Abstract: A method for generating digital setups for an orthodontic treatment path. The method includes receiving a digital 3D model of teeth, performing interproximal reduction (IPR) on the model and, after performing the IPR, generating an initial treatment path with stages including an initial setup, a final setup, and a plurality of intermediate setups. The method also includes computing IPR accessibility for each tooth at each stage of the initial treatment path, applying IPR throughout the initial treatment path based upon the computed IPR accessibility, and dividing the initial treatment path into steps of feasible motion of the teeth resulting in a final treatment path with setups corresponding with the steps. The setups can be used to make orthodontic appliances, such as clear tray aligners, for each stage of the treatment path.

Abstract: Methods and apparatus for obtaining representations of proteins and small molecule drugs for synthesis; wherein input queries into trained mixed modality protein and natural language models are augmented with relevant query-related documents. In one embodiment, the relevant query-related documents are obtained by maximum inner product search of an embedding latent vector space into which the query and the documents are projected. The top-k most relevant documents to the query are then combined with the query as input into the trained mixed modality language model. In one embodiment, the mixed modality model is an autoregressive multicapitate transformer whose decoder output heads correspond to the represented modalities. The method returns mixed modality output representations of proteins or small molecule drugs for synthesis or manufacture.

Abstract: A method for nucleic acid sequencing includes receiving a plurality of observed or measured signals indicative of a parameter observed or measured for a plurality of defined spaces; determining, for at least some of the defined spaces, whether the defined space comprises one or more sample nucleic acids; processing, for at least some of the defined spaces, the observed or measured signal to improve a quality of the observed or measured signal; generating, for at least some of the defined spaces, a set of candidate sequences of bases for the defined space using one or more metrics adapted to associate a score or penalty to the candidate sequences of bases; and selecting the candidate sequence leading to a highest score or a lowest penalty as corresponding to the correct sequence for the one or more sample nucleic acids in the defined space.

Abstract: The present disclosure provides methods for determining a probability that after any of a number of therapeutic interventions, an initial state of a subject, such as somatic cell mutational status of a subject with cancer, will develop a subsequent state. Such probabilities can be used to inform a health care provider as to particular courses of treatment to maximize probability of a desired outcome for the subject.

Abstract: Time-series data formed by acquiring values indicating amounts or states of a plurality of biological materials for each biological material at a plurality of time points is prepared, the plurality of biological materials are divided into a plurality of groups on the basis of temporal variations of time-series data of the respective biological materials, representative time-series data indicating a state of each group is generated on the basis of time-series data of at least one biological material included in each group, and dependencies between the groups are estimated on the basis of the representative time-series data of each group.

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: Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.

Abstract: A plasma piwi-interacting RNA (piRNA) combination for early diagnosis of gastric cancer and application thereof are provided. Based on the plasma piRNA expression profile of the Chinese population, the present invention obtains a plasma piRNA combination for early diagnosis of gastric cancer, and establishes an early diagnosis model for gastric cancer based on the plasma piRNA combination. The model can predict the incidence risk of gastric cancer with relatively high accuracy, which helps to reduce the cost of detection. At the same time, the present invention uses a Lasso Logistic regression model, which greatly reduces the number of variables included in the model and facilitates the application and popularization of the model.

Abstract: A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention, incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and/or genetic data taken from other related individuals.

Abstract: Training a protein diffusion model includes receiving a representation of a protein as training data, the representation comprising at least three dimensions. It further includes training a protein diffusion model at least in part by performing rotational diffusion based at least in part on the representation of the protein. Generating proteins includes receiving protein conditioning information. It further includes, based at least in part on the protein conditioning information, performing conditional sampling of a protein diffusion model. The protein diffusion model is trained at least in part by performing rotational diffusion. Based at least in part on the conditional sampling of the protein diffusion model, the protein diffusion model generates one or more of a protein structure or a protein sequence.

Abstract: Integrated glucose monitoring systems, comprising a memory configured to store data relating to at least two glucose measurements of a user, a glucose safe range, and exogenous data. Wherein the at least two glucose measurements of the user are at different time points t1 and t2; a user interface comprising a display; and a processor comprising computer-executable instructions. Wherein the computer-executable instructions determine a rate of change based on the at least two glucose measurements of the user; determine, based on the at least two glucose measurements of the user and the determined rate of change, a projected glucose level at a future time t3; and provide an alarm at the user interface if, based on at least one point of exogenous data, the projected glucose level at future time t3 is outside of the glucose safe range.

Abstract: Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.

Abstract: This invention pertains to arthropods that cause disease in humans and animals or that serve as vectors of human and animal disease-causing pathogens. It comprises a novel method, wherein acquiring, processing, identifying and determining the pathogen burden in said arthropods is integrated into a single seamless sequence that ends with the provision of data and information that can be used to improve understanding and to develop and deliver recommendations for remedial treatment of both the arthropods and humans and animals that are afflicted with disease-causing arthropods or diseases that they transmit. The novel integrated method can be offered as a unified commercial service.

Abstract: The purpose of the present invention is to provide a service on the basis of genetic information on a user group. A method of operating an electronic device may comprise: an operation for grouping genetic information on a plurality of users belonging to a user group; an operation for determining genetic characteristics of the user group on the basis of the grouped genetic information; and an operation for providing data generated on the basis of the genetic characteristics of the user group.

Abstract: Disclosed herein is a system and method for increasing the fidelity of measured genetic data, for making allele calls, and for determining the state of aneuploidy, in one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available. Poorly or incorrectly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related individuals. In accordance with one embodiment, incomplete genetic data from an embryonic cell are reconstructed at a plurality of loci using the more complete genetic data from a larger sample of diploid cells from one or both parents, with or without haploid genetic data from one or both parents. In another embodiment, the chromosome copy number can be determined from the measured genetic data, with or without genetic information from one or both parents.

Abstract: Processes and materials to detect cancer, transplant rejection, or fetal genetic abnormalities from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences indicative of a neoplasm, transplant rejection, or fetal genetic abnormality. Detection of somatic variants occurring in phase and/or insertions and deletions (indels) can indicate the presence of cancer, transplant rejection, or fetal genetic abnormalities in a diagnostic scan, and a clinical intervention can be performed.

Abstract: A computer implemented method and a machine learning model for predicting the likelihood that a subject having breast cancer will experience a relapse following treatment, predicting a tumor within a whole slide image, and/or predicting a status of a biomarker in breast cancer tissue is provided.

Abstract: The present invention provides methods for personalized therapeutic management of a disease in order to optimize therapy and/or monitor therapeutic efficacy. In particular, the present invention comprises measuring an array of one or a plurality of biomarkers at a plurality of time points over the course of therapy with a therapeutic agent to determine a mucosal healing index for selecting therapy, optimizing therapy, reducing toxicity, and/or monitoring the efficacy of therapeutic treatment. In certain instances, the therapeutic agent is a TNF? inhibitor for the treatment of a TNF?-mediated disease or disorder.

Abstract: Exemplary embodiments provide methods, mediums, and systems for processing multiplexed image data from a fluorescence in-situ hybridization (FISH) experiment. According to exemplary embodiments, a convolutional neural network (CNN) may be applied to the image data to localize and identify hybridization spots in images corresponding to different sets of targeting probes. The CNN is configured in such a way that it is able to discriminate hybridization spots in situations that are difficult for conventional techniques. The CNN may be trained on a relatively small amount of data by exploiting the nature of the FISH codebook.

Abstract: A health and wellness system for a non-human subject comprising analyzing genetic data and phenotypic data of the non-human subject with a machine learning algorithm and making a recommendation or recommendation for products or activities for the non-human subject.