Biodiscovery, Inc

Hughes Electronics Corporation

Other

Hughes Aircraft Company

Soheil Shams

James Darrell Park

Yi-Xiong Zhou

David B Shu

Anton Petrov

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.

Apparatus, method, and computer program product for determining gene function and functional groups using chromosomal distribution patterns

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 microarry 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.

Apparatus, method, and computer program product for determining confidence measures and combined confidence measures for assessing the quality of microarrays

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.

System and method for automatically processing microarrays

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.

Automated DNA array image segmentation and analysis

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.

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 diaplays 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.

Automated DNA array segmentation and analysis

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.

Independently non-homogeneously dynamically reconfigurable two

A method of detection and tracking of targets using multiple angle-only sensors is disclosed. The method is computationally efficient and is capable of detecting and tracking multiple targets in true three dimensional space. The method comprises distributing a set of modules in space and associating those modules with bearing lines from each sensor to each target. Through repetitive iterative associations between modules and bearing lines, the modules converge on the targets present.

Search method for detection and tracking of targets using multiple

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.

Multiple elastic feature net and method for target deghosting and

In a parallel processing architecture following the Single Instruction stream Multiple Data stream execution paradigm where a controller element is connected to at least one processing element with a local memory having a local memory address shift register adapted to receive and retain therein a globally broadcast memory base register address value received from the controller element for use by the processing element for access and transfer of data between the processing element and its respective local memory, a computer architecture for implementing indirect addressing and look-up tables includes a processing element shift register associated with the at least one processing element and adapted to receive and retain therein a local memory offset address value calculated or loaded by the associated processing element in accord with a first predetermined set of instructions. The processing element shift register transfers its contents bitwise to the local memory shift register of the local memory associated with the processing element, with the bit value of the most significant bit position being sequentially transferred to the least significant bit position of the local memory shift register in accord with a second predetermined set of instructions. A parallel transfer of the contents of the two shift registers is also disclosed.

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Redondo Beach, CA, United States of America

Soheil Shams