 180 μm bore capillary with a ∼2-cm long illuminated volume shows over a 50-fold gain in signal-to-noise (S/N) compared to a single-pass on-tube configuration with the same capillary. The limit of detection (LOD) is 4.4 fmol (2.6 pg, 1 μL of 22.0 nM injected dye) BTB under pulseless (pneumatic) flow conditions. The cells behave as multipath devices where the effective path lengths are greater at low absorbance values. In our experiments, where non-coherent light is launched through optical fibers that are large compared to capillary bore dimensions, increase in the effective path length of the cell do not occur in a predictable fashion with the angle of incidence of the light beam. Although the effective path length almost linearly increases with increasing distance between the light entry and exit windows, the absolute values of the effective path lengths are always lower than this physical distance, suggesting that after some passage through the solution, light largely travels through or along the glass wall. Square capillaries have better light transmission and offer some performance advantages. Multi-reflection cells can indeed be of value for sensitive detection in microflow systems.     

The directional contact distance of two ellipsoids: coarse-grained potentials for anisotropic interactions

We obtain the distance of closest approach of the surfaces of two arbitrary ellipsoids valid at any orientation and separation measured along their intercenter vector. This directional distance is derived from the elliptic contact function. The geometric meaning behind this approach is clarified. An elliptic pair potential for modeling arbitrary mixtures of elliptic particles, whether hard or soft, is proposed based on this distance. Comparisons with Gay-Berne potentials are discussed. Analytic expressions for the forces and torques acting on the elliptic particles are given.     

Computing the distribution of the Robinson-Foulds distance

With the exponential growth of genome databases, the importance of phylogenetics has increased dramatically over the past years. Studying phylogenetic trees enables us not only to understand how genes, genomes, and species evolve, but also helps us predict how they might change in future. One of the crucial aspects of phylogenetics is the comparison of two or more phylogenetic trees. There are different metrics for computing the dissimilarity between a pair of trees. The Robinson-Foulds (RF) distance is one of the widely used metrics on the space of labeled trees. The distribution of the RF distance from a given tree has been studied before, but the fastest known algorithm for computing this distribution is a slow, albeit polynomial-time, O(l⁵) algorithm. In this paper, we modify the dynamic programming algorithm for computing the distribution of this distance for a given tree by leveraging the number-theoretic transform (NTT), and improve the running time from O(l⁵) to O(l³ log l), where l is the number of tips of the tree. In addition to its practical usefulness, our method represents a theoretical novelty, as it is, to our knowledge, one of the rare applications of the number-theoretic transform for solving a computational biology problem.     

Scaled Euclidian distances: a general dissimilarity index with a suitably defined geometrical foundation

A simple manipulation of the Euclidian distance expression permits to obtain a scaled dissimilarity index measure, varying within a range of values lying in the interval [0,1]. Here is presented the theoretical background, its application to quantum similarity and use for artificial intelligence general purposes as well. The origin of Hodgkin-Richards index is analyzed and compared with quantum similarity Carbó index.     

Optimizing heterosurface adsorbent synthesis for liquid chromatography

The structural and geometric parameters of a silica matrix (SM) for the synthesis of heterosurface adsorbents (HAs) are optimized. Modification is performed by shielding the external surfaces of alkyl-modified silica (AS) using human serum albumin and its subsequent crosslinking. The structural and geometric characteristics of the SM, AS, and HA are measured via low-temperature nitrogen adsorption. It is found that the structural characteristics of AS pores with diameters D < 6 nm do not change during HA synthesis, while the volume of pores with diameters of 6 nm < D < 9 nm shrinks slightly due to the adsorption of albumin in the pore orifices. It is established that the volume of pores with diameters D > 9 nm reduces significantly due to adsorption of albumin. It is concluded that silica gel with a maximum pore size distribution close to 5 nm and a minimal proportion of pores with D > 9 nm is optimal for HA synthesis; this allows us to achieve the greatest similarity between the chromatographic retention parameters for HA and AS. The suitability of the synthesized adsorbents for analyzing drugs in biological fluids through direct sample injection is confirmed by chromatography. It was found that the percentage of the protein fraction detected at the outlet of the chromatographic column is 98%.     

Constrained and unconstrained chirality functions. A new method, going from discrete to continuous space, to find the best overlap between enantiomer atoms

This paper provides two different functions for quantifying geometric chirality. Both are based on Euclidean distances between enantiomer atoms and the best associated RMS, but, depending on the function, atoms are paired without or with constraint. In the first, the best match between the enantiomer atoms is sought by means of a completely new method in which one enantiomer is fitted onto a spline approximation of the other. This method reestablishes the continuity between similarity and dissimilarity, broken in discrete space by atom-per-atom shape recognition treatments. In the second, each enantiomer atom is paired with its mirror image and only the mirror location is optimized. Congruity-based chirality measures are grouped into two classes according to whether the discrimination function between the chiral object and the reference object takes some constraint into account (second class) or does not (first class). In this paper, our constrained or unconstrained chirality function is compared with the continuous chirality measure (second class). It is inferred that only chirality scales of the same class can be correlated.     

Effect of sample to detector geometry on the accuracy of instrumental neutron activation analysis and implications for the design of a simple automatic sample-changing wheel suitable for the routine counting of low activity geological samples

The effect of small geometric errors in positioning samples in front of gamma detectors during instrumental neutron activation analysis is discussed and it is shown that, for example, a 0.2 mm repositioning discrepancy for a source to detector distance of 10 mm can cause errors in measured activity of as much as 4 per cent. This calculation has been undertaken for a range of sample-detector distances (5–50 mm) in order to emphasise the importance of sample counting geometry on the accuracy of INAA calibrations. Criteria derived from this investigation have been used to design and construct a simple samplechanging wheel suitable for the routine analysis of low activity geological samples. The effect of the choice of sample wheel size on the magnitude of spectral interference between counting and non-counting samples mounted in the wheel has been considered.     

Damaging processes in polypropylene compound: Experiment and modeling

The aim of this paper is to present a procedure of construction of constitutive equations within the framework of Continuum Mechanics. The main focus of our effort is to introduce the geometric change at a high level of strain and the damage which are generally developed in simple tests (tension, shear) of polymeric materials such as polypropylene compounds or copolymers (PP). High-resolution strain-mapping techniques are employed to determine the surface strain fields and, consequently, a measurement of the volume change. A phenomenological model based upon experimental observations was developed to reproduce the main behavior, e.g., the stress strain curves, including the volume change and their consequences. State Variables are defined and related to their evolution in relation with the state laws. The identification of the resulting model was made by reproducing the data issued from basic tests (Tension, Iosipescu Shear). Published in Russian in Vysokomolekulyarnye Soedineniya, Ser. A. 2008, Vol. 50, No. 5, pp. 850–861. This article was submitted by the authors in English.     

Influence of the distance between a spectrometer and sample on the intensity of X-ray fluorescence

Expressions for calculating the extreme point coordinates of focal spots of X-ray tubes and a detector’s sensitive area are found. These coordinates are used in calculations of the sample area. The dependence of the X-ray fluorescence intensity on the distance between a spectrometer and an analyzed sample is studied experimentally. The intensities of the FeK _α spectral lines in iron-containing materials are calculated at different geometric parameters of a spectrometer. It is found that the distance between a sample and detector at which the maximum of the measured intensity is observed depends on the size and position of the detector and X-ray tube collimators, as well as on the relative position of the X-ray tube and detector. Recommendations on how to achieve the maximum intensity of X-ray fluorescence are proposed. The results of the present work can be used for the development of X-ray fluorescence analysis techniques applicable for free-flowing materials directly in technological processes.     

The molecular and crystal structure of stable 5-methyl-2-methylsulfonyl-3-thiophenecarbonitrile oxide

A stable thiophene derivative, 5-methyi-2-methylsulfonyl-3-thiophenecarbonitrile oxide, which is active in reactions with dipolarophiles, was studied by means of X-ray structural analysis. In the crystalline state the structure includes two independent molecules with similar values of geometric and conformation parameters. The bond angle at the C atom of the nitrile oxide group is significantly different from 180°. The intramolecular distances between the C and S atoms in the nitrile oxide and sulfonyl groups are well below the equilibrium distance. The stability of the molecule is thought to be increased by electrostatic or donor-acceptor interactions between the atoms of these groups. The mutual orientation of the two independent molecules in the crystal is nearly orthogonal.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 4, pp. 725–727, April, 1993.