公开(公告)号：US07587516B2

公开(公告)日：2009-09-08

申请号：US10468999

申请日：2002-02-25

申请人： Gyan Bhanot ,  Matthias A. Blumrich ,  Dong Chen ,  Paul W. Coteus ,  Alan G. Gara ,  Mark E. Giampapa ,  Philip Heidelberger ,  Burkhard D. Steinmacher-Burow ,  Todd E. Takken ,  Pavlos M. Vranas

发明人： Gyan Bhanot ,  Matthias A. Blumrich ,  Dong Chen ,  Paul W. Coteus ,  Alan G. Gara ,  Mark E. Giampapa ,  Philip Heidelberger ,  Burkhard D. Steinmacher-Burow ,  Todd E. Takken ,  Pavlos M. Vranas

IPC分类号： G06F15/173 ,  H04L12/66 ,  H04L12/50

CPC分类号： H04L45/16 ,  H04L45/06

摘要： Class network routing is implemented in a network such as a computer network comprising a plurality of parallel compute processors at nodes thereof. Class network routing allows a compute processor to broadcast a message to a range (one or more) of other compute processors in the computer network, such as processors in a column or a row. Normally this type of operation requires a separate message to be sent to each processor. With class network routing pursuant to the invention, a single message is sufficient, which generally reduces the total number of messages in the network as well as the latency to do a broadcast. Class network routing is also applied to dense matrix inversion algorithms on distributed memory parallel supercomputers with hardware class function (multicast) capability. This is achieved by exploiting the fact that the communication patterns of dense matrix inversion can be served by hardware class functions, which results in faster execution times.

摘要翻译： 在诸如包括在其节点处的多个并行计算处理器的计算机网络的网络中实现类网络路由。 类网络路由允许计算处理器将消息广播到计算机网络中的其他计算处理器的范围（一个或多个），例如列或行中的处理器。 通常这种类型的操作需要单独的消息发送到每个处理器。 根据本发明的类网络路由，单个消息是足够的，这通常减少了网络中的消息总数以及进行广播的延迟。 类网络路由也适用于具有硬件类功能（组播）能力的分布式存储并行超级计算机上的密集矩阵求逆算法。 这是通过利用密集矩阵反演的通信模式可以通过硬件类功能来实现的，这导致更快的执行时间。

公开(公告)号：US07313582B2

公开(公告)日：2007-12-25

申请号：US10468991

申请日：2002-02-25

申请人： Gyan Bhanot ,  Matthias A. Blumrich ,  Dong Chen ,  Alan G. Gara ,  Mark E. Giampapa ,  Philip Heidelberger ,  Burkhard D. Steinmacher-Burow ,  Pavlos M. Vranas

发明人： Gyan Bhanot ,  Matthias A. Blumrich ,  Dong Chen ,  Alan G. Gara ,  Mark E. Giampapa ,  Philip Heidelberger ,  Burkhard D. Steinmacher-Burow ,  Pavlos M. Vranas

IPC分类号： G06F7/38

CPC分类号： G06F15/17337

摘要： Methods and systems for performing arithmetic functions. In accordance with a first aspect of the invention, methods and apparatus are provided, working in conjunction of software algorithms and hardware implementation of class network routing, to achieve a very significant reduction in the time required for global arithmetic operation on the torus. Therefore, it leads to greater scalability of applications running on large parallel machines. The invention involves three steps in improving the efficiency and accuracy of global operations: (1) Ensuring, when necessary, that all the nodes do the global operation on the data in the same order and so obtain a unique answer, independent of roundoff error; (2) Using the topology of the torus to minimize the number of hops and the bidirectional capabilities of the network to reduce the number of time steps in the data transfer operation to an absolute minimum; and (3) Using class function routing to reduce latency in the data transfer. With the method of this invention, every single element is injected into the network only once and it will be stored and forwarded without any further software overhead. In accordance with a second aspect of the invention, methods and systems are provided to efficiently implement global arithmetic operations on a network that supports the global combining operations. The latency of doing such global operations are greatly reduced by using these methods.

摘要翻译： 用于执行算术功能的方法和系统。 根据本发明的第一方面，提供了方法和装置，其结合软件算法和类网络路由的硬件实现，以实现对环面上的全局算术运算所需的时间的非常显着的减少。 因此，它可以提高在大型并行机上运行的应用程序的可扩展性。 本发明涉及提高全球运营效率和准确性三个步骤：（1）在必要时确保所有节点按照相同顺序对数据进行全局运算，从而获得独立的回答，而不考虑舍入误差; （2）使用环面的拓扑来最小化跳数和网络的双向能力，将数据传输操作中的时间步数减少到绝对最小值; 和（3）使用类函数路由来减少数据传输中的延迟。 利用本发明的方法，每个单个元件仅被注入到网络中一次，并且它将被存储和转发而没有任何进一步的软件开销。 根据本发明的第二方面，提供了用于在支持全局组合操作的网络上有效地实现全局算术运算的方法和系统。 通过使用这些方法大大减少了进行这种全局操作的延迟。

公开(公告)号：US20060101104A1

公开(公告)日：2006-05-11

申请号：US10963101

申请日：2004-10-12

申请人： Gyan Bhanot ,  Alan Gara ,  Philip Heidelberger ,  Eoin Lawless ,  James Sexton ,  Robert Walkup

发明人： Gyan Bhanot ,  Alan Gara ,  Philip Heidelberger ,  Eoin Lawless ,  James Sexton ,  Robert Walkup

IPC分类号： G06F1/16

CPC分类号： G06F9/5066

摘要： A general computer-implement method and apparatus to optimize problem layout on a massively parallel supercomputer is described. The method takes as input the communication matrix of an arbitrary problem in the form of an array whose entries C(i, j) are the amount to data communicated from domain i to domain j. Given C(i, j), first implement a heuristic map is implemented which attempts sequentially to map a domain and its communications neighbors either to the same supercomputer node or to near-neighbor nodes on the supercomputer torus while keeping the number of domains mapped to a supercomputer node constant (as much as possible). Next a Markov Chain of maps is generated from the initial map using Monte Carlo simulation with Free Energy (cost function) F=Σi,jC(i,j)H(i,j)—where H(i,j) is the smallest number of hops on the supercomputer torus between domain i and domain j. On the cases tested, found was that the method produces good mappings and has the potential to be used as a general layout optimization tool for parallel codes. At the moment, the serial code implemented to test the method is un-optimized so that computation time to find the optimum map can be several hours on a typical PC. For production implementation, good parallel code for our algorithm would be required which could itself be implemented on supercomputer.

摘要翻译： 描述了在大型并行超级计算机上优化问题布局的通用计算机实现方法和装置。 该方法采用数组形式的任意问题的通信矩阵作为输入，其条目C（i，j）是从域i到域j传送的数据量。 给定C（i，j），首先实现启发式映射，其尝试顺序地将域及其通信邻居映射到超级计算机节点或超级计算机环面上的近邻节点，同时保持域的数量映射到 超级计算机节点常数（尽可能多）。 接下来，使用具有自由能量（成本函数）的蒙特卡罗模拟，从初始映射生成马尔可夫链映射，其中F =Σi，j C（i，j）H（i，j） H（i，j）是域i和域j之间的超级计算机环面上的最小跳数。 在测试的情况下，发现该方法产生良好的映射，并且有可能被用作并行代码的通用布局优化工具。 此时，实现测试方法的序列号未优化，以便在典型的PC上找到最佳映射的计算时间可以为几个小时。 对于生产实现，将需要我们的算法的良好的并行代码，这本身可以在超级计算机上实现。

公开(公告)号：US20130005597A1

公开(公告)日：2013-01-03

申请号：US13516105

申请日：2010-12-20

申请人： W. Kimryn Rathmell ,  A. Rose Brannon ,  Gyan Bhanot ,  Anupama Reddy

发明人： W. Kimryn Rathmell ,  A. Rose Brannon ,  Gyan Bhanot ,  Anupama Reddy

IPC分类号： C40B30/04 ,  C40B40/10 ,  C40B40/06

CPC分类号： G01N33/57438 ,  G01N2800/52 ,  G01N2800/60

摘要： Methods for generating a prognostic signature for a subject with clear cell renal cell carcinoma (ccRCC) are disclosed. The methods include determining expression levels for three or more genes disclosed in ccRCC cells obtained from the subject, wherein the determining provides a prognostic signature for the subject. Also provided are methods for assessing risk of an adverse outcome of a subject clear cell renal cell carcinoma (ccRCC), method for predicting a clinical outcome of a treatment in a subject diagnosed with clear cell renal cell carcinoma (ccRCC), and arrays that include polynucleotides that hybridize to at least three genes disclosed or that include specific peptide or polypeptide gene products of at least three of the genes disclosed.

摘要翻译： 公开了用于产生具有透明细胞肾细胞癌（ccRCC）的受试者的预后特征的方法。 所述方法包括确定从受试者获得的ccRCC细胞中公开的三种或更多种基因的表达水平，其中该确定提供了该受试者的预后特征。 还提供了用于评估受试者透明细胞肾细胞癌（ccRCC）的不良结果的风险的方法，用于预测诊断为透明细胞肾细胞癌（ccRCC）的受试者的治疗的临床结果的方法，以及包括 与所公开的至少三种基因杂交或包括所公开的至少三种基因的特异性肽或多肽基因产物杂交的多核苷酸。

公开(公告)号：US20120052508A1

公开(公告)日：2012-03-01

申请号：US13220434

申请日：2011-08-29

申请人： Erhan Bilal ,  Gyan Bhanot ,  Shrider Ganesan

发明人： Erhan Bilal ,  Gyan Bhanot ,  Shrider Ganesan

IPC分类号： C12Q1/68 ,  G06F19/00

CPC分类号： C12Q1/6886 ,  A61K31/138 ,  A61K45/06 ,  C12Q2600/106 ,  C12Q2600/118 ,  C12Q2600/156 ,  C12Q2600/158 ,  Y02A90/26

摘要： This application provides a method to identify genetic markers associated with increased sensitivity or resistance to hormonal therapies using an outlier analysis. More specifically, this application discloses that amplifications on chromosomes 8 and 17 are associated with increased proliferation and poor outcome in ER-positive breast cancer, and amplicons 17q21.33-q25.1, 8p11.2 and 8q24.3 may be responsible for higher proliferation and poor outcome in the setting of antiestrogen, in particular Tamoxifen, treatment clinically observed in a subset of ER-positive, HER2-negative breast cancers. The invention also provides use of the identified genetic markers in the development of targeted treatments for antiestrogen-resistant ER-positive breast cancers as well as in improving current methods of drug response prediction.

摘要翻译： 该应用提供了一种使用异常值分析来鉴定与激素治疗增加的敏感性或抗性相关的遗传标记的方法。 更具体地，本申请公开了染色体8和17上的扩增与增殖增加和ER阳性乳腺癌的不良结果相关，扩增子17q21.33-q25.1,8p11.2和8q24.3可能负责更高 在抗雌激素，特别是他莫昔芬的设置中的增殖和不良结果，在ER阳性，HER2阴性乳腺癌的一个亚组中临床观察到的治疗。 本发明还提供了鉴定的遗传标记在开发用于抗雌激素抵抗性ER阳性乳腺癌的靶向治疗中的用途以及改进目前的药物反应预测方法。