Abstract: A machine learning model is generated for drug efficacy prediction in treatment of genetic disease from a dataset correlating gene expression data for disease-cell samples with drug efficacy values for the samples. Bias weights are stored that correspond to respective genes in the samples. Each bias weight is dependent on predetermined relevance of the respective gene to drug efficacy. The model is generated by processing the dataset via a tree ensemble method wherein decision trees are grown with splits corresponding to respective genes in the samples. The gene for each split is chosen from a respective subset of the genes, and genes are selected for inclusion in this subset with respective probabilities dependent on the corresponding bias weights. The model is stored, and can be applied to gene expression data measured for a patient to obtain a personalized drug efficacy prediction for devising a personalized course of treatment.

Abstract: Provide a reinforcement learning model including an agent and a critic; the critic includes a neural network pre-trained to generate, from input biomolecular data characterizing tissue cells and input compound data defining a compound molecule, a property value for said biomolecular action of that molecule on those tissue cells. The agent includes a neural network adapted to generate the compound data in dependence on input biomolecular data. Supply biomolecular data characterizing patient tissue cells to the agent and supply that data, and the compound data generated therefrom, to the critic to obtain a property value in an iterative training process in which reward values, dependent on the property values, are used to progressively train the agent to optimize the reward value. After training the agent, supply target biomolecular data, characterizing the target tissue cells, to the agent to generate compound data corresponding to a set of drug compounds.

Abstract: A neural network model is generated for drug efficacy prediction in treatment of genetic disease from a dataset correlating biomolecular data for disease-cell samples with drug efficacy values for a plurality of drugs, including defining training data pairs each including biomolecular data for a sample represented in the dataset and a string representation of a drug represented in the dataset; and using the training data pairs and the drug efficacy values corresponding to respective pairs to train weights of the model including a first attention-based encoder which encodes the biomolecular data of each pair, to produce encoded biomolecular data, a second attention-based encoder which encodes the string representation of each pair, to produce encoded string data, and a set of neural network layers which process the encoded biomolecular and string data for each pair, to produce a model output corresponding to drug efficacy.

Abstract: Analysis of genetic disease progression may be provided. Data about a set of molecular status may be received. A dynamic prediction model of molecular interactions may be provided over time. The molecular statuses of the set over time may be determined using the dynamic prediction model. The determined molecular statuses may be clustered by applying an interaction-aware metric for the analysis of the genetic disease progression.

Abstract: A computer-implemented method for inferring a 3D structure of a genome is provided. The method includes providing genome interaction data and operating an autoencoder including a structured sequence of n autoencoder units, each of which including an encoder unit and a decoder unit, each of which is implemented as a recurrent neural network unit. The method includes additionally training the autoencoder by feeding all vectors of genome interaction data to the encoder units. Thereby, the training of the auto-encoder units is performed stepwise by using inner state of respective previous autoencoder units in the cascaded sequence of autoencoder units and performing backpropagation within each of the plurality of autoencoder units after all autoencoder units have processed their respective input values, and using the output values of the encoder units for deriving a 3D model for a visualization of the genome.

Abstract: Computer-implemented methods are provided for generating a personalized Boolean model for a genetic disease of a patient. The method includes storing specification data and reference model data. The reference model includes gene nodes, representing genes, connected to Boolean circuitry and a plurality of inputs for receiving binary input values. Each gene node in the reference model comprises a multiplexer. The multiplexer has a first input and an output, a second input for receiving a binary mutation value, and a control input for receiving a binary selector value. The method further comprises using a model checker to determine if the specification is reachable in the reference model. If the specification is reachable, the method includes identifying each multiplexer whose second input was connected to its output in the path reaching the specification to obtain mutation data for the patient, generating a personalized Boolean model, and outputting personal model data.

Abstract: A computer-implemented method for inferring a 3D structure of a genome is provided. The method includes providing genome interaction data and operating an autoencoder including a structured sequence of n autoencoder units, each of which including an encoder unit and a decoder unit, each of which is implemented as a recurrent neural network unit. The method includes additionally training the autoencoder by feeding all vectors of genome interaction data to the encoder units. Thereby, the training of the auto-encoder units is performed stepwise by using inner state of respective previous autoencoder units in the cascaded sequence of autoencoder units and performing backpropagation within each of the plurality of autoencoder units after all autoencoder units have processed their respective input values, and using the output values of the encoder units for deriving a 3D model for a visualization of the genome.

Abstract: Methods and systems are provided for identifying drug compounds for targeting proteins in tissue cells. Such a method includes providing a neural network model which comprises an attention-based protein encoder and a molecular decoder. The protein encoder is pretrained in an autoencoder architecture to encode an input protein sequence into an output vector in a latent space representing proteins. The molecular decoder is pretrained in an autoencoder architecture to generate compound data, defining a compound molecule, from an input vector in a latent space representing molecules. The protein encoder and molecular decoder are coupled such that the input vector of the molecular decoder is dependent on the output vector of the protein encoder for an input protein sequence.

Abstract: A neural network model is generated for drug efficacy prediction in treatment of genetic disease from a dataset correlating biomolecular data for disease-cell samples with drug efficacy values for a plurality of drugs, including defining training data pairs each including biomolecular data for a sample represented in the dataset and a string representation of a drug represented in the dataset; and using the training data pairs and the drug efficacy values corresponding to respective pairs to train weights of the model including a first attention-based encoder which encodes the biomolecular data of each pair, to produce encoded biomolecular data, a second attention-based encoder which encodes the string representation of each pair, to produce encoded string data, and a set of neural network layers which process the encoded biomolecular and string data for each pair, to produce a model output corresponding to drug efficacy.

Abstract: Provide a reinforcement learning model including an agent and a critic; the critic includes a neural network pre-trained to generate, from input biomolecular data characterizing tissue cells and input compound data defining a compound molecule, a property value for said biomolecular action of that molecule on those tissue cells. The agent includes a neural network adapted to generate the compound data in dependence on input biomolecular data. Supply biomolecular data characterizing patient tissue cells to the agent and supply that data, and the compound data generated therefrom, to the critic to obtain a property value in an iterative training process in which reward values, dependent on the property values, are used to progressively train the agent to optimize the reward value. After training the agent, supply target biomolecular data, characterizing the target tissue cells, to the agent to generate compound data corresponding to a set of drug compounds.

Abstract: Analysis of genetic disease progression may be provided. Data about a set of molecular status may be received. A dynamic prediction model of molecular interactions may be provided over time. The molecular statuses of the set over time may be determined using the dynamic prediction model. The determined molecular statuses may be clustered by applying an interaction-aware metric for the analysis of the genetic disease progression.

Abstract: A machine learning model is generated for drug efficacy prediction in treatment of genetic disease from a dataset correlating gene expression data for disease-cell samples with drug efficacy values for the samples. Bias weights are stored that correspond to respective genes in the samples. Each bias weight is dependent on predetermined relevance of the respective gene to drug efficacy. The model is generated by processing the dataset via a tree ensemble method wherein decision trees are grown with splits corresponding to respective genes in the samples. The gene for each split is chosen from a respective subset of the genes, and genes are selected for inclusion in this subset with respective probabilities dependent on the corresponding bias weights. The model is stored, and can be applied to gene expression data measured for a patient to obtain a personalized drug efficacy prediction for devising a personalized course of treatment.

Abstract: The present disclosure relates to a system and method for extracting information from text data. The method comprises: obtaining a plurality of text elements. A word embedding algorithm may be applied to the obtained text elements by mapping each text element of at least part of the text elements into a vector of a predefined dimension. The mapped text elements may be clustered into groups using the distances between the respective vectors. For each text element of a set of text elements of the mapped text elements a respective distribution of neighbors across the groups may be built. Similarity scores may be computed using the distributions thereby for determining relations between the set of text elements.

Abstract: The present disclosure relates to a system and method for extracting information from text data. The method comprises: obtaining a plurality of text elements. A word embedding algorithm may be applied to the obtained text elements by mapping each text element of at least part of the text elements into a vector of a predefined dimension. The mapped text elements may be clustered into groups using the distances between the respective vectors. For each text element of a set of text elements of the mapped text elements a respective distribution of neighbors across the groups may be built. Similarity scores may be computed using the distributions thereby for determining relations between the set of text elements.

Abstract: Computer-implemented methods are provided for generating a personalized Boolean model for a genetic disease of a patient. The method includes storing specification data and reference model data. The reference model includes gene nodes, representing genes, connected to Boolean circuitry and a plurality of inputs for receiving binary input values. Each gene node in the reference model comprises a multiplexer. The multiplexer has a first input and an output, a second input for receiving a binary mutation value, and a control input for receiving a binary selector value. The method further comprises using a model checker to determine if the specification is reachable in the reference model. If the specification is reachable, the method includes identifying each multiplexer whose second input was connected to its output in the path reaching the specification to obtain mutation data for the patient, generating a personalized Boolean model, and outputting personal model data.

Abstract: The present invention concerns the biotechnology sector and more specifically human healthcare. In particular, the present invention describes a vaccine composition for therapeutic use thereof on cancer patients. The vaccine composition described in the present invention has as active principle a chemical conjugate of human recombining Epidermic Growth Factor (hrEGF) and are combining protein P64k. In addition, specific conditions are described for performing a conjugation reaction which produces said chemical conjugate in a controlled and reproducible manner. In another embodiment, the present invention concerns a method for purification of the chemical conjugate which not only provides greater purity for the therapeutic composition, but surprisingly increases the immunogenic activity causing significant increases in the anti-EGF antibody titers in humans.

Abstract: The present invention relates to the biotechnological field and particularly to the human health. More particularly, the present invention relates to a vaccine composition for therapeutic use in cancer patients. The vaccine composition of the present invention has as active principle a chemical conjugated between the human recombinant Epidermal Growth Factor (hrEGF) and the P64K recombinant protein. In another embodiment, the present invention relates to the conjugation procedure to obtain, a chemical conjugated under controlled and reproducible parameters. In a preferred embodiment, the present invention relates to the procedure for purifying the chemical conjugated with a higher purity of the therapeutical vaccine composition, and a surprisingly increased immunogenic activity, inducing a significant increase of the anti-EGF antibody titers in humans.