Abstract: Aspects of the disclosure relate to methods for improving compatibility of nucleic acid sequencing data obtained using different techniques. The disclosure is based, in part, on methods for mapping expression levels for genes expressed in a biological sample and obtained from a subject using a first protocol to expression levels as would have been determined through a second protocol if the second protocol were used to process the biological sample instead of the first protocol.

Abstract: Implementations include evaluating a first sub-set of rules based on a first sub-set of facts to provide a first set of impacts, evaluating including applying the first sub-set of facts to each rule using a hash join operation to determine whether a rule results in an impact, indexes of arguments of facts being used in a probe phase of the hash join operation, evaluating a second sub-set of rules using impacts of the first set of impacts to provide a second set of impacts, determining whether each goal in a set of goals has been achieved using the first set of impacts and the second set of impacts, each goal being provided as an impact, in response to determining that each goal in the set of goals has been achieved, removing paths of the AAG, each of the paths resulting in an impact that is not a goal.

Abstract: Implementations include receiving an AAG that at least partially defines a digital twin of an enterprise network and includes rule nodes each representing an attack tactic that can be used to move along a path, determining security controls each mitigating at least one rule node, executing an iteration of a simulation of a sub-set of security controls in the enterprise network, the iteration including: for each security control in the set of security controls, determining, an influence score that represents a change in a security risk from implementing the security control and a rule distribution, defining the sub-set of security controls based on the first influence scores, and reducing the AAG based on the sub-set of security controls to provide a residual AAG, determining a decrease in a graph risk value and the first AAG, and selectively implementing the sub-set of security controls in the enterprise network.

Abstract: Aspects of the disclosure relate to methods for determining whether or a subject is likely to respond to certain adoptive cell therapies (e.g., chimeric antigen receptor (CAR) T-cell therapy, etc.). In some embodiments, the methods comprise the steps of identifying a subject as having a tumor microenvironment (TME) type based upon a molecular-functional (MF) expression signature of the subject, and determining whether or not the subject is likely to respond to a chimeric antigen receptor (CAR) T-cell therapy based upon the TME type. In some embodiments, the methods comprise determining the lymphoma microenvironment (LME) type of a lymphoma (e.g., Diffuse Large B cell lymphoma (DLBCL)) subject and identifying the subjects prognosis based upon the LME type determination.

Abstract: Aspects of the disclosure relate to methods for determining whether or a subject is likely to respond to certain adoptive cell therapies (e.g., chimeric antigen receptor (CAR) T-cell therapy, etc.). In some embodiments, the methods comprise the steps of identifying a subject as having a tumor microenvironment (TME) type based upon a molecular-functional (MF) expression signature of the subject, and determining whether or not the subject is likely to respond to a chimeric antigen receptor (CAR) T-cell therapy based upon the TME type. In some embodiments, the methods comprise determining the lymphoma microenvironment (LME) type of a lymphoma (e.g., Diffuse Large B cell lymphoma (DLBCL)) subject and identifying the subject's prognosis based upon the LME type determination.

Abstract: Aspects of the disclosure relate to methods for improving compatibility of nucleic acid sequencing data obtained using different techniques. The disclosure is based, in part, on methods for mapping expression levels for genes expressed in a biological sample and obtained from a subject using a first protocol to expression levels as would have been determined through a second protocol if the second protocol were used to process the biological sample instead of the first protocol.

Abstract: Implementations include evaluating a first sub-set of rules based on a first sub-set of facts to provide a first set of impacts, evaluating including applying the first sub-set of facts to each rule using a hash join operation to determine whether a rule results in an impact, indexes of arguments of facts being used in a probe phase of the hash join operation, evaluating a second sub-set of rules using impacts of the first set of impacts to provide a second set of impacts, determining whether each goal in a set of goals has been achieved using the first set of impacts and the second set of impacts, each goal being provided as an impact, in response to determining that each goal in the set of goals has been achieved, removing paths of the AAG, each of the paths resulting in an impact that is not a goal.

Abstract: Implementations include evaluating a first sub-set of rules based on a first sub-set of facts to provide a first set of impacts, evaluating including applying the first sub-set of facts to each rule using a hash join operation to determine whether a rule results in an impact, indexes of arguments of facts being used in a probe phase of the hash join operation, evaluating a second sub-set of rules using impacts of the first set of impacts to provide a second set of impacts, determining whether each goal in a set of goals has been achieved using the first set of impacts and the second set of impacts, each goal being provided as an impact, in response to determining that each goal in the set of goals has been achieved, removing paths of the AAG, each of the paths resulting in an impact that is not a goal.

Abstract: Implementations include evaluating a first sub-set of rules based on a first sub-set of facts to provide a first set of impacts, evaluating including applying the first sub-set of facts to each rule using a hash join operation to determine whether a rule results in an impact, indexes of arguments of facts being used in a probe phase of the hash join operation, evaluating a second sub-set of rules using impacts of the first set of impacts to provide a second set of impacts, determining whether each goal in a set of goals has been achieved using the first set of impacts and the second set of impacts, each goal being provided as an impact, in response to determining that each goal in the set of goals has been achieved, removing paths of the AAG, each of the paths resulting in an impact that is not a goal.

Abstract: Aspects of the disclosure relate to methods for determining whether or a subject is likely to respond to certain adoptive cell therapies (e.g., chimeric antigen receptor (CAR) T-cell therapy, etc.). In some embodiments, the methods comprise the steps of identifying a subject as having a tumor microenvironment (TME) type based upon a molecular-functional (MF) expression signature of the subject, and determining whether or not the subject is likely to respond to a chimeric antigen receptor (CAR) T-cell therapy based upon the TME type. In some embodiments, the methods comprise determining the lymphoma microenvironment (LME) type of a lymphoma (e.g., Diffuse Large B cell lymphoma (DLBCL)) subject and identifying the subject's prognosis based upon the LME type determination.

Abstract: Implementations include receiving an AAG that at least partially defines a digital twin of an enterprise network and includes rule nodes each representing an attack tactic that can be used to move along a path, determining security controls each mitigating at least one rule node, executing an iteration of a simulation of a sub-set of security controls in the enterprise network, the iteration including: for each security control in the set of security controls, determining, an influence score that represents a change in a security risk from implementing the security control and a rule distribution, defining the sub-set of security controls based on the first influence scores, and reducing the AAG based on the sub-set of security controls to provide a residual AAG, determining a decrease in a graph risk value and the first AAG, and selectively implementing the sub-set of security controls in the enterprise network.