Abstract: Systems and methods for phenotyping clinical data are provided. The method includes obtaining episodic records comprising unstructured clinical data from an electronic medical record (EMR) or electronic health record (EHR) for patients. The method also includes filtering the episodic records by language pattern recognition to identify episodic records that each includes an expression related to a clinical condition. The method also includes splitting each episodic record to obtain snippets comprising tokens. The method also includes predicting if an episodic record represents an instance of the clinical condition using a trained classifier. The trained classifier includes an aggregation function that aggregates the snippets to output a corresponding representation for the episodic record, and an interpretation function that interprets the corresponding representation to output a corresponding prediction for whether the episodic record represents an instance of the clinical condition.

Abstract: A method for determining cardiology disease risk from electrocardiogram trace data and clinical data includes receiving electrocardiogram trace data associated with a patient, receiving the patient's clinical data, providing both sets of data to a trained machine learning composite model that is trained to evaluate the data with respect to each disease of a set of cardiology diseases including three or more of cardiac amyloidosis, aortic stenosis, aortic regurgitation, mitral stenosis, mitral regurgitation, tricuspid regurgitation, abnormal reduced ejection fraction, or abnormal interventricular septal thickness, generating, by the model and based on the evaluation, a composite risk score reflecting a likelihood of the patient being diagnosed with one or more of the cardiology diseases within a predetermined period of time from when the electrocardiogram trace data was generated, and outputting the composite risk score to at least one of a memory or a display.

Abstract: Techniques for detecting low ejection fraction (EF) from electrocardiogram (ECG) data using artificial intelligence (AI) are disclosed. ECG data is obtained for a patient. The ECG data is provided as input to a plurality of trained AI models, wherein each trained AI model is trained to determine a score of low EF based on the ECG data. A score of low EF is determined using each trained AI model based on the ECG data. An overall score of low EF is determined based on a combination of the scores of low EF determined by each of the trained AI models. An operating point threshold is obtained for the patient based on a plurality of patient characteristics. The overall score of low EF is compared to the operating point threshold. A low EF prediction is made for the patient based on the comparison.

Abstract: Systems and methods are provided for performing quality control analysis. The method obtains, in electronic form, a batch dataset comprising, for each respective sample in a batch of samples, a corresponding plurality of sequence reads derived from the respective sample by targeted or whole transcriptome RNA sequencing and corresponding metadata for the respective sample. The method determines for the batch dataset a cohort-matched reference batch, where the cohort-matched reference batch is balanced for tissue site, tumor purity, cancer type, sequencer identity, or date sequenced. The method performs one or more global batch quality control tests on the batch dataset using at least the cohort-matched reference batch. The method removes respective samples from the batch dataset that fail any one of the one or more global batch quality control tests or flagging for manual inspection respective samples that fail any one of the one or more global batch quality control tests.

Abstract: A computer system receives, from a user, a set of clinical eligibility criteria. The computer system retrieves, from a database, medical records for a plurality of subjects. The computer system inputs, into a model comprising 1000 parameters: information corresponding to the set of clinical eligibility criteria; and information corresponding to the medical records for at least a first subset of the plurality of subjects. The computer system receives, from the model, responsive to the inputting, a ranking of the first subset of the plurality of subjects indicative of relative relevance of the respective medical histories of the plurality of subjects to the set of clinical eligibility criteria. The computer system selects, based on the ranking, a second subset of the plurality of subjects for inclusion in the cohort.

Abstract: A method includes the step of receiving electrocardiogram (ECG) data associated with a plurality of patients and an electrocardiogram configuration including a plurality of leads and a time interval. The electrocardiogram data includes, for each lead included in the plurality of leads, voltage data associated with at least a portion of the time interval. The method also includes training an artificial intelligence model on the ECG data, tuning the artificial intelligence model using data from a device having fewer leads than the plurality of leads, and evaluating the artificial intelligence model on additional data received from the ECG data.

Abstract: A method and system for determining cardiac disease risk from electrocardiogram trace data is provided. The method includes receiving electrocardiogram trace data associated with a patient, the electrocardiogram trace data having an electrocardiogram configuration including a plurality of leads. One or more leads of the plurality of leads that are derivable from a combination of other leads of the plurality of leads are identified, and a portion of the electrocardiogram trace data does not include electrocardiogram trace data of the one or more leads. The portion of the electrocardiogram data is provided to a trained machine learning model, to evaluate the portion of the electrocardiogram trace data with respect to one or more cardiac disease states. A risk score reflecting a likelihood of the patient being diagnosed with a cardiac disease state within a predetermined period of time is generated by the trained machine learning model based on the evaluation.

Abstract: Techniques are provided for replacing image assays using real world data and real word evidence RNA-seq analysis for assessing biologic pathways for identifying molecular subtypes. Systems of a methods diagnose HER2 status for a patient, by identifying discordant HER2 status result between the HER2 status from immunohistochemistry (IHC) and the HER2 status from fluorescence in-situ hybridization (FISH) and diagnosing HER2 status based gene expression data.

Abstract: A platform to perform normalization and correction on gene expression datasets and combines different datasets into a standard dataset using a framework configured to continuously incorporate new gene expression data. The framework determines a series of conversion factors that are used to on-board new gene expression datasets, such as unpaired datasets, where these conversion factors are able to correct for variations in data type, variations in gene expressions, and variations in collection systems.

Abstract: In the disclosed systems and methods for categorizing medical data, a computer system obtains, in electronic form, a plurality of medical records. Each medical record includes corresponding medical data from a respective medical evaluation and corresponding metadata comprising a plurality of attributes about the respective medical evaluation. Each respective attribute comprises a corresponding string of text. The computer system determines, for each respective pair of medical records consisting of a first medical record and a second medical record, a corresponding pairwise similarity between, for each respective attribute in a set of attributes, the corresponding string of text for the first medical record and the corresponding string of text for the second medical record. The computer system identifies a first subset of the plurality of medical records. Each respective medical record in the first subset is connected to each other through pairwise similarities that each satisfies a similarity threshold.

Abstract: A system for personalized depression disorder treatment is disclosed herein. The system includes a server configured to communicate with existing healthcare resources and to receive patient data corresponding to a patient, the server including an analytics module. The system further includes a first database configured to store empirical patient outcomes, and further configured to communicate with the analytics module. Additionally, the system includes a user device having a graphical user interface (GUI) configured to communicate with the server and to display at least one output generated by the analytics module. The analytics module is configured to determine at least one of a personalized depression treatment and a personalized depression state prediction based on the empirical patient outcomes and the patient data.

Abstract: A system and method, the method comprising receiving a laboratory diagnostic testing result associated with a specimen of a subject, the steps of receiving a clinomic profile of the subject, identifying a cohort of similar subjects based at least in part on the clinomic profile of the subject, providing the diagnostic testing results, clinomic profile, and the cohort of similar subjects to a smart output module to generate a personalized, precision medicine based laboratory diagnostic testing result as a smart output and displaying the smart output to a user.

Abstract: A method for characterizing cancer organoid response to an immune cell based therapy, includes providing a panel of different combinations of cancer organoid cells and immune cells to culturing wells and culturing the different combination under conditions that support organoid growth. Brightfield and corresponding fluorescence images of the culturing wells are captured and provided to one or more trained machine learning algorithms that identify and distinguish cancer organoid cells from immune cells and characterize cancer organoid morphology changes caused by an immune cell based therapies, from which an analytical report including a characterization of cancer organoid cell death caused by the immune cell based therapy is provided.

Abstract: Disclosed herein are systems, methods, and compositions for treating a subject diagnosed with, or suffering from cancer. In some embodiments, the method comprises determining whether a tumor sample from the subject includes a cytotoxic gene signature, and treating the subject based on the determination. In some embodiments, the subject has or is suspected of having a loss of heterozygosity in human leukocyte antigen (HLA) class I genes. In some embodiments, the therapy comprises one or more checkpoint inhibitors. In some embodiments, the cancer is colorectal, uterine, stomach, lung, skin, head or neck, or non-small cell lung carcinoma.

Abstract: Methods for determining a cancer composition of a subject are provided that include generating machine-learning models configured to identify cell types based on respective cell-type RNA expression profiles, and using the models to determine the cancer composition of the subject.

Abstract: A computer-implemented method, computing system and computer-readable medium include receiving training data and training a machine learning model to generate a cell expression map. A computer-implemented method, computing system and computer-readable medium includes receiving a histology image and a cell segmentation map and processing them using a trained machine learning model.

Abstract: Methods, systems, and software are provided for determining a homologous recombination pathway status of a cancer in a test subject, e.g., to improve cancer treatment predictions and outcomes. In some embodiments, classifiers using one or more of (i) a heterozygosity status for DNA damage repair genes in a cancerous tissue, (ii) a measure of the loss of heterozygosity across the genome of the cancerous tissue, (iii) a measure of variant alleles detected in a second plurality of DNA damage repair genes in the genome of the cancerous tissue, (iv) a measure of variant alleles detected in the second plurality of DNA damage repair genes in the genome of a non-cancerous tissue, and (v) tumor sample purity are provided.

Abstract: A method includes displaying a cohort report; receiving a request to determine a therapy identification; causing information to be transmitted to a remote cloud server; receiving clinical trial data; and updating the cohort report. A computing system includes a processor; and a memory having stored thereon computer-executable instructions that, when executed by the one or more processors, cause the computing system to: display a cohort report; receive a request to determine a therapy identification; cause information to be transmitted to a remote cloud server; receive clinical trial data; and update the cohort report. A computer-readable medium having stored thereon a set of computer-executable instructions that, when executed by one or more processors, cause a computer to: display a cohort report; receive a request to determine a therapy identification; cause information to be transmitted to a remote cloud server; receive clinical trial data; and update the cohort report.

Abstract: In the disclosed systems and methods for characterizing a cancer condition of a tissue in a subject, a computer system inputs information into an ensemble model. The information includes, for each respective class of radiomics features in a plurality of classes of radiomics features, a corresponding value for each respective radiomic feature in a corresponding plurality of radiomics features of the respective class of radiomics features obtained from a medical imaging dataset. The ensemble model comprises a plurality of component models. The computer system obtains as output from each respective component model in the plurality of component models a corresponding component prediction for the cancer condition, thereby obtaining a plurality of component predictions for the cancer condition. The computer system combines the plurality of component predictions to obtain as output of the ensemble model a characterization of the cancer condition.

Abstract: This application describes, amongst other things, methods and systems for building and deploying agents. An example method includes obtaining orchestration data about a set of task-specific components selected to provide a response to the prompt, where each respective task-specific components in the set of task-specific components is configured to assist with a respective clinical task of the one or more clinical tasks. The method further includes, determining an order in which each respective task-specific components of the set of task-specific components should be utilized to prepare a complete response to the prompt that address the one or more clinical tasks based on the obtained orchestration data about the set of task-specific components. The method also includes, in accordance with the determined order, providing first data related to the prompt to a first task-specific component and receiving a first response from the first task-specific component.