Patents by Inventor Dexter Roydon Pratt
Dexter Roydon Pratt has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
-
Publication number: 20140297573Abstract: One or more measurement signatures are derived from a knowledge base of casual biological facts, where a signature is a collection of measured node entities and their expected directions of change with respect to a reference node. The knowledge base may be a directed network of experimentally-observed casual relationships among biological entities and processes, and a reference node represents a perturbation. A degree of activation of a signature is then assessed by scoring one or more “differential” data sets against the signature to compute an amplitude score. The amplitude score quantifies fold-changes of measurements in the signature. In one particular embodiment, the amplitude score is a weighted average of adjusted log-fold changes of measured node entities in the signature, wherein an adjustment applied to the log-fold changes is based on their expected direction of change. In an alternative embodiment, the amplitude score is based on quantity effects.Type: ApplicationFiled: June 16, 2014Publication date: October 2, 2014Inventors: Ty Matthew Thomson, Dexter Roydon Pratt, William M. Ladd
-
Patent number: 8843420Abstract: A “Specificity” statistic (or metric) is computed as a means to identify amplitude scores associated with a signature that can be attributed with high probability to a specific biological entity or process represented by the signature. Preferably, Specificity is computed by assessing a likelihood of a given null hypothesis, namely, that an amplitude score is not representative of the specific signature but, instead, is representative of a general trend in the applicable data set that can be measured by any signature that is comparable to the signature of interest. In a typical implementation, a first step to compute the Specificity metric is to construct a set of comparable signatures. Next, an amplitude score is computed for each of these signatures, preferably using the same data set. Then, the Specificity metric is computed, preferably as a two-tailed p-value, by placing the amplitude score for the signature of interest on a distribution of scores for the comparable signatures.Type: GrantFiled: August 19, 2011Date of Patent: September 23, 2014Assignee: Selventa, Inc.Inventors: Ty Matthew Thomson, Dexter Roydon Pratt
-
Patent number: 8812430Abstract: To directly compare two or more network perturbation amplitude scores and identify whether the difference between them is meaningful, an Uncertainty (confidence interval) for each of the scores is computed. According to this disclosure, experimental replicates of the measurements are used to compute the score Uncertainty, based on an assumption that variability between measurement replicates represents a largest source of error in the score. Preferably, at least three (3) experimental replicates for both treated and control conditions are used to compute Uncertainty.Type: GrantFiled: August 20, 2012Date of Patent: August 19, 2014Assignee: Selventa, Inc.Inventors: Ty Matthew Thomson, Dexter Roydon Pratt, David Drubin
-
Patent number: 8756182Abstract: One or more measurement signatures are derived from a knowledge base of casual biological facts, where a signature is a collection of measured node entities and their expected directions of change with respect to a reference node. The knowledge base may be a directed network of experimentally-observed casual relationships among biological entities and processes, and a reference node represents a perturbation. A degree of activation of a signature is then assessed by scoring one or more “differential” data sets against the signature to compute an amplitude score. The amplitude score quantifies fold-changes of measurements in the signature. In one particular embodiment, the amplitude score is a weighted average of adjusted log-fold changes of measured node entities in the signature, wherein an adjustment applied to the log-fold changes is based on their expected direction of change. In an alternative embodiment, the amplitude score is based on quantity effects.Type: GrantFiled: May 31, 2011Date of Patent: June 17, 2014Assignee: Selventa, Inc.Inventors: Ty Matthew Thomson, Dexter Roydon Pratt, William M. Ladd
-
Patent number: 8417661Abstract: One or more measurement signatures are derived from a knowledge base of casual biological facts, where a signature is a collection of measured node entities and their expected directions of change with respect to a reference node. The knowledge base may be a directed network of experimentally-observed casual relationships among biological entities and processes, and a reference node represents a perturbation. A degree of activation of a signature is then assessed by scoring one or more “differential” data sets against the signature to compute an amplitude score. The amplitude score quantifies fold-changes of measurements in the signature. In one particular embodiment, the amplitude score is a weighted average of adjusted log-fold changes of measured node entities in the signature, wherein an adjustment applied to the log-fold changes is based on their expected direction of change. In an alternative embodiment, the amplitude score is based on quantity effects.Type: GrantFiled: May 4, 2012Date of Patent: April 9, 2013Assignee: Selventa, Inc.Inventors: Ty Matthew Thomson, Dexter Roydon Pratt, William M. Ladd
-
Publication number: 20130046726Abstract: A “Specificity” statistic (or metric) is computed as a means to identify amplitude scores associated with a signature that can be attributed with high probability to a specific biological entity or process represented by the signature. Preferably, Specificity is computed by assessing a likelihood of a given null hypothesis, namely, that an amplitude score is not representative of the specific signature but, instead, is representative of a general trend in the applicable data set that can be measured by any signature that is comparable to the signature of interest. In a typical implementation, a first step to compute the Specificity metric is to construct a set of comparable signatures. Next, an amplitude score is computed for each of these signatures, preferably using the same data set. Then, the Specificity metric is computed, preferably as a two-tailed p-value, by placing the amplitude score for the signature of interest on a distribution of scores for the comparable signatures.Type: ApplicationFiled: August 19, 2011Publication date: February 21, 2013Applicant: SELVENTA, INC.Inventors: Ty Matthew Thomson, Dexter Roydon Pratt
-
Publication number: 20120221506Abstract: One or more measurement signatures are derived from a knowledge base of casual biological facts, where a signature is a collection of measured node entities and their expected directions of change with respect to a reference node. The knowledge base may be a directed network of experimentally-observed casual relationships among biological entities and processes, and a reference node represents a perturbation. A degree of activation of a signature is then assessed by scoring one or more “differential” data sets against the signature to compute an amplitude score. The amplitude score quantifies fold-changes of measurements in the signature. In one particular embodiment, the amplitude score is a weighted average of adjusted log-fold changes of measured node entities in the signature, wherein an adjustment applied to the log-fold changes is based on their expected direction of change. In an alternative embodiment, the amplitude score is based on quantity effects.Type: ApplicationFiled: May 4, 2012Publication date: August 30, 2012Applicant: SELVENTA, INC.Inventors: Ty Matthew Thomson, Dexter Roydon Pratt, William M. Ladd
-
Publication number: 20120030162Abstract: One or more measurement signatures are derived from a knowledge base of casual biological facts, where a signature is a collection of measured node entities and their expected directions of change with respect to a reference node. The knowledge base may be a directed network of experimentally-observed casual relationships among biological entities and processes, and a reference node represents a perturbation. A degree of activation of a signature is then assessed by scoring one or more “differential” data sets against the signature to compute an amplitude score. The amplitude score quantifies fold-changes of measurements in the signature. In one particular embodiment, the amplitude score is a weighted average of adjusted log-fold changes of measured node entities in the signature, wherein an adjustment applied to the log-fold changes is based on their expected direction of change. In an alternative embodiment, the amplitude score is based on quantity effects.Type: ApplicationFiled: May 31, 2011Publication date: February 2, 2012Applicant: SELVENTA, INC.Inventors: Ty Matthew Thomson, Dexter Roydon Pratt, William M. Ladd
-
Publication number: 20070225956Abstract: Disclosed are software assisted systems and methods for analyzing biological data sets to generate hypotheses potentially explanatory of the data. Active causative relationships in the biology of complex living systems are discovered by providing a data base of biological assertions comprising a multiplicity of nodes representative of a network of biological entities, actions, functional activities, and concepts, and relationship links between the nodes. Simulating perturbation of individual root nodes in the network initiates a cascade of virtual activity through the relationship links to discern plural branching paths within the data base. Operational data, e.g., experimental data, representative of a real or hypothetical perturbations of one or more nodes are mapped onto the data base. The branching paths then are prioritized as hypotheses on the basis of how well they predict the operational data. Logic based criteria are applied to the graphs to reject graphs as not likely representative of real biology.Type: ApplicationFiled: March 27, 2006Publication date: September 27, 2007Inventors: Dexter Roydon Pratt, William McClure Ladd, Suresh Toby Segaran, Jack Pollard