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

https://www2.econ.iastate.edu/tesfatsi/DeepLearningInNeuralNetworksOverview.JSchmidhuber2015.pdf

Deep learning in neural networks

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

Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

Publisher Summary This chapter focuses on the modern notion of short-term memory, called working memory. Working memory refers to the temporary maintenance of information that was just experienced or just retrieved from long-term memory but no longer exists in the external environment. These internal representations are short-lived, but can be maintained for longer periods of time through active rehearsal strategies, and can be subjected to various operations that manipulate the information in such a way that makes it useful for goal-directed behavior. Working memory is a system that is critically important in cognition and seems necessary in the course of performing many other cognitive functions, such as reasoning, language comprehension, planning, and spatial processing. This chapter demonstrates the functional importance of dopamine to working memory function in several ways. Elucidation of the cognitive and neural mechanisms underlying human working memory is an important focus of cognitive neuroscience and neurology for much of the past decade. One conclusion that arises from research is that working memory, a faculty that enables temporary storage and manipulation of information in the service of behavioral goals, can be viewed as neither a unitary, nor a dedicated system. Data from numerous neuropsychological and neurophysiological studies in animals and humans demonstrates that a network of brain regions, including the prefrontal cortex, is critical for the active maintenance of internal representations.

Chapter 11 Working memory

A fundamental challenge for systems neuroscience is to quantitatively relate its three major branches of research: brain-activity measurement, behavioral measurement, and computational modeling. Using measured brain-activity patterns to evaluate computational network models is complicated by the need to define the correspondency between the units of the model and the channels of the brain-activity data, e.g. single-cell recordings or voxels from functional magnetic resonance imaging (fMRI). Similar correspondency problems complicate relating activity patterns between different modalities of brain-activity measurement, and between subjects and species. In order to bridge these divides, we suggest abstracting from the activity patterns themselves and computing representational dissimilarity matrices, which characterize the information carried by a given representation in a brain or model. We propose a new experimental and data-analytical framework called representational similarity analysis (RSA), in which multi-channel measures of neural activity are quantitatively related to each other and to computational theory and behavior by comparing representational dissimilarity matrices. We demonstrate RSA by relating representations of visual objects as measured with fMRI to computational models spanning a wide range of complexities. We argue that these ideas, which have deep roots in psychology and neuroscience, will allow the integrated quantitative analysis of data from all three branches, thus contributing to a more unified systems neuroscience.

https://www.mrc-cbu.cam.ac.uk/wp-content/uploads/2013/01/kriegeskorte_RSA_frontiersSN20081.pdf

Representational Similarity Analysis – Connecting the Branches of Systems Neuroscience

A neuroscientific experiment typically generates a large amount of data, of which only a small fraction is analyzed in detail and presented in a publication. However, selection among noisy measurements can render circular an otherwise appropriate analysis and invalidate results. Here we argue that systems neuroscience needs to adjust some widespread practices to avoid the circularity that can arise from selection. In particular, ‘double dipping’, the use of the same dataset for selection and selective analysis, will give distorted descriptive statistics and invalid statistical inference whenever the results statistics are not inherently independent of the selection criteria under the null hypothesis. To demonstrate the problem, we apply widely used analyses to noise data known to not contain the experimental effects in question. Spurious effects can appear in the context of both univariate activation analysis and multivariate pattern-information analysis. We suggest a policy for avoiding circularity.

/pdf/circular-analysis-in-systems-neuroscience-the-dangers-of-vhuzaaene1.pdf

Circular analysis in systems neuroscience: the dangers of double dipping.

The development of high-resolution neuroimaging and multielectrode electrophysiological recording provides neuroscientists with huge amounts of multivariate data. The complexity of the data creates a need for statistical summary, but the local averaging standardly applied to this end may obscure the effects of greatest neuroscientific interest. In neuroimaging, for example, brain mapping analysis has focused on the discovery of activation, i.e., of extended brain regions whose average activity changes across experimental conditions. Here we propose to ask a more general question of the data: Where in the brain does the activity pattern contain information about the experimental condition? To address this question, we propose scanning the imaged volume with a "searchlight," whose contents are analyzed multivariately at each location in the brain.

https://www.pnas.org/content/pnas/103/10/3863.full.pdf

Information-based functional brain mapping

http://lsr-web-02.mrc-cbu.cam.ac.uk/personal/nikolaus.kriegeskorte/kriegeskorte_hmIT_neuron2008.pdf

Matching Categorical Object Representations in Inferior Temporal Cortex of Man and Monkey

Inferior temporal (IT) cortex in human and nonhuman primates serves visual object recognition. Computational object-vision models, although continually improving, do not yet reach human performance. It is unclear to what extent the internal representations of computational models can explain the IT representation. Here we investigate a wide range of computational model representations (37 in total), testing their categorization performance and their ability to account for the IT representational geometry. The models include well-known neuroscientific object-recognition models (e.g. HMAX, VisNet) along with several models from computer vision (e.g. SIFT, GIST, self-similarity features, and a deep convolutional neural network). We compared the representational dissimilarity matrices (RDMs) of the model representations with the RDMs obtained from human IT (measured with fMRI) and monkey IT (measured with cell recording) for the same set of stimuli (not used in training the models). Better performing models were more similar to IT in that they showed greater clustering of representational patterns by category. In addition, better performing models also more strongly resembled IT in terms of their within-category representational dissimilarities. Representational geometries were significantly correlated between IT and many of the models. However, the categorical clustering observed in IT was largely unexplained by the unsupervised models. The deep convolutional network, which was trained by supervision with over a million category-labeled images, reached the highest categorization performance and also best explained IT, although it did not fully explain the IT data. Combining the features of this model with appropriate weights and adding linear combinations that maximize the margin between animate and inanimate objects and between faces and other objects yielded a representation that fully explained our IT data. Overall, our results suggest that explaining IT requires computational features trained through supervised learning to emphasize the behaviorally important categorical divisions prominently reflected in IT.

https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003915&type=printable

Nikolaus Kriegeskorte

Papers

Representational Similarity Analysis – Connecting the Branches of Systems Neuroscience

Circular analysis in systems neuroscience: the dangers of double dipping.

Information-based functional brain mapping

Matching Categorical Object Representations in Inferior Temporal Cortex of Man and Monkey

Deep supervised, but not unsupervised, models may explain IT cortical representation.