arXiv subjects

Yi-Kuo Yu

Publications and source records attributed to Yi-Kuo Yu.

26 records · Page 2Linked to original sources

arXiv2008

The effectiveness of position- and composition-specific gap costs for protein similarity searches

The flexibility in gap cost enjoyed by Hidden Markov Models (HMMs) is expected to afford them better retrieval accuracy than position-specific scoring matrices (PSSMs). We attempt to quantify the effect of more general gap parameters by separately examining the influence of position- and composition-specific gap scores, as well as by comparing the retrieval accuracy of the PSSMs constructed using an iterative procedure to that of the HMMs provided by Pfam and SUPERFAMILY, curated ensembles of multiple alignments. We found that position-specific gap penalties have an advantage over uniform gap costs. We did not explore optimizing distinct uniform gap costs for each query. For Pfam, PSSMs iteratively constructed from seeds based on HMM consensus sequences perform equivalently to HMMs that were adjusted to have constant gap transition probabilities, albeit with much greater variance. We observed no effect of composition-specific gap costs on retrieval performance.

q-bio.BM↗

arXiv2007

Geometric Aspects of Biological Sequence Comparison

We propose a general framework for converting global and local similarities between biological sequences to quasi-metrics. In contrast to previous works, our formulation allows asymmetric distances, originating from uneven weighting of strings, that may induce non-trivial partial orders on sets of biosequences. Furthermore, the $\ell^p$-type distances considered are more general than traditional generalized string edit distances corresponding to the $\ell^1$ case, and enable conversion of sequence similarities to distances for a much wider class of scoring schemes. Our constructions require much less restrictive gap penalties than the ones regularly used. Numerous examples are provided to illustrate the concepts introduced and their potential applications.

q-bio.QM↗

arXiv2006

Decoding Information from noisy, redundant, and intentionally-distorted sources

Advances in information technology reduce barriers to information propagation, but at the same time they also induce the information overload problem. For the making of various decisions, mere digestion of the relevant information has become a daunting task due to the massive amount of information available. This information, such as that generated by evaluation systems developed by various web sites, is in general useful but may be noisy and may also contain biased entries. In this study, we establish a framework to systematically tackle the challenging problem of information decoding in the presence of massive and redundant data. When applied to a voting system, our method simultaneously ranks the raters and the ratees using only the evaluation data, consisting of an array of scores each of which represents the rating of a ratee by a rater. Not only is our appraoch effective in decoding information, it is also shown to be robust against various hypothetical types of noise as well as intentional abuses.

cond-mat.dis-nn↗

arXiv2005

A new method for analyzing second-order phase transitions applied to the ferromagnetic transition of a polaronic system

A new method for analyzing second-order phase transitions is presented and applied to the polaronic system La$_{0.7}$Ca$_{0.3}$MnO$_{3}$. It utilizes heat capacity and thermal expansion data simultaneously to correctly predict the critical temperature's pressure dependence. Analysis of the critical phenomena reveals second-order behavior and an unusually large heat capacity exponent.

cond-mat.str-el↗

arXiv2002

Buyer feedback as a filtering mechanism for reputable sellers

We propose a continuum model for the description of buyer and seller dynamics in an Internet market. The relevant variables are the research effort of buyers and the sellers' reputation building process. We show that, if a commercial web-site gives consumers the possibility to rate credibly sellers they bargained with, vendors are forced to be more honest. This leads to mutual beneficial symbiosis between buyers and sellers; the overall enhanced volume of transactions contributes ultimately to the web-site, which facilitates the matchmaking service.

physics.soc-ph↗

arXiv2001

On the Anti-Wishart distribution

We provide the probability distribution function of matrix elements each of which is the inner product of two vectors. The vectors we are considering here are independently distributed but not necessarily Gaussian variables. When the number of components M of each vector is greater than the number of vectors N, one has a $N\times N$ symmetric matrix. When $M\ge N$ and the components of each vector are independent Gaussian variables, the distribution function of the $N(N+1)/2$ matrix elements was obtained by Wishart in 1928. When N > M, what we called the ``Anti-Wishart'' case, the matrix elements are no longer completely independent because the true degrees of freedom becomes smaller than the number of matrix elements. Due to this singular nature, analytical derivation of the probability distribution function is much more involved than the corresponding Wishart case. For a class of general random vectors, we obtain the analytical distribution function in a closed form, which is a product of various factors and delta function constraints, composed of various determinants. The distribution function of the matrix element for the $M\ge N$ case with the same class of random vectors is also obtained as a by-product. Our result is closely related to and should be valuable for the study of random magnet problem and information redundancy problem.

cond-mat.stat-mech↗

arXiv1998

Are Directed Waves Multifractal?

Wave propagation is studied in a sufficiently anisotropic random medium that backscattering along one direction can be neglected. A Fokker-Planck equation is derived the solution to which would provide a complete statistical description of such directed waves. The Fokker-Planck equation is mapped onto an su(1,1) ferromagnet and its symmetries are identified. Using the symmetries asymptotic wave function distributions are computed and used to show that directed wave functions fill space uniformly and do not have multifractal character.

cond-mat.dis-nn↗

arXiv1996

Nonuniversal Critical Conductance Fluctuations of Chiral Surface States in the Bulk Integral Quantum Hall Effect -- An Exact Calculation

The chiral surface electrons in the bulk quantum Hall effect probably form the first extended system in which conductance fluctuations can be calculated non-perturbatively in the presence of disorder. By use of the Kubo formula with appropriate boundary conditions, we calculate exactly the variance of conductance with non-perturbative methods. We find that the conductance fluctuations of this system are ``nonuniversal'' and the variance of the conductance scales in a very peculiar way. This result can be checked with exact computation using the Landauer-Buttiker formula and both methods show the same scaling behavior. We have also calculated the diffusion constant fluctuations exactly. We find that the diffusion constant fluctuations vanish and thus play no role in the conductance fluctuations.

cond-mat.mes-hall↗