Methods, computer-accessible medium and systems to model disease progression using biomedical data from multiple patients

Abstract

An exemplary embodiment of system, method and computer-accessible medium can be provided to reconstruct models based on the probabilistic notion of causation, which can differ fundamentally from that can be based on correlation. A general reconstruction setting can be complicated by the presence of noise in the data, owing to the intrinsic variability of biological processes as well as experimental or measurement errors. To gain immunity to noise in the reconstruction performance, it is possible to use a shrinkage estimator. On synthetic data, the exemplary procedure can outperform currently known procedures and, for some real cancer datasets, there are biologically significant differences revealed by the exemplary reconstructed progressions. The exemplary system, method and computer accessible medium can be efficient even with a relatively low number of samples and its performance quickly converges to its asymptote as the number of samples increases.

What is claimed is: 
     
         1 . A non-transitory computer-accessible medium having stored thereon computer-executable instructions for generating a model of progression of at least one disease using biomedical data of at least one patient, wherein, when a computer arrangement executes the instructions, the computer arrangement is configured to perform procedures comprising:
 obtaining the biomedical data; and   generating the model of progression, which includes at least one of (i) states of the at least one disease or (ii) transitions among the states, based on the obtained biomedical data.   
     
     
         2 . The computer-accessible medium of  claim 1 , wherein the model of progression further includes a progression graph. 
     
     
         3 . The computer-accessible medium of  claim 2 , wherein the progression graph is based on a causal graph. 
     
     
         4 . The computer-accessible medium of  claim 2 , wherein the model of progression further includes at least one of a directed acyclic graph (DAG), a disconnected DAG, a tree or a forest. 
     
     
         5 . The computer-accessible medium of  claim 4 , wherein nodes of the DAG are atomic events and edges represent a progression between the atomic events. 
     
     
         6 . The computer-accessible medium of  claim 1 , wherein the model of progression is further based on a noise model. 
     
     
         7 . The computer-accessible medium of  claim 6 , wherein the noise model includes a biological noise model. 
     
     
         8 . The computer-accessible medium of  claim 7 , wherein the computer arrangement is further configured to use the biological noise model to distinguish spurious causes from genuine causes. 
     
     
         9 . The computer-accessible medium of  claim 6 , wherein the noise model includes an experimental noise model. 
     
     
         10 . The computer-accessible medium of  claim 6 , wherein the noise model includes an experimental noise model and a biological noise model. 
     
     
         11 . The computer-accessible medium of  claim 1 , wherein the biomedical data includes at least one of genomics, transcriptomics, epigeneomics or imaging data. 
     
     
         12 . The computer-accessible medium of  claim 1 , wherein the biomedical data includes information pertaining to at least one of at least one normal cell, at least one tumor cell, cell-free circulating DNA or at least one circulating tumor cell. 
     
     
         13 . The computer-accessible medium of  claim 1 , wherein the computer arrangement is further configured to determine the states of the disease by at least one of genomics, transcriptomics or epigeneomics mutational profiles. 
     
     
         14 . The computer-accessible medium of  claim 1 , wherein the computer arrangement is further configured to determine transitions of the states by a causality relationship whose strength is estimated by probability-raising by at least one unbiased estimator. 
     
     
         15 . The computer-accessible medium of  claim 14 , wherein the unbiased estimator includes at least one shrinkage estimator. 
     
     
         16 . The computer-accessible medium of  claim 15 , wherein the shrinkage estimator is a measure of causation among any pair of events atomic events. 
     
     
         17 . The computer-accessible medium of  claim 1 , wherein the at least one disease includes cancer. 
     
     
         18 . The computer-accessible medium of  claim 1 , wherein the computer arrangement is further configured to (i) receive further biomedical data related to at least one further patient, and (ii) generate information about the at least one further patient based on the model of progression and the further biomedical data. 
     
     
         19 . The computer-accessible medium of  claim 18 , wherein the information includes a classification of at least one further disease of the at least one further patient. 
     
     
         20 . A method for modeling a progression of at least one disease using biomedical data for one or more patients, comprising:
 (a) obtaining the biomedical data; and   (b) using a computer hardware arrangement, generating the model of progression, which includes at least one of (i) states of the disease or (ii) transitions among the states, based on the obtained biomedical data.   
     
     
         21 - 38 . (canceled) 
     
     
         39 . A system for modeling a progression of at least one disease using biomedical data for one or more patients, comprising:
 a computer hardware arrangement configured to:   (a) obtaining the biomedical data; and   (b) using a computer hardware arrangement, generating the model of progression, which includes at least one of (i) states of the disease or (ii) transitions among the states, based on the obtained biomedical data.   
     
     
         40 - 57 . (canceled)