抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Suppose x is an unknown vector in Ropfm (a digital image or signal); we plan to measure n general linear functionals of x and then reconstruct. If x is known to be compressible by transform coding with a known transform, and we reconstruct via the nonlinear procedure defined here, the number of measurements n can be dramatically smaller than the size m. Thus, certain natural classes of images with m pixels need only n=O(m1/4log5/2(m)) nonadaptive nonpixel samples for faithful recovery, as opposed to the usual m pixel samples. More specifically, suppose x has a sparse representation in some orthonormal basis (e.g., wavelet, Fourier) or tight frame (e.g., curvelet, Gabor)-so the coefficients belong to an lscrp ball for 0<ples1. The N most important coefficients in that expansion allow reconstruction with lscr2 error O(N1/2-1p/). It is possible to design n=O(Nlog(m)) nonadaptive measurements allowing reconstruction with accuracy comparable to that attainable with direct knowledge of the N most important coefficients. Moreover, a good approximation to those N important coefficients is extracted from the n measurements by solving a linear program-Basis Pursuit in signal processing. The nonadaptive measurements have the character of "random" linear combinations of basis/frame elements. Our results use the notions of optimal recovery, of n-widths, and information-based complexity. We estimate the Gel'fand n-widths of lscrp balls in high-dimensional Euclidean space in the case 0<ples1, and give a criterion identifying near- optimal subspaces for Gel'fand n-widths. We show that "most" subspaces are near-optimal, and show that convex optimization (Basis Pursuit) is a near-optimal way to extract information derived from these near-optimal subspaces

Compressed sensing

Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Machine learning

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

The structure and dynamics of multilayer networks

An iterative algorithm for the multiuser detection problem that arises in code division multiple access (CDMA) systems is developed on the basis of Pearl's belief propagation (BP). We show that the BP-based algorithm exhibits nearly optimal performance in a practical time scale by utilizing the central limit theorem and self-averaging property appropriately, whereas direct application of BP to the detection problem is computationally difficult and far from practical. We further present close relationships of the proposed algorithm to the Thouless–Anderson–Palmer approach and replica analysis known in spin-glass research.

/pdf/a-cdma-multiuser-detection-algorithm-on-the-basis-of-belief-5a3x8vsq3v.pdf

A CDMA multiuser detection algorithm on the basis of belief propagation

We consider the problem of reconstructing an N-dimensional continuous vector x from P constraints which are generated from its linear transformation under the assumption that the number of non-zero elements of x is typically limited to ρN (0≤ρ≤1). Problems of this type can be solved by minimizing a cost function with respect to the Lp-norm , subject to the constraints under an appropriate condition. For several values of p, we assess a typical case limit αc(ρ), which represents a critical relation between α = P/N and ρ for successfully reconstructing the original vector by the minimization for typical situations in the limit while keeping α finite, utilizing the replica method. For p = 1, αc(ρ) is considerably smaller than its worst case counterpart, which has been rigorously derived in the existing literature on information theory.

A typical reconstruction limit for compressed sensing based onLp-norm minimization

We employ two different methods, based on belief propagation and TAP,for decoding corrupted messages encoded by employing Sourlas's method, where the code word comprises products of K bits selected randomly from the original message. We show that the equations obtained by the two approaches are similar and provide the same solution as the one obtained by the replica approach in some cases K=2. However, we also show that for K>=3 and unbiased messages the iterative solution is sensitive to the initial conditions and is likely to provide erroneous solutions; and that it is generally beneficial to use Nishimori's temperature, especially in the case of biased messages.

/pdf/belief-propagation-vs-tap-for-decoding-corrupted-messages-2mb56o9fa3.pdf

Belief propagation vs. TAP for decoding corrupted messages

We investigate the performance of error-correcting codes, where the code word comprises products of K bits selected from the original message and decoding is carried out utilizing a connectivity tensor with C connections per index. Shannon's bound for the channel capacity is recovered for large K and zero temperature when the code rate K/C is finite. Close to optimal error-correcting capability is obtained for finite K and C. We examine the finite-temperature case to assess the use of simulated annealing for decoding and extend the analysis to accommodate other types of noisy channels.

/pdf/statistical-mechanics-of-error-correcting-codes-31dkragscl.pdf

Statistical mechanics of error-correcting codes

An approach to analyze the performance of the code division multiple access (CDMA) scheme, which is a core technology used in modern wireless communication systems, is provided. The approach characterizes the objective system by the eigenvalue spectrum of a cross-correlation matrix composed of signature sequences used in CDMA communication, which enable us to handle a wider class of CDMA systems beyond the basic model reported by Tanaka in Europhys. Lett., 54 (2001) 540. The utility of the scheme is shown by analyzing a system in which the generation of signature sequences is designed for enhancing the orthogonality.

https://iopscience.iop.org/article/10.1209/epl/i2006-10380-5/pdf

Yoshiyuki Kabashima

Papers

A CDMA multiuser detection algorithm on the basis of belief propagation

A typical reconstruction limit for compressed sensing based onLp-norm minimization

Belief propagation vs. TAP for decoding corrupted messages

Statistical mechanics of error-correcting codes

Analysis of CDMA systems that are characterized by eigenvalue spectrum