Abstract: 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.

Abstract: A method, an apparatus, and a computer program product for facilitating local signaling among a plurality of agents are presented. An agent 100 including a digital processor 102 a transmitter 104, and a directional receiver 106 comprising a plurality of angular regions 108 is configured to enable the selection of a signal from a plurality of signals received on the basis of local data such as the strength of the received signal. The local data may be incorporated into a cumulative data portion of a signal that is passed from local agent 100 to local agent 100 across a plurality of agents 100 in order to provide a gradient across the plurality of agents 100. The gradient could be used, for example, to determine a shortest path across the agents. The signaling techniques described can also be used to determine the distance and direction to objects in the signaling path.

Abstract: An apparatus, a method, and a computer program product for plotting proteomic and genomic data are presented. The apparatus comprises a computer system for generating data to display in a visual form. The computer system receives a set of proteomic and genomic data including data samples and schemes for partitioning the data samples into data partitions. Various operations are performed by the computer system in response to user commands, including adjusting the view of partition schemes in response to the selection of a particular partition scheme in order to allow a user to visually detect correlations among data. The system also allows for the performance of set operations on the proteomic and genomic data, and for displaying the results. Additionally, the computer system allows for operations for determining partition schemes and partitions in which a particular data sample are located, and for generating and modifying partition schemes.

Abstract: The present invention provides an apparatus, a method, and a computer program product for clustering proteomic and genomic data. The apparatus comprises a computer system including a processor, a memory, an input, and an output coupled. The apparatus further comprises means, modules, or steps, for (a) receiving a set of data; (b) producing a one-dimensional ordering of the data samples,; (c) configuring a dendrogram from the linearly ordered set of data samples; and (d) outputting the one-dimensional ordering of the data samples and the configuration of the dendrogram; whereby the data samples are clustered in order to allow for efficient analysis to be performed thereon.

Abstract: A method and apparatus for computing properties of a physical environment is provided, using a plurality of agents forming a distributed network embedded within the environment. The method comprises determining an initiating agent 200, transmitting a signal including a cumulative cost value to neighboring agents 202, and processing the signal at each neighboring agent to augment the cumulative cost value with local information 204. If multiple signals are received, determining which has the best cumulative cost value for generating a new signal 206, then treating the neighboring agent as an initiating agent 208 and transmitting the new signal to neighboring agents 208 and retaining the best augmented cost value in memory 210. Methods further include determining paths using shortest path computations, using dual gradients for aligning agents on a path between two reference agents, and discovering and converging agents on choke points.

Abstract: A method for dynamic auto-calibration of a multi-sensor tracking system and apparatus incorporating it therein are presented. The method and apparatus utilize information from complementary sensors, filtered by a simultaneously running filter that combines the sensor data into an estimate of the state of the monitored system to iteratively tune the bias estimate. To track a dynamic system, complimentary or redundant sensors may be combined with a model of the system so that the uncertainty in the estimated state of the dynamic system is less than the noise in the individual sensors. In addition to noise, the sensors may have bias, which has the same value whenever the system is in a particular state. While estimating the actual value of the state, the present invention allows the estimator to determine the bias. The present invention, in its most general embodiment requires complex computations.

Abstract: Systems and methods of analyzing data and for specifying and applying user-selected, user-variable sequences of mathematical data preparation operations to data and methods for normalizing data that include dividing the data into a plurality of groups where the number of groups is a function of the range and number of values and for calculating a normalization correction for each group are disclosed.

Abstract: A method for controlling the movement of agents using local communications is provided. Generally, each agent maintains an optimal distance from other local neighbor agents by, for each agent 200, selecting a local agent 202, measuring the distance and angle to the agent 204, performing a distance maintenance calculation 218, and repeating the distance maintenance calculation 218 for each local agent. In the distance maintenance calculation 218, an attraction/repulsion map is used in order to determine whether an agent is attracted to or repelled from other agents. A motion vector is used to determine agent responses to the attraction or repulsion. Over time, the agents settle into a neutral configuration where each is optimally distanced from the other agents. Reference agents and leader agents can be designated to direct the movement of other agents, and agents can be designated as blocking beacons to repel other agents from undesirable areas.

Abstract: A method for controlling the movement of agents using local communications is provided. Generally, each agent maintains an optimal distance from other local neighbor agents by, for each agent 200, selecting a local agent 202, measuring the distance and angle to the agent 204, performing a distance maintenance calculation 218, and repeating the distance maintenance calculation 218 for each local agent. In the distance maintenance calculation 218, an attraction/repulsion map is used in order to determine whether an agent is attracted to or repelled from other agents. A motion vector is used to determine agent responses to the attraction or repulsion. Over time, the agents settle into a neutral configuration where each is optimally distanced from the other agents. Reference agents and leader agents can be designated to direct the movement of other agents, and agents can be designated as blocking beacons to repel other agents from undesirable areas.

Abstract: A method and apparatus for computing properties of a physical environment is provided, using a plurality of agents forming a distributed network embedded within the environment. The method comprises determining an initiating agent 200, transmitting a signal including a cumulative cost value to neighboring agents 202, and processing the signal at each neighboring agent to augment the cumulative cost value with local information 204. If multiple signals are received, determining which has the best cumulative cost value for generating a new signal 206, then treating the neighboring agent as an initiating agent 208 and transmitting the new signal to neighboring agents 208 and retaining the best augmented cost value in memory 210. Methods further include determining paths using shortest path computations, using dual gradients for aligning agents on a path between two reference agents, and discovering and converging agents on choke points.

Abstract: A method, an apparatus, and a computer program product for facilitating local signaling among a plurality of agents are presented. An agent 100 including a digital processor 102 a transmitter 104, and a directional receiver 106 comprising a plurality of angular regions 108 is configured to enable the selection of a signal from a plurality of signals received on the basis of local data such as the strength of the received signal. The local data may be incorporated into a cumulative data portion of a signal that is passed from local agent 100 to local agent 100 across a plurality of agents 100 in order to provide a gradient across the plurality of agents 100. The gradient could be used, for example, to determine a shortest path across the agents. The signaling techniques described can also be used to determine the distance and direction to objects in the signaling path.