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

Tree boosting is a highly effective and widely used machine learning method. In this paper, we describe a scalable end-to-end tree boosting system called XGBoost, which is used widely by data scientists to achieve state-of-the-art results on many machine learning challenges. We propose a novel sparsity-aware algorithm for sparse data and weighted quantile sketch for approximate tree learning. More importantly, we provide insights on cache access patterns, data compression and sharding to build a scalable tree boosting system. By combining these insights, XGBoost scales beyond billions of examples using far fewer resources than existing systems.

/pdf/xgboost-a-scalable-tree-boosting-system-48ocu6x4c7.pdf

XGBoost: A Scalable Tree Boosting System

In this paper, we present Google, a prototype of a large-scale search engine which makes heavy use of the structure present in hypertext. Google is designed to crawl and index the Web efficiently and produce much more satisfying search results than existing systems. The prototype with a full text and hyperlink database of at least 24 million pages is available at http://google.stanford.edu/. To engineer a search engine is a challenging task. Search engines index tens to hundreds of millions of web pages involving a comparable number of distinct terms. They answer tens of millions of queries every day. Despite the importance of large-scale search engines on the web, very little academic research has been done on them. Furthermore, due to rapid advance in technology and web proliferation, creating a web search engine today is very different from three years ago. This paper provides an in-depth description of our large-scale web search engine -- the first such detailed public description we know of to date. Apart from the problems of scaling traditional search techniques to data of this magnitude, there are new technical challenges involved with using the additional information present in hypertext to produce better search results. This paper addresses this question of how to build a practical large-scale system which can exploit the additional information present in hypertext. Also we look at the problem of how to effectively deal with uncontrolled hypertext collections where anyone can publish anything they want.

/pdf/the-anatomy-of-a-large-scale-hypertextual-web-search-engine-496poj789d.pdf

The anatomy of a large-scale hypertextual Web search engine

The importance of a Web page is an inherently subjective matter, which depends on the readers interests, knowledge and attitudes. But there is still much that can be said objectively about the relative importance of Web pages. This paper describes PageRank, a mathod for rating Web pages objectively and mechanically, effectively measuring the human interest and attention devoted to them. We compare PageRank to an idealized random Web surfer. We show how to efficiently compute PageRank for large numbers of pages. And, we show how to apply PageRank to search and to user navigation.

The PageRank Citation Ranking : Bringing Order to the Web

Audio sources frequently concentrate much of their energy into a relatively small proportion of the available time-frequency cells in a short-time Fourier transform (STFT). This sparsity makes it possible to separate sources, to some degree, simply by selecting STFT cells dominated by the desired source, setting all others to zero (or to an estimate of the obscured target value), and inverting the STFT to a waveform. The problem of source separation then becomes identifying the cells containing good target information. We treat this as a classification problem, and train a Relevance Vector Machine (a probabilistic relative of the Support Vector Machine) to perform this task. We compare the performance of this classifier both against SVMs (it has similar accuracy but is not as efficient as RVMs), and against a traditional Computational Auditory Scene Analysis (CASA) technique based on a noise-robust pitch tracker, which the RVM outperforms significantly. Differences between the RVM- and pitch-tracker-based mask estimation suggest benefits to be obtained by combining both.

/pdf/estimating-single-channel-source-separation-masks-relevance-iw1mh9dwqf.pdf

Estimating Single-Channel Source Separation Masks: Relevance Vector Machine Classifiers vs. Pitch-Based Masking

In recent years, rapid progress has been made on the problem of single-channel sound separation using supervised training of deep neural networks. In such supervised approaches, a model is trained to predict the component sources from synthetic mixtures created by adding up isolated ground-truth sources. Reliance on this synthetic training data is problematic because good performance depends upon the degree of match between the training data and real-world audio, especially in terms of the acoustic conditions and distribution of sources. The acoustic properties can be challenging to accurately simulate, and the distribution of sound types may be hard to replicate. In this paper, we propose a completely unsupervised method, mixture invariant training (MixIT), that requires only single-channel acoustic mixtures. In MixIT, training examples are constructed by mixing together existing mixtures, and the model separates them into a variable number of latent sources, such that the separated sources can be remixed to approximate the original mixtures. We show that MixIT can achieve competitive performance compared to supervised methods on speech separation. Using MixIT in a semi-supervised learning setting enables unsupervised domain adaptation and learning from large amounts of real world data without ground-truth source waveforms. In particular, we significantly improve reverberant speech separation performance by incorporating reverberant mixtures, train a speech enhancement system from noisy mixtures, and improve universal sound separation by incorporating a large amount of in-the-wild data.

Unsupervised Sound Separation Using Mixture Invariant Training

The lack of precise numerical information for the values of biological parameters severely limits the development and analysis of models of genetic regulatory networks. To deal with this problem, we propose a method for the analysis of genetic regulatory networks with parameter uncertainty. We consider models based on piecewise-multiaffine differential equations, dynamical properties expressed in temporal logic, and intervals for the values of uncertain parameters. The problem is then either to guarantee that the system satisfies the expected properties for every possible parameter value - the corresponding parameter set is then called valid - or to find valid subsets of a given parameter set. The proposed method uses discrete abstractions and model checking, and allows for efficient search of the parameter space. This approach has been implemented in a tool for robust verification of gene networks (RoVerGeNe) and applied to the tuning of a synthetic network build in E. coli.

/pdf/model-checking-genetic-regulatory-networks-with-parameter-3ml6dxm0fh.pdf

Model checking genetic regulatory networks with parameter uncertainty

Making recommendations by learning to rank is becoming an increasingly studied area. Approaches that use stochastic gradient descent scale well to large collaborative filtering datasets, and it has been shown how to approximately optimize the mean rank, or more recently the top of the ranked list. In this work we present a family of loss functions, the k-order statistic loss, that includes these previous approaches as special cases, and also derives new ones that we show to be useful. In particular, we present (i) a new variant that more accurately optimizes precision at k, and (ii) a novel procedure of optimizing the mean maximum rank, which we hypothesize is useful to more accurately cover all of the user's tastes. The general approach works by sampling N positive items, ordering them by the score assigned by the model, and then weighting the example as a function of this ordered set. Our approach is studied in two real-world systems, Google Music and YouTube video recommendations, where we obtain improvements for computable metrics, and in the YouTube case, increased user click through and watch duration when deployed live on www.youtube.com.

https://dl.acm.org/doi/pdf/10.1145/2507157.2507210

Learning to rank recommendations with the k-order statistic loss

A long-standing goal of synthetic biology is to rapidly engineer new regulatory circuits from simpler devices. As circuit complexity grows, it becomes increasingly important to guide design with quantitative models, but previous efforts have been hindered by lack of predictive accuracy. To address this, we developed Empirical Quantitative Incremental Prediction (EQuIP), a new method for accurate prediction of genetic regulatory network behavior from detailed characterizations of their components. In EQuIP, precisely calibrated time-series and dosage-response assays are used to construct hybrid phenotypic/mechanistic models of regulatory processes. This hybrid method ensures that model parameters match observable phenomena, using phenotypic formulation where current hypotheses about biological mechanisms do not agree closely with experimental observations. We demonstrate EQuIP’s precision at predicting distributions of cell behaviors for six transcriptional cascades and three feed-forward circuits in mamma...

Ron Weiss

Papers

Estimating Single-Channel Source Separation Masks: Relevance Vector Machine Classifiers vs. Pitch-Based Masking

Unsupervised Sound Separation Using Mixture Invariant Training

Model checking genetic regulatory networks with parameter uncertainty

Learning to rank recommendations with the k-order statistic loss

Accurate predictions of genetic circuit behavior from part characterization and modular composition.