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

TensorFlow is a machine learning system that operates at large scale and in heterogeneous environments. Tensor-Flow uses dataflow graphs to represent computation, shared state, and the operations that mutate that state. It maps the nodes of a dataflow graph across many machines in a cluster, and within a machine across multiple computational devices, including multicore CPUs, general-purpose GPUs, and custom-designed ASICs known as Tensor Processing Units (TPUs). This architecture gives flexibility to the application developer: whereas in previous "parameter server" designs the management of shared state is built into the system, TensorFlow enables developers to experiment with novel optimizations and training algorithms. TensorFlow supports a variety of applications, with a focus on training and inference on deep neural networks. Several Google services use TensorFlow in production, we have released it as an open-source project, and it has become widely used for machine learning research. In this paper, we describe the TensorFlow dataflow model and demonstrate the compelling performance that TensorFlow achieves for several real-world applications.

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TensorFlow: a system for large-scale machine learning

TensorFlow is an interface for expressing machine learning algorithms, and an
implementation for executing such algorithms. A computation expressed using
TensorFlow can be executed with little or no change on a wide variety of
heterogeneous systems, ranging from mobile devices such as phones and tablets
up to large-scale distributed systems of hundreds of machines and thousands of
computational devices such as GPU cards. The system is flexible and can be used
to express a wide variety of algorithms, including training and inference
algorithms for deep neural network models, and it has been used for conducting
research and for deploying machine learning systems into production across more
than a dozen areas of computer science and other fields, including speech
recognition, computer vision, robotics, information retrieval, natural language
processing, geographic information extraction, and computational drug
discovery. This paper describes the TensorFlow interface and an implementation
of that interface that we have built at Google. The TensorFlow API and a
reference implementation were released as an open-source package under the
Apache 2.0 license in November, 2015 and are available at www.tensorflow.org.

/pdf/tensorflow-large-scale-machine-learning-on-heterogeneous-2yk4fgchw6.pdf

TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems

TensorFlow is a machine learning system that operates at large scale and in heterogeneous environments. TensorFlow uses dataflow graphs to represent computation, shared state, and the operations that mutate that state. It maps the nodes of a dataflow graph across many machines in a cluster, and within a machine across multiple computational devices, including multicore CPUs, general-purpose GPUs, and custom designed ASICs known as Tensor Processing Units (TPUs). This architecture gives flexibility to the application developer: whereas in previous "parameter server" designs the management of shared state is built into the system, TensorFlow enables developers to experiment with novel optimizations and training algorithms. TensorFlow supports a variety of applications, with particularly strong support for training and inference on deep neural networks. Several Google services use TensorFlow in production, we have released it as an open-source project, and it has become widely used for machine learning research. In this paper, we describe the TensorFlow dataflow model in contrast to existing systems, and demonstrate the compelling performance that TensorFlow achieves for several real-world applications.

TensorFlow: A system for large-scale machine learning

Robust and powerful software instrumentation tools are essential for program analysis tasks such as profiling, performance evaluation, and bug detection. To meet this need, we have developed a new instrumentation system called Pin. Our goals are to provide easy-to-use, portable, transparent, and efficient instrumentation. Instrumentation tools (called Pintools) are written in C/C++ using Pin's rich API. Pin follows the model of ATOM, allowing the tool writer to analyze an application at the instruction level without the need for detailed knowledge of the underlying instruction set. The API is designed to be architecture independent whenever possible, making Pintools source compatible across different architectures. However, a Pintool can access architecture-specific details when necessary. Instrumentation with Pin is mostly transparent as the application and Pintool observe the application's original, uninstrumented behavior. Pin uses dynamic compilation to instrument executables while they are running. For efficiency, Pin uses several techniques, including inlining, register re-allocation, liveness analysis, and instruction scheduling to optimize instrumentation. This fully automated approach delivers significantly better instrumentation performance than similar tools. For example, Pin is 3.3x faster than Valgrind and 2x faster than DynamoRIO for basic-block counting. To illustrate Pin's versatility, we describe two Pintools in daily use to analyze production software. Pin is publicly available for Linux platforms on four architectures: IA32 (32-bit x86), EM64T (64-bit x86), Itanium®, and ARM. In the ten months since Pin 2 was released in July 2004, there have been over 3000 downloads from its website.

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Pin: building customized program analysis tools with dynamic instrumentation

Loop interchange is an important code optimization that improves data locality and extracts parallelism. While previous research in compilers has tried to automate the selection of which loops to interchange, existing methods have an important limitation. They use less precise machine models. This is mainly because developing a model to predict whether to interchange two loops is challenging since such a prediction depends on many factors. While state-of-the-art methods try to avoid this problem by using a deep-learning based cost model, they suffer from another limitation. They scale proportionally with the number of loop levels of a given loop nest. This is mainly because they use the model to evaluate all the possible loop interchanges (or a subset of the most promising ones). In this paper, we propose a novel deep-learning model for loop interchange that addresses the previous limitations. It takes a code representation as input and predicts the best pair of loops to interchange. Compared to state-of-the-art deep-learning based cost models, it requires constant time to predict the best loop interchange. This is in contrast to state-of-the-art deep learning models that are used to evaluate all the loop pairs and then pick the best one. The proposed model is the first deep learning model that requires a constant time to predict the best loops to interchange. The model is implemented and evaluated in the Tiramisu compiler, a state-of-the-art polyhedral compiler. We evaluate the proposed model on a benchmark of Tiramisu programs and show an accuracy of 78.57% for 1-shot and 85.71% for 2-shots. Experiments show that our model outperforms the cost model currently used by the Tiramisu compiler by 8.57% in terms of 1-shot accuracy, and 5.71% with 2-shots accuracy, while at the same time reducing the total execution time needed for predicting the best pair of loops to interchange.

A Deep Learning Model for Loop Interchange

With the increasing miniaturization of transistors, wire delays are becoming a dominant factor in microprocessor performance. To address this issue, a number of emerging architectures contain replicated processing units with softwareexposed communication between one unit and another (e.g., Raw, SmartMemories, TRIPS). However, for their use to be widespread, it will be necesary to develop a common machine language to allow programmers to express an algorithm in a way that can be efficiently mapped across these architectures. We propose a new common machine language for grid-based software-exposed architectures: StreamIt. StreamIt is a high-level programming language with explicit support for streaming computation. Unlike sequential programs with obscured dependence information and complex communication patterns, a stream program is naturally written as a set of concurrent filters with regular steady-state communication. The language imposes a hierarchical structure on the stream graph that enables novel representations and optimizations within the StreamIt compiler. We have implemented a fully functional compiler that parallelizes StreamIt applications for Raw, including several loadbalancing transformations. Though StreamIt exposes the parallelism and communication patterns of stream programs, analysis is needed to adapt a stream program to a software-exposed processor. We describe a partitioning algorithm that employs fission and fusion transformations to adjust the granularity of a stream graph, a layout algorithm that maps a stream graph to a given network topology, and a scheduling strategy that generates a fine-grained static communication pattern for each computational element. Using the cycle-accurate Raw simulator, we demonstrate that the StreamIt compiler can automatically map a high-level stream abstraction to Raw. We consider this work to be a first step towards a portable programming model for communication-exposed architectures.

StreamIt: A Language and Compiler for Communication-Exposed Architectures

In 1957, the FORTRAN language and compiler introduced multidimensional dense arrays or dense tensors. Subsequent programming languages added a myriad of data structures from lists, sets, hash tables, trees, to graphs. Still, when dealing with extremely large data sets, dense tensors are the only simple and practical solution. However, modern data is anything but dense. Real world data, generated by sensors, produced by computation, or created by humans, often contain underlying structure, such as sparsity, runs of repeated values, or symmetry. In this talk I will describe how programming languages and compilers can support large data sets with structure. I will introduce TACO, a compiler for sparse data computing. TACO is the first system to automatically generate kernels for any tensor algebra operation on tensors in any of the commonly used formats. It pioneered a new technique for compiling compound tensor expressions into efficient loops in a systematic way. TACO generated code has competitive performance to best-in-class hand-written codes for tensor and matrix operations. With TACO, I will show how to put sparse array programming on the same compiler transformation and code generation footing as dense array codes. Structured data has immense potential for hardware acceleration. However, instead of one-off single-operation compute engines, with compilers frameworks such as TACO, I believe that it is possible to create hardware for an entire class of sparse computations. With the help of the FPGA community, I am looking forward to such a future.

Compiler Support for Structured Data

This document describes an attempt to develop a compiler-based approach for computations with symmetric tensors. Given a computation and the symmetries of its input tensors, we derive formulas for random access under a storage scheme that eliminates redundancies; construct intermediate representations to describe the loop structure; and translate this information, using the taco tensor algebra compiler, into code. While we achieve a framework for reasoning about a fairly general class of symmetric computations, the resulting code is not performant when the symmetries are misaligned.

An Attempt to Generate Code for Symmetric Tensor Computations.

Many applications, from social network graph analytics to control flow analysis, compute on sparse data that evolves over the course of program execution. Such data can be represented as dynamic sparse tensors and efficiently stored in formats (data layouts) that utilize pointer-based data structures like block linked lists, binary search trees, B-trees, and C-trees among others. These specialized formats support fast in-place modification and are thus better suited than traditional, array-based data structures like CSR for storing dynamic sparse tensors. However, different dynamic sparse tensor formats have distinct benefits and drawbacks, and performing different computations on tensors that are stored in different formats can require vastly dissimilar code that are not straightforward to correctly implement and optimize. This paper shows how a compiler can generate efficient code to compute tensor algebra operations on dynamic sparse tensors that may be stored in a wide range of disparate formats. We propose a language for precisely specifying recursive, pointer-based data structures, and we show how this language can express many different dynamic data structures, including all the ones named above as well as many more. We then describe how, given high-level specifications of such dynamic data structures, a compiler can emit code to efficiently access and compute on dynamic sparse tensors that are stored in the aforementioned data structures. We evaluate our technique and find it generates efficient dynamic sparse tensor algebra kernels that have performance comparable to, if not better than, state-of-the-art libraries and frameworks such as PAM, Aspen, STINGER, and Terrace. At the same time, our technique supports a wider range of tensor algebra operationsÐ such as those that simultaneously compute with static and dynamic sparse tensorsÐthan Aspen, STINGER, and Terrace, while also achieving significantly better performance than PAM for those same operations.

Saman Amarasinghe

Papers

A Deep Learning Model for Loop Interchange

StreamIt: A Language and Compiler for Communication-Exposed Architectures

Compiler Support for Structured Data

An Attempt to Generate Code for Symmetric Tensor Computations.

175 Compilation of Dynamic Sparse Tensor Algebra