公开(公告)号：US6145072A

公开(公告)日：2000-11-07

申请号：US309565

申请日：1994-09-20

申请人： Soheil Shams ,  David B. Shu

发明人： Soheil Shams ,  David B. Shu

IPC分类号： G06F15/16 ,  G06F15/173 ,  G06F15/80 ,  G06F13/00

CPC分类号： G06F15/17343 ,  G06F15/17381

摘要： In a SIMD architecture having a two dimensional array of processing elements, where a controller broadcasts instructions to all processing elements in the array, a dynamically reconfigurable switching means useful to connect four of the processing elements in the array into a group in accordance with either the broadcast instruction of the controller or a special communication instruction held in one processing element of the group, the switch includes at least one dataline connected to each processing element in the group. A multiplexer is connected to each data line and to the controller and to a configuration register. It is adapted to load the special communication instruction from the one processing element in the group into a configuration register and to operate in accord with either the broadcast instruction from the controller or the contents of the configuration register to select one of the four data lines as a source of data and applying the data therefrom to a source output port. A demultiplexer is connected to each data line and to the controller and to said configuration register, and to the source output port of the multiplexer means, and adapted to operate in accord with either the broadcast instruction from the controller or the contents of the configuration register to select one of the four data lines as a source of data and applying the data therefrom to a selected data line. The switch also acts to connect processing elements that cross chip partitions forming the processor array. Up to four such switches can be used to connect a group of four processing elements.

摘要翻译： 在具有处理元件的二维阵列的SIMD架构中，其中控制器向阵列中的所有处理元件广播指令，可动态重新配置的切换装置用于根据以下任何一种将阵列中的四个处理元件连接到组中： 所述控制器的广播指令或保持在所述组的一个处理元件中的特殊通信指令，所述交换机包括连接到所述组中的每个处理元件的至少一个数据线。 多路复用器连接到每个数据线以及控制器和配置寄存器。 它适用于将特殊通信指令从组中的一个处理单元加载到配置寄存器中，并根据来自控制器的广播指令或配置寄存器的内容进行操作，以选择四条数据线之一作为 数据源并将数据应用于源输出端口。 解复用器连接到每个数据线以及控制器和配置寄存器以及多路复用器装置的源输出端口，并且适于根据来自控制器的广播指令或配置寄存器的内容进行操作 选择四条数据线之一作为数据源，并将数据应用于所选择的数据线。 该交换机还用于连接形成处理器阵列的跨芯片分区的处理元件。 最多可以使用四个这样的开关来连接一组四个处理元件。

公开(公告)号：US20100191473A1

公开(公告)日：2010-07-29

申请号：US12661920

申请日：2010-03-26

申请人： Soheil Shams

发明人： Soheil Shams

IPC分类号： G06F19/00

CPC分类号： G06F19/20 ,  G06F19/18

摘要： A method, apparatus, and computer program product for analyzing gene expressions is presented. An operation is performed for determining a gene expression pattern for a condition, wherein the gene expression pattern comprises a gene expression. Next, a spatial-expression pattern is formed by selecting a chromosomal region having an exon; and associating the gene expression within the gene expression pattern with its corresponding exon. A further operation may be performed, where in the forming of the spatial-expression pattern, a spatial-expression pattern signal is created as a representation of the spatial-expression pattern. The magnitude of the spatial-expression pattern signal at any point is determined by an expression level of the corresponding exon. Spatial patterns may be identified in the signal by means of various signal processing techniques such as Fourier or Wavelet transforms. Also, multiple regions and/or conditions may be tested and their reaction patterns compared to determine related genetic regions.

公开(公告)号：US20090204339A1

公开(公告)日：2009-08-13

申请号：US12380911

申请日：2009-03-05

申请人： Soheil Shams ,  Anton Petrov

发明人： Soheil Shams ,  Anton Petrov

IPC分类号： G01N33/48 ,  G06F19/00

CPC分类号： G06T7/0006 ,  G06T2207/30072 ,  G16B40/00

摘要： An apparatus, method, and computer program product are provided for determining a confidence measure for the output of a process for assessing proteomic and genomic information samples. Typically, data is received as the results from a microarryi experiment. The confidence measure is intended to determine whether the results of the experiment have been degraded due to experimental error. Several criteria are used by which quality is determined. The criteria are preferably combined into a combined quality measure in order to account for several possible sources of error.

摘要翻译： 提供了一种装置，方法和计算机程序产品，用于确定用于评估蛋白质组和基因组信息样本的过程的输出的置信度度量。 通常，数据作为microarryi实验的结果收到。 置信度测量旨在确定实验结果是否由于实验误差而退化。 使用几个标准来确定质量。 这些标准优选地组合成组合的质量度量，以便考虑几个可能的误差源。

公开(公告)号：US06731781B1

公开(公告)日：2004-05-04

申请号：US09416634

申请日：1999-10-12

申请人： Soheil Shams ,  James Darrell Park ,  Yi-Xiong Zhou

发明人： Soheil Shams ,  James Darrell Park ,  Yi-Xiong Zhou

IPC分类号： G06K900

CPC分类号： G06K9/00 ,  G06T5/50 ,  G06T7/0012 ,  G06T7/12 ,  G06T2207/10056 ,  G06T2207/10064 ,  G06T2207/20061 ,  G06T2207/30072

摘要： A digital image processing-based system and method for quantitatively processing a plurality of nucleic acid species expressed in a microarray are disclosed. The microarray is a grid of a plurality of sub-grids of the nucleic acid species. The system includes a scanner that has a digital scanning sensor that scans the microarray and transmits from an output a digital image of the microarray, and a processor that receives the digital image of the microarray from the scanner and then processes the digital image, identifying each of the microarray's sub-grids. The processor then detects in each of the sub-grids a center-representing pixel of a signal of a chemical material and an approximate radius of the signal. Then, the processor segments the signal and calculates a characterizing measure for the segmented signal.

公开(公告)号：US06577956B1

公开(公告)日：2003-06-10

申请号：US09591915

申请日：2000-06-09

申请人： Soheil Shams

发明人： Soheil Shams

IPC分类号： G01N3348

CPC分类号： G06T7/0012 ,  G06T7/11 ,  G06T7/70 ,  G06T2207/10056 ,  G06T2207/10064 ,  G06T2207/30072 ,  Y10S707/99933 ,  Y10S707/99945

摘要： A segmentation method of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots. The image information includes image intensity level information corresponding to said DNA spots. The frame is stored in a memory device and a set of image information within said frame including a selected set of the DNA spot images is selected. A grid including a plurality of spaced grid points corresponding to said selected DNA spot images is generated, such that each grid point includes position information indicating the position of the grid point within said frame. The current position of one or more grid points are adjusted by: selecting a first bounding area in the frame around the current position of the grid point; generating a first position update including position information for updating a current position of said grid point to a first new position within the first bounding area, the location of said first new position relative to said current position being a function of intensity level of at least a portion of the image within the first bounding area; generating a second position update including position information for updating said current position to a second new position in the frame, said second new position being in a geometric arrangement with the position of grid points around said grid point; and updating said current position with the position information of the first and the second position updates, thereby shifting said grid point toward the corresponding spot image. A display method displays image information corresponding to a plurality of DNA spot images of at least one DNA spot, the image information including image characteristic values including background and signal intensity levels. For each DNA spot image: (1) background and signal intensity levels are extracted from the image characteristic values for the spot image, and (2) difference values between the background intensity levels and signal intensity levels are determined. For each DNA spot: (1) the corresponding difference values are related a range of graphic values, (2) a graphic value for each difference value is selected; and (3) the selected graphic values are displayed.

公开(公告)号：US07689365B2

公开(公告)日：2010-03-30

申请号：US10609137

申请日：2003-06-26

申请人： Soheil Shams

发明人： Soheil Shams

IPC分类号： G06F19/00 ,  G11C17/00 ,  G06F15/00

CPC分类号： G06F19/20 ,  G06F19/18

摘要： A method, apparatus, and computer program product for analyzing gene expressions is presented. An operation is performed for determining a gene expression pattern for a condition, wherein the gene expression pattern comprises a gene expression. Next, a spatial-expression pattern is formed by selecting a chromosomal region having an exon; and associating the gene expression within the gene expression pattern with its corresponding exon. A further operation may be performed, where in the forming of the spatial-expression pattern, a spatial-expression pattern signal is created as a representation of the spatial-expression pattern. The magnitude of the spatial-expression pattern signal at any point is determined by an expression level of the corresponding exon. Spatial patterns may be identified in the signal by means of various signal processing techniques such as Fourier or Wavelet transforms. Also, multiple regions and/or conditions may be tested and their reaction patterns compared to determine related genetic regions.

摘要翻译： 提出了一种用于分析基因表达的方法，装置和计算机程序产品。 进行用于确定条件的基因表达模式的操作，其中所述基因表达模式包含基因表达。 接下来，通过选择具有外显子的染色体区域形成空间表达模式; 并将基因表达模式中的基因表达与其相应的外显子相关联。 可以进行进一步的操作，其中在形成空间表达模式时，创建空间表达模式信号作为空间表达模式的表示。 任何点的空间表达模式信号的幅度由相应的外显子的表达水平确定。 可以通过各种信号处理技术（例如傅立叶变换或小波变换）在信号中识别空间模式。 此外，可以测试多个区域和/或条件，并比较它们的反应模式以确定相关的遗传区域。

公开(公告)号：US07099502B2

公开(公告)日：2006-08-29

申请号：US10761938

申请日：2004-01-21

申请人： Soheil Shams ,  James Darrell Park ,  Yi-Xiong Zhou

发明人： Soheil Shams ,  James Darrell Park ,  Yi-Xiong Zhou

IPC分类号： G06K9/00

CPC分类号： G06K9/00 ,  G06T5/50 ,  G06T7/0012 ,  G06T2207/20068 ,  G06T2207/30072

摘要： A digital image processing-based system and method for quantitatively processing a plurality of nucleic acid species expressed in a microarray are disclosed. The microarray is a grid of a plurality of sub-grids of the nucleic acid species. The system includes a scanner that has a digital scanning sensor that scans the microarray and transmits from an output a digital image of the microarray, and a processor that receives the digital image of the microarray from the scanner and then processes the digital image, identifying each of the microarray's sub-grids. The processor then detects in each of the sub-grids a center-representing pixel of a signal of a chemical material and an approximate radius of the signal. Then, the processor segments the signal and calculates a characterizing measure for the segmented signal.

摘要翻译： 公开了一种用于定量处理微阵列中表达的多种核酸物质的基于数字图像处理的系统和方法。 微阵列是核酸物种的多个子网格的网格。 该系统包括具有数字扫描传感器的扫描仪，其扫描微阵列并从输出端传送微阵列的数字图像，以及处理器，其从扫描器接收微阵列的数字图像，然后处理数字图像，识别每个 的微阵列子网。 然后，处理器在每个子网格中检测化学材料的信号的中心表示像素和信号的近似半径。 然后，处理器对信号进行分段，并计算分段信号的特征度量。

公开(公告)号：US06674882B1

公开(公告)日：2004-01-06

申请号：US09992687

申请日：2001-11-16

申请人： Soheil Shams

发明人： Soheil Shams

IPC分类号： G06K900

CPC分类号： G06T7/0012 ,  G06T7/11 ,  G06T7/70 ,  G06T2207/10056 ,  G06T2207/10064 ,  G06T2207/30072 ,  Y10S707/99933 ,  Y10S707/99945

摘要： A segmentation method of a frame of image information including a plurality of spaced DNA spot images corresponding to a plurality of DNA spots. The image information includes image intensity level information corresponding to said DNA spots. A grid including a plurality of spaced grid points corresponding to selected DNA spot images is generated, such that each grid point includes position information indicating the position of the grid point within said frame. For each DNA spot image: (1) background and signal intensity levels are extracted from image characteristic values for the spot image, and (2) difference values between the background intensity levels and signal intensity levels are determined. For each DNA spot: (1) the corresponding difference values are related a range of graphic values, (2) a graphic value for each difference value is selected; and (3) the selected graphic values are displayed.

摘要翻译： 一种图像信息的分割方法，包括对应于多个DNA斑点的多个间隔的DNA斑点图像。 图像信息包括对应于所述DNA斑点的图像强度等级信息。 生成包括对应于选定的DNA斑点图像的多个间隔网格点的网格，使得每个网格点包括指示网格点在所述帧内的位置的位置信息。 对于每个DNA斑点图像：（1）从斑点图像的图像特征值中提取背景和信号强度水平，并且（2）确定背景强度水平和信号强度水平之间的差值。 对于每个DNA斑点：（1）相应的差值与图形值的范围相关，（2）选择每个差值的图形值; 和（3）显示所选择的图形值。

公开(公告)号：US5680514A

公开(公告)日：1997-10-21

申请号：US311373

申请日：1994-09-23

申请人： Soheil Shams

发明人： Soheil Shams

IPC分类号： G01S5/04 ,  G01S7/36 ,  G01S7/41 ,  G01S13/68 ,  G01S13/72 ,  G06E1/00 ,  G06E3/00 ,  G06F15/18

CPC分类号： G01S5/04 ,  G01S13/723 ,  G01S7/417 ,  G01S13/68 ,  G01S7/36

摘要： A multiple elastic feature network having N independent sets of M feature specific neurons that respond to the temporal properties of a number of targets. The targets are represented by sets of M feature specific coordinates. Each of the neurons and its coordinates are labeled with a different one of the feature types, and have an associated receptive field and distortion, locking and expectation parameters. A sequence of candidate coordinates, which include the targets' coordinates as well as false or ghost coordinates, is input to the MEFN. Each successive candidate coordinate selects the closest neuron that has the same feature type and whose receptive field includes the candidate coordinates. The coordinates of the selected neuron and the other neurons in its set are adjusted towards the candidate coordinates. The distortion, expectation and locking parameters measure the distortion in the neurons' coordinates, the elapsed time since each neuron was last selected and the changes in the neurons' coordinates, respectively. As the sets of neurons converge towards respective targets, the expectation, distortion and locking parameters are reduced, and hence the receptive fields are reduced, causing the neurons to lock onto and track the targets.

摘要翻译： 具有N个独立的M组的多重弹性特征网络具有对多个目标的时间特性作出响应的特定特征神经元。 目标由一组M特征特定坐标表示。 每个神经元及其坐标都用不同的特征类型进行标记，并具有相关的接收场和失真，锁定和期望参数。 包括目标坐标以及虚假或重心坐标的候选坐标序列被输入到MEFN。 每个连续的候选坐标选择具有相同特征类型的最接近的神经元，其接收场包括候选坐标。 所选神经元和其集合中的其他神经元的坐标被调整为候选坐标。 失真，期望和锁定参数测量神经元坐标中的失真，分别是每个神经元最后一次被选择的经过时间和神经元坐标的变化。 随着神经元集合到各个目标，预期，失真和锁定参数被减少，因此接收场减少，导致神经元锁定并跟踪目标。

公开(公告)号：US20090299646A1

公开(公告)日：2009-12-03

申请号：US12459702

申请日：2009-07-07

申请人： Soheil Shams ,  Bruce Hoff

发明人： Soheil Shams ,  Bruce Hoff

IPC分类号： G06F19/00

CPC分类号： G16B5/00 ,  G16B25/00

摘要： The invention provides system and methods for analyzing the perturbation of one or more biological pathways. In one embodiment, expression values for each of a plurality of genes for one or more experimental conditions may be received. Gene differential regulation values may then be calculated for each of the plurality of genes across each of the one or more experimental conditions. The gene differential regulation values may then be grouped by the biological pathway and experimental condition from which each gene differential regulation value originated yielding one or more pathway-condition data sets. Pathway perturbation values may then for each of the one or more pathway-condition data sets using the gene differential regulation values. These pathway perturbation values may be clustered, used to identify biological pathways or experimental conditions for further analysis, and/or utilized to build a classifier for classifying additional experimental data.

摘要翻译： 本发明提供了用于分析一个或多个生物学途径的扰动的系统和方法。 在一个实施方案中，可以接收用于一个或多个实验条件的多个基因中的每一个的表达值。 然后可以针对所述一个或多个实验条件中的每一个针对所述多个基因中的每一个计算基因差异调节值。 然后可以通过生物学途径和每个基因差异调节值产生的实验条件将基因差异调节值分组，产生一个或多个途径条件数据集。 然后可以使用基因差异调节值对每个一个或多个途径条件数据集进行路径扰动值。 这些通路扰动值可以是聚类的，用于鉴定用于进一步分析的生物学途径或实验条件，和/或用于建立用于分类附加实验数据的分类器。