AIM To develop a framework to incorporate background domain knowledge into classification rule learning for knowledge discovery in biomedicine.METHODS Bayesian rule learning(BRL) is a rule-based classifier that uses a...AIM To develop a framework to incorporate background domain knowledge into classification rule learning for knowledge discovery in biomedicine.METHODS Bayesian rule learning(BRL) is a rule-based classifier that uses a greedy best-first search over a space of Bayesian belief-networks(BN) to find the optimal BN to explain the input dataset, and then infers classification rules from this BN. BRL uses a Bayesian score to evaluate the quality of BNs. In this paper, we extended the Bayesian score to include informative structure priors, which encodes our prior domain knowledge about the dataset. We call this extension of BRL as BRL_p. The structure prior has a λ hyperparameter that allows the user to tune the degree of incorporation of the prior knowledge in the model learning process. We studied the effect of λ on model learning using a simulated dataset and a real-world lung cancer prognostic biomarker dataset, by measuring the degree of incorporation of our specified prior knowledge. We also monitored its effect on the model predictive performance. Finally, we compared BRL_p to other stateof-the-art classifiers commonly used in biomedicine.RESULTS We evaluated the degree of incorporation of prior knowledge into BRL_p, with simulated data by measuring the Graph Edit Distance between the true datagenerating model and the model learned by BRL_p. We specified the true model using informative structurepriors. We observed that by increasing the value of λ we were able to increase the influence of the specified structure priors on model learning. A large value of λ of BRL_p caused it to return the true model. This also led to a gain in predictive performance measured by area under the receiver operator characteristic curve(AUC). We then obtained a publicly available real-world lung cancer prognostic biomarker dataset and specified a known biomarker from literature [the epidermal growth factor receptor(EGFR) gene]. We again observed that larger values of λ led to an increased incorporation of EGFR into the final BRL_p model. This relevant background knowledge also led to a gain in AUC.CONCLUSION BRL_p enables tunable structure priors to be incorporated during Bayesian classification rule learning that integrates data and knowledge as demonstrated using lung cancer biomarker data.展开更多
Based on the existing pivot rules,the simplex method for linear programming is not polynomial in the worst case.Therefore,the optimal pivot of the simplex method is crucial.In this paper,we propose the optimal rule to...Based on the existing pivot rules,the simplex method for linear programming is not polynomial in the worst case.Therefore,the optimal pivot of the simplex method is crucial.In this paper,we propose the optimal rule to find all the shortest pivot paths of the simplex method for linear programming problems based on Monte Carlo tree search.Specifically,we first propose the SimplexPseudoTree to transfer the simplex method into tree search mode while avoiding repeated basis variables.Secondly,we propose four reinforcement learning models with two actions and two rewards to make the Monte Carlo tree search suitable for the simplex method.Thirdly,we set a new action selection criterion to ameliorate the inaccurate evaluation in the initial exploration.It is proved that when the number of vertices in the feasible region is C_(n)^(m),our method can generate all the shortest pivot paths,which is the polynomial of the number of variables.In addition,we experimentally validate that the proposed schedule can avoid unnecessary search and provide the optimal pivot path.Furthermore,this method can provide the best pivot labels for all kinds of supervised learning methods to solve linear programming problems.展开更多
基金Supported by National Institute of General Medical Sciences of the National Institutes of Health,No.R01GM100387
文摘AIM To develop a framework to incorporate background domain knowledge into classification rule learning for knowledge discovery in biomedicine.METHODS Bayesian rule learning(BRL) is a rule-based classifier that uses a greedy best-first search over a space of Bayesian belief-networks(BN) to find the optimal BN to explain the input dataset, and then infers classification rules from this BN. BRL uses a Bayesian score to evaluate the quality of BNs. In this paper, we extended the Bayesian score to include informative structure priors, which encodes our prior domain knowledge about the dataset. We call this extension of BRL as BRL_p. The structure prior has a λ hyperparameter that allows the user to tune the degree of incorporation of the prior knowledge in the model learning process. We studied the effect of λ on model learning using a simulated dataset and a real-world lung cancer prognostic biomarker dataset, by measuring the degree of incorporation of our specified prior knowledge. We also monitored its effect on the model predictive performance. Finally, we compared BRL_p to other stateof-the-art classifiers commonly used in biomedicine.RESULTS We evaluated the degree of incorporation of prior knowledge into BRL_p, with simulated data by measuring the Graph Edit Distance between the true datagenerating model and the model learned by BRL_p. We specified the true model using informative structurepriors. We observed that by increasing the value of λ we were able to increase the influence of the specified structure priors on model learning. A large value of λ of BRL_p caused it to return the true model. This also led to a gain in predictive performance measured by area under the receiver operator characteristic curve(AUC). We then obtained a publicly available real-world lung cancer prognostic biomarker dataset and specified a known biomarker from literature [the epidermal growth factor receptor(EGFR) gene]. We again observed that larger values of λ led to an increased incorporation of EGFR into the final BRL_p model. This relevant background knowledge also led to a gain in AUC.CONCLUSION BRL_p enables tunable structure priors to be incorporated during Bayesian classification rule learning that integrates data and knowledge as demonstrated using lung cancer biomarker data.
基金supported by National Key R&D Program of China(Grant No.2021YFA1000403)National Natural Science Foundation of China(Grant No.11991022)+1 种基金the Strategic Priority Research Program of Chinese Academy of Sciences(Grant No.XDA27000000)the Fundamental Research Funds for the Central Universities。
文摘Based on the existing pivot rules,the simplex method for linear programming is not polynomial in the worst case.Therefore,the optimal pivot of the simplex method is crucial.In this paper,we propose the optimal rule to find all the shortest pivot paths of the simplex method for linear programming problems based on Monte Carlo tree search.Specifically,we first propose the SimplexPseudoTree to transfer the simplex method into tree search mode while avoiding repeated basis variables.Secondly,we propose four reinforcement learning models with two actions and two rewards to make the Monte Carlo tree search suitable for the simplex method.Thirdly,we set a new action selection criterion to ameliorate the inaccurate evaluation in the initial exploration.It is proved that when the number of vertices in the feasible region is C_(n)^(m),our method can generate all the shortest pivot paths,which is the polynomial of the number of variables.In addition,we experimentally validate that the proposed schedule can avoid unnecessary search and provide the optimal pivot path.Furthermore,this method can provide the best pivot labels for all kinds of supervised learning methods to solve linear programming problems.
