# US 8,572,018 B2 · Method, system and software arrangement for reconstructing formal descriptive models of processes from functional/modal data using suitable ontology > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 8,572,018 B2 - Document ID: US8572018B2 - Status: Granted - Kind: B2 - Application number: 12/803,195 - Filed: 2010-06-21 - Published: 2011-05-19 - Granted: 2013-10-29 - Earliest claimed: 2005-06-20 - Assignees: New York University - Applicants: Bhubaneswar Mishra; Marco Antoniotti; Naren Ramakrishnan - Inventors: Bhubaneswar Mishra; Marco Antoniotti; Naren Ramakrishnan - Web page: https://patentgrep.com/patent/US8572018B2 ## CPC - G06N 5/048: Fuzzy inferencing - G06F 40/30: Semantic analysis - G06N: COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS - G06F: ELECTRIC DIGITAL DATA PROCESSING (computer systems based on specific computational models G06N) ## Abstract A method, system and software arrangement in accordance with an exemplary embodiment of the present invention are provided to extract descriptive narrative from numerical experimental data augmented with ontological controlled vocabulary. One exemplary application of such system, method and software arrangement is in organizing gene-expression time course data in terms of biological processes that may be activated and deactivated as the biological system responds to its normal or perturbed environment. The present invention may also have biological applications to drug-or-vaccine discovery, understanding behavior of a cell in an altered diseased state (e.g., cancer, neuro-degeneration or auto-immune disease, etc.), genetically modifying a natural wild-type organism, genetic-engineering, etc. Other exemplary applications may include understanding neural behavior, market behavior of a population of users interacting on the Internet, etc. ## Claims ### Claim 1 A method for at least one of generating or utilizing a model associated with a data set using predetermined semantics, comprising: organizing the data set into a plurality of states and a plurality of state transitions, wherein at least one transition of the plurality of state transitions is associated with each of the states; associating each of the states with at least one label relating to the predetermined semantics; assigning at least one probability to at least one state of the plurality of states based on a likelihood that the at least one state follows the at least one transition associated with the at least one state; determining at least one invariant associated with the model as a function of the at least one probability; and re-organizing the data set into a plurality of further states and a plurality of further state transitions based at least in part on the at least one probability assigned to the at least one state, wherein at least one further transition of the plurality of further state transitions is associated with each of the further states. ### Claim 2 (depends on 1) The method of claim 1, further comprising: receiving a query relating to the data set; and providing a response to the query based at least in part on the model. ### Claim 3 (depends on 1) The method of claim 1, wherein the data set comprises at least one of modal data, temporal data or functional data. ### Claim 4 (depends on 1) The method of claim 1, wherein the data set is associated with at least one of a gene expression, a probe value, a click on a web link, or a cellular event. ### Claim 5 (depends on 1) The method of claim 1, wherein the data set is arranged in a form of a matrix. ### Claim 6 (depends on 1) The method of claim 1, wherein the data set is organized using at least one of a clustering procedure, a K-means procedure, an SOM procedure, an agglomerative procedure, a graph-based procedure, a biclustering procedure, or an information-bottleneck-based procedure. ### Claim 7 (depends on 1) The method of claim 1, wherein the predetermined semantics are provided by at least one of a controlled vocabulary, an ontology, a gene ontology, a prior knowledge relating to the data set, a procedure which operates on gene expression data, or a statistical text mining procedure. ### Claim 8 (depends on 1) The method of claim 1, wherein the at least one probability is determined using at least one of a Fisher exact test or a Jacquard coefficient technique. ### Claim 9 (depends on 1) The method of claim 1, wherein the at least one invariant is determined using at least one of a modal logic technique, a linear-time temporal logic technique, a branching-time temporal logic technique, or a fuzzy logic technique. ### Claim 10 (depends on 1) The method of claim 1, wherein the at least one invariant is determined by combining at least two labels. ### Claim 11 (depends on 10) The method of claim 10, further comprising combining at least two labels using at least one of a model checking technique or an iterative extension technique. ### Claim 12 A system for at least one of generating or utilizing a model associated with a data set using predetermined semantics, comprising: a computer hardware arrangement configured to; (a) organize the data set into a plurality of states and a plurality of state transitions, wherein at least one transition of the plurality of state transitions is associated with each of the states; (b) associate each of the states with at least one label relating to the predetermined semantics; (c) assign at least one probability to at least one state of the plurality of states based on a likelihood that the at least one state follows the at least one transition associated with the at least one state; (d) determine at least one invariant associated with the model as a function of the at least one probability; and re-organize the data set into a plurality of further states and a plurality of further state transitions based at least in part on the at least one probability assigned to the at least one state, wherein at least one further transition of the plurality of further state transitions is associated with each of the further states. ### Claim 13 (depends on 12) The system of claim 12, wherein the computer hardware arrangement is further configured to: (e) receive a query relating to the data set; and (f) provide a response to the query based at least in part on the model. ### Claim 14 (depends on 12) The system of claim 12, wherein the computer hardware arrangement is further configured to organize the data set using at least one of a clustering procedure, a K-means procedure, an SOM procedure, an agglomerative procedure, a graph-based procedure, a biclustering procedure, or an information-bottleneck-based procedure. ### Claim 15 A non-transitory computer-accessible medium having stored thereon computer-executable instructions for at least one of generating or utilizing a model associated with a data set using predetermined semantics, wherein, when a computer hardware arrangement executes the instructions, the computer arrangement is configured to perform procedures comprising: organizing the data set into a plurality of states and a plurality of state transitions, wherein at least one transition of the plurality of state transitions is associated with each of the states; associating each of the states with at least one label relating to the predetermined semantics; assigning at least one probability to at least one state of the plurality of states based on a likelihood that the at least one state follows the at least one transition associated with the at least one state; determining at least one invariant associated with the model as a function of the at least one probability; and re-organizing the data set into a plurality of further states and a plurality of further state transitions based at least in part on the at least one probability assigned to the at least one state, wherein at least one further transition of the plurality of further state transitions is associated with each of the further states. ### Claim 16 (depends on 15) The computer-accessible medium of claim 15, wherein the processing arrangement is further configured to: receive a query relating to the data set; and provide a response to the query based at least in part on the model. ### Claim 17 (depends on 15) The computer-accessible medium of claim 15, wherein the processing arrangement is further configured to organize the data set using at least one of a clustering procedure, a K-means procedure, an SOM procedure, an agglomerative procedure, a graph-based procedure, a biclustering procedure, or an information-bottleneck-based procedure.