Abstract: Disclosed herein are methods for predicting tumor-specific neoantigen MHC class I or MHC class II immunogenicity by jointly predicting MHC class I or MHC class II binding affinity and predicting the likelihood a tumor-specific neoantigen will be presented by a MHC class I or class II protein on a cell-surface.

Abstract: Disclosed herein are methods for profiling a cancerous tumor using a high-throughput sequencing technique.

Abstract: Immunogenic response prediction techniques are described. In an example, a system receives first training data that identifies a peptide, a first set of multiple major histocompatibility complex (MHC) molecules, and an immunogenic response associated with the peptide and the first set. The system updates a parameter of a first model based at least in part on the first training data. The first model is configured to determine a probability of causing the immunogenic response by a pair formed by the peptide and a MHC molecule from the first set. The system also receives second data that identifies a second set of MHC molecules, and generates, by using the first model and a second model, an immunologic response prediction of pairing the peptide with a MHC molecule from the second set. The second model is configured to generate at least one of peptide-MHC binding predictions or peptide-MHC cell surface presentation predictions.

Abstract: Approaches for predicting manufacturability of a peptide are provided. A request for information related to manufacturability of a peptide can be received. A determination as to whether the peptide is predicted to be synthesizable can be made, such as by using a machine learning model. The machine learning model can be trained on data including manufacturer specifications and descriptions associated with a peptide and features for peptides. A second determination can be made as to whether the peptide is predicted to be soluble, using the same or different machine learning model trained with solubility data for peptides. If the peptide is predicted to be soluble and synthesizable, a manufacturability score for the peptide can be determined. The manufacturability score can correspond to or be indicative of a chance of successfully manufacturing the peptide.

Abstract: This disclosure relates to methods of non-invasively measuring the degree of cellular energy metabolism. The methods disclosed herein comprise applying monitoring devices to a bodily surface or solution containing cells (e.g., a dermal surface of a subject), generating a radio frequency, detecting operating values of the circuitry of the device, maintaining contact between the monitoring device and the bodily surface or solution containing cells for a desired length of time, and collecting data that corresponds to the degree of cellular energy metabolism. Methods of this disclosure can be used to correlate the degree of cellular energy metabolism to other physiological or cellular phenomena (e.g., cellular respiration, cell viability).

Abstract: Methods and systems are disclosed for selecting a set of peptides from a plurality of peptides for producing a drug product. A request may be received to produce a vaccine that meets specific requirements, including the desired immune response and the inclusion of certain types of peptides. The system may rank peptides using one or more metrics that factor in immunogenicity and/or manufacturability. Based on the ranking, the system may select a group of peptides for inclusion in a manufacturing simulation process, which returns a set of peptides that are predicted to be successfully manufactured. The system refines its selection to a subset of manufacturable peptides based on specific criteria. This iterative process continues until predefined conditions are met, such as the convergence of the simulation results. Based on these results, the system identifies an optimal or near-optimal set of peptides that can be used for effective drug production.

Abstract: Disclosed herein is a method for determining tumor margins relative to non-tumorous tissue using a deep-learning platform. Also disclosed herein are methods for removing a tumor from a tumor biopsy.

Abstract: Data about concentration of one or more types of molecules present within a human body are determined noninvasively using radio frequency signals. These signals at several different frequencies are generated at very low power levels are emitted and acquired using an antenna mounted to a wearable device. Information about changes to the signals, such as phase variances of the signals at different frequencies is indicative of the concentration of one or more types molecules within the user. The antenna includes concentric elements with one or more being used to emit the signal(s) while one or more are used to acquire the signal(s). Concentrations at different depths may be measured by selectively using particular concentric elements. A maximum depth may approximately equal the spacing between the elements being used at a given time. Other sensors may be emplaced or operate through windows located between one or more of the concentric elements.

Abstract: Disclosed herein are methods of scoring predicted immunogenicity of neoantigens from biological samples of a subject. Methods can include the steps of preparing biological samples for nucleic acid sequencing; nucleic acid sequencing; evaluating the initial sequencing results by analyzing (e.g., comparing) sequencing parameters of the results; based on an analysis (e.g., a comparison) of sequencing parameters, combining the initial sequencing results to yield union sequencing results or selecting a representative biological sample; and scoring the predicted immunogenicity of neoantigens in the biological samples based on either the union sequencing results or the sequencing results of the representative sample. Methods can further include the step of comparing sequencing parameters of union sequencing results and the initial sequencing results.

Abstract: A wearable device may compress the skin of a user when worn, which may affect values determined using sensors of the device. To determine the effect of skin compression on the values, a time-of-flight signal, images, or frames of video data that depict a portion of the body having indentations from wearing the device may be acquired. Characteristics of the images, such as shadows associated with the indentations, may be processed using a machine learning algorithm or mathematical function to determine a depth of various portions of the indentations. Depth data from the time of flight signal may be used to refine or modify these determined depths. The amount of skin compression associated with the indentations may be used to modify signals acquired using sensors, or output a recommendation for a band or other method for securing the device.

Abstract: Provided herein are immunogenic compositions comprising tumor-specific neoantigen long peptides, tumor-specific neoantigen short peptides, and adjuvant, optionally a helper peptide, and optionally a tumor-specific peptide. The disclosure also provides methods of using these immunogenic compositions for treating cancer.

Abstract: Disclosed herein are methods for classifying a cell present in a sample. such as a tumor, of a subject. comprising: sequencing bulk DNA from first and second (e.g., tumor and healthy) a subject's tissue samples; classifying somatic variants as first or second sample alleles; sequencing RNA from the cell; aligning each RNA sequence with the bulk DNA; classifying each RNA sequence as a first, a second, or an unknown allele sequence, depending on whether it substantially aligns with the first, the second sample allele, or cannot be determined; and identifying the cell as a first, a second, or an unknown cell, based on the classifying of each of the plurality of RNA sequences. Methods can comprise validating identification by allelic frequency of germ-line variants in the RNA sequences. The methods provide improved characterization of heterogenous cell populations, such as cell populations contaminated with cells from different sources, or tumor populations.

Abstract: Disclosed herein is a method, comprising administering to a subject in need thereof an initial immunogenic composition comprising a plurality of tumor-specific neoantigens, each corresponding to a member of a first set of tumor-associated mutations in a subject, and none corresponding to a member of a second set of tumor-associated mutations in the subject; and quantifying each member of the first set of tumor-associated mutations and each member of the second set of tumor-associated mutations in circulating material comprising tumor-associated mutations isolated from the subject at each of multiple time points.

Abstract: Data about concentration of one or more types of molecules present within a human body are determined noninvasively using radio frequency (RF) signals. Signals at several different frequencies at very low power levels are emitted using an antenna mounted to a wearable device. Operating values, such as changes to the impedance of the antenna resulting from interaction between the RF signals and the user, are associated with the concentration of one or more types of molecules within the user. These changes in impedance may be relatively small. Circuitry in the device determines internal impedance of the circuitry, compensating for internal impedances and improving overall accuracy of the measured impedance resulting from interaction with the user.

Abstract: Disclosed herein are methods for evaluating the efficacy of an immunogenic composition by monitoring circulating tumor DNA. The disclosure also relates to methods for treating a subject having cancer.

Abstract: Techniques are described and relate to anisotropic pooling for contextual embedding of a protein sequence. In an example, a system receives a first biological sequence and determines a sequence arrangement that comprises a component of the first biological sequence and a second biological sequence of components. By using an artificial intelligence (AI) model, the system determines a third sequence that comprises a contextual embedding vector corresponding to the component of the first biological sequence. The AI model generates the third sequence based at least in part on the sequence arrangement and by at least using a convolution and anisotropic pooling.

Abstract: Data about concentration of one or more types of molecules present within a human body are determined noninvasively using radio frequency signals. Signals at several different frequencies at very low power levels are emitted using an antenna mounted to a wearable device. The antenna includes nested elements of different sizes. Operating values, such as changes to the impedance of the antenna, are associated with the concentration of one or more types molecules within the user. Concentrations at different depths may be measured by using different sets of the nested elements at different times. Operating values at those times are measured and used to determine information indicative of concentration of the molecules. During use, a long axis of the antenna may be aligned with a long axis of a user's arm.

Abstract: Disclosed herein are methods for selecting tumor-specific neoantigens from a tumor of a subject that are suitable for subject-specific immunogenic compositions.

Abstract: Described is a system and method that determines character sequences from speech, without determining the words of the speech, and processes the character sequences to determine sentiment data indicative of emotional state of a user that output the speech. The emotional state may then be presented or provided as an output to the user.

Abstract: Systems, devices, and methods are provided for detecting and correcting eating behavior. A device may receive audio data, determine that the audio data is indicative of consumption of a product by a user. The device may determine, based on the product, a measureable attribute associated with the user. The device may receive first data associated with the measureable attribute. The device may determine that the first data exceeds a threshold. The device may generate a message for presentation.