├── README.md └── src ├── A1_training_of_PEDLA_for_H1.m ├── A2_prediction_of_PEDLA_for_H1.m ├── A2o_transform_prediction_of_H1_into_Bed.pl ├── B1_training_of_PEDLA_for_multiple_cells_and_tissues.m ├── B2_performance_evaluation_of_on_training_or_test_set.m ├── B2o1_merge_performance_of_training_or_test_set.m ├── B2o2_performance_of_learnt_model_for_one_cell.m ├── B3_prediction_of_PEDLA_for_multiple_cells_and_tissues.m ├── B3o_transform_prediction_into_Bed.pl ├── Matlab_code_for_PEDLA ├── EM_init_kmeans.m ├── dbnsetup.m ├── dbntrain.m ├── emgm.m ├── gaussian_prob.m ├── isposdef.m ├── lf_HMMSupervisedLearning.m ├── lf_HMMSupervisedLearning_FromExistedModel - 鍓湰.m ├── lf_HMMSupervisedLearning_FromExistedModel.m ├── lf_HMMViterbi.m ├── logdet.m ├── logsumexp.m ├── minFunc │ ├── ArmijoBacktrack.m │ ├── WolfeLineSearch.m │ ├── autoGrad.m │ ├── autoHess.m │ ├── autoHv.m │ ├── autoTensor.m │ ├── callOutput.m │ ├── conjGrad.m │ ├── dampedUpdate.m │ ├── example_minFunc.m │ ├── example_minFunc_LR.m │ ├── isLegal.m │ ├── lbfgs.m │ ├── lbfgsC.c │ ├── lbfgsC.mexa64 │ ├── lbfgsC.mexglx │ ├── lbfgsC.mexmac │ ├── lbfgsC.mexmaci │ ├── lbfgsC.mexmaci64 │ ├── lbfgsC.mexw32 │ ├── lbfgsC.mexw64 │ ├── lbfgsUpdate.m │ ├── logistic │ │ ├── LogisticDiagPrecond.m │ │ ├── LogisticHv.m │ │ ├── LogisticLoss.m │ │ ├── mexutil.c │ │ ├── mexutil.h │ │ ├── mylogsumexp.m │ │ ├── repmatC.c │ │ ├── repmatC.dll │ │ ├── repmatC.mexglx │ │ └── repmatC.mexmac │ ├── mchol.m │ ├── mcholC.c │ ├── mcholC.mexmaci64 │ ├── mcholC.mexw32 │ ├── mcholC.mexw64 │ ├── mcholinc.m │ ├── minFunc.m │ ├── minFunc_processInputOptions.m │ ├── polyinterp.m │ ├── precondDiag.m │ ├── precondTriu.m │ ├── precondTriuDiag.m │ ├── rosenbrock.m │ └── taylorModel.m ├── mixgauss_prob.m ├── params2stack.m ├── rbmtrain.m ├── rbmup.m ├── sigm.m ├── sigmrnd.m ├── softmaxCost.m ├── softmaxtrain.m ├── softmaxtup.m ├── sqdist.m ├── stack2params.m ├── supervisedfinetuning.m ├── supervisedlearnig.m ├── supervisedstackedAECost.m ├── supervisedstackedAEPredict.m ├── unsupervisedfinetuning.asv ├── unsupervisedfinetuning.m ├── unsupervisedlearnig.asv ├── unsupervisedlearnig.m ├── unsupervisedstackedAECost.asv ├── unsupervisedstackedAECost.m ├── unsupervisedstackedAEPredict.asv └── unsupervisedstackedAEPredict.m ├── O10_combine_data.pl ├── O10_combine_data_of_H1.pl ├── O1a_tag_count_for_histone_modification.pl ├── O1b_RPKM_calculation_for_histone_modification.pl ├── O1c_merge_RPKM_of_replicates_for_histone_modification.pl ├── O2a_tag_count_for_phastCons46way.pl ├── O2b_RPKM_calculation_for_phastCons46way.pl ├── P1_extract_training_feature_and_label_for_PEDLA.pl ├── P1_extract_training_feature_and_label_for_PEDLA_of_H1.pl ├── P2_load_training_feature_and_label_for_PEDLA.m ├── P2_load_training_feature_and_label_for_PEDLA_of_H1.m ├── P2o_calculate_quantile_of_twentytwo_training_cells.m ├── P3_extract_unlabelled_data_for_PEDLA.pl ├── P3_extract_unlabelled_data_for_PEDLA_of_H1.pl ├── 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