Kwan-yuet Ho

National Institutes of Health, Division of Computational Bioscience, Department Member

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Papers by Kwan-yuet Ho

P194 Recommendations for prioritising expert review of free-text job descriptions that underwent computer-based coding using the soccer algorithm

Occupational and Environmental Medicine, 2016

Computer-based coding of free-text job descriptions to efficiently identify occupations in epidemiological studies

Occupational and environmental medicine, Jan 21, 2016

Mapping job titles to standardised occupation classification (SOC) codes is an important step in ... more Mapping job titles to standardised occupation classification (SOC) codes is an important step in identifying occupational risk factors in epidemiological studies. Because manual coding is time-consuming and has moderate reliability, we developed an algorithm called SOCcer (Standardized Occupation Coding for Computer-assisted Epidemiologic Research) to assign SOC-2010 codes based on free-text job description components. Job title and task-based classifiers were developed by comparing job descriptions to multiple sources linking job and task descriptions to SOC codes. An industry-based classifier was developed based on the SOC prevalence within an industry. These classifiers were used in a logistic model trained using 14 983 jobs with expert-assigned SOC codes to obtain empirical weights for an algorithm that scored each SOC/job description. We assigned the highest scoring SOC code to each job. SOCcer was validated in 2 occupational data sources by comparing SOC codes obtained from SO...

Phase Transition and Critical Phenomena

HTJoinSolver: Human immunoglobulin VDJ partitioning using approximate dynamic programming constrained by conserved motifs

BMC bioinformatics, Jan 23, 2015

Partitioning the human immunoglobulin variable region into variable (V), diversity (D), and joini... more Partitioning the human immunoglobulin variable region into variable (V), diversity (D), and joining (J) segments is a common sequence analysis step. We introduce a novel approximate dynamic programming method that uses conserved immunoglobulin gene motifs to improve performance of aligning V-segments of rearranged immunoglobulin (Ig) genes. Our new algorithm enhances the former JOINSOLVER algorithm by processing sequences with insertions and/or deletions (indels) and improves the efficiency for large datasets provided by high throughput sequencing. In our simulations, which include rearrangements with indels, the V-matching success rate improved from 61% for partial alignments of sequences with indels in the original algorithm to over 99% in the approximate algorithm. An improvement in the alignment of human VDJ rearrangements over the initial JOINSOLVER algorithm was also seen when compared to the Stanford.S22 human Ig dataset with an online VDJ partitioning software evaluation too...

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Computer-Based Coding of Occupation Codes for Epidemiological Analyses

2014 IEEE 27th International Symposium on Computer-Based Medical Systems, 2014

Mapping job titles to standardized occupation classification (SOC) codes is an important step in ... more Mapping job titles to standardized occupation classification (SOC) codes is an important step in evaluating changes in health risks over time as measured in inspection databases. However, manual SOC coding is cost prohibitive for very large studies. Computer based SOC coding systems can improve the efficiency of incorporating occupational risk factors into large-scale epidemiological studies. We present a novel method of mapping verbatim job titles to SOC codes using a large table of prior knowledge available in the public domain that included detailed description of the tasks and activities and their synonyms relevant to each SOC code. Job titles are compared to our knowledge base to find the closest matching SOC code. A soft Jaccard index is used to measure the similarity between a previously unseen job title and the knowledge base. Additional information such as standardized industrial codes can be incorporated to improve the SOC code determination by providing additional context to break ties in matches.

Properties of Metallic Helimagnets

This dissertation investigates various aspects of helimagnets. Helimagnets are magnets with spins... more This dissertation investigates various aspects of helimagnets. Helimagnets are magnets with spins aligned in helical order at low temperatures. It exists in materials of crystal structure lacking the spatial inversion symmetry. The helical order is due to the Dzyaloshinskii-Moriya (DM) mechanism. Examples of helimagnets include MnSi, FeGe and Fe 1−x Co x Si.

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Quantum Entanglement in Continuous System

Influence of Goldstone modes on the electronic properties of helical magnets

Bulletin of the American Physical Society, Jan 1, 2011

We have investigated the influence of Goldstone modes on the electronic properties of helical mag... more

Skyrmions and Their Sizes in Helimagnets

arXiv preprint arXiv:1112.5991, Jan 1, 2011

Skyrmion gases and lattices in helimagnets are studied, and the size of a Skyrmion in various pha... more Skyrmion gases and lattices in helimagnets are studied, and the size of a Skyrmion in various phases is estimated. For isolated Skyrmions, the long distance tail is related to the magnetization correlation functions and exhibits power-law decay if the phase spontaneously breaks a continuous symmetry, but decays exponentially otherwise. The size of a Skyrmion is found to depend on a number of length scales. These length scales are related to the strength of Dzyaloshinskii-Moriya (DM) interaction, the thermal correlation lengths, and the strength of the external magnetic field. An Abrikosov lattice of Skyrmions is found to exist near the helimagnetic phase boundary, and the core-to-core distance is estimated.

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Entanglement between a Two-level System and a Quantum Harmonic Oscillator

arXiv preprint arXiv:0801.0310, Jan 1, 2008

The entanglement between a Pauli-like two-level system and a quantum harmonic oscillator enhanced... more The entanglement between a Pauli-like two-level system and a quantum harmonic oscillator enhanced by an interaction between them and a δ-pulse sequence is studied, with the decoherence due to their coupling with a Markovian bath. Without the Markovian bath, the entanglement is enhanced to maximum possible values. With the Markovian bath, the entanglement is enhanced up to some time and then dissipated, with the system in thermal equilibrium with the Markovian bath after a very long time. The time for achieving the maximum entanglement shows discontinuous jumps over the parameters of decoherence.

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Vortex formation in a two-dimensional Bose gas

Journal of Physics B: Atomic, Molecular …, Jan 1, 2010

We discuss the stability of a homogeneous two-dimensional Bose gas at finite temperature against ... more We discuss the stability of a homogeneous two-dimensional Bose gas at finite temperature against formation of isolated vortices. We consider a patch of several healing lengths in size and compute its free energy using the Euclidean formalism. Since we deal with an open system, which is able to exchange particles and angular momentum with the rest of the condensate, we use the symmetrybreaking (as opposed to the particle number conserving) formalism, and include configurations with all values of angular momenta in the partition function. At finite temperature, there appear sphaleron configurations associated to isolated vortices. The contribution from these configurations to the free energy is computed in the dilute gas approximation. We show that the Euclidean action of linearized perturbations of a vortex is not positive definite. As a consequence the free energy of the 2D Bose gas acquires an imaginary part. This signals the instability of the gas. This instability may be identified with the Berezinskii, Kosterlitz and Thouless (BKT) transition. PACS numbers: 67.85.-d, 64.60.Q-, 03.75.Lm, 67.25.dj, 31.15.xk

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Ordered phases of itinerant Dzyaloshinsky-Moriya magnets and their electronic properties

Physical Review B, Jan 1, 2010

A field theory appropriate for magnets that display helical order due to the Dzyaloshinsky-Moriya... more A field theory appropriate for magnets that display helical order due to the Dzyaloshinsky-Moriya mechanism, a class that includes MnSi and FeGe, is used to derive the phase diagram in a meanfield approximation. The helical phase, the conical phase in an external magnetic field, and recent proposals for the structure of the A-phase and the non-Fermi-liquid region in the paramagnetic phase are discussed. It is shown that the orientation of the helical pitch vector along an external magnetic field within the conical phase occurs via two distinct phase transitions. The Goldstone modes that result from the long-range order in the various phases are determined, and their consequences for electronic properties, in particular the specific heat, the single-particle relaxation time, and the electrical and thermal conductivities, are derived. Various aspects of the ferromagnetic limit, and qualitative differences between the transport properties of helimagnets and ferromagnets, are also discussed.

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