Multi-evaluation Binary Classifier #15
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since classifications are binary many of the individual nodes actually don't affect training classification and we can remove those resulting in a much smaller easier to analyze tree
mjohnson541
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hwpang
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May 7, 2024
| if node.depth <= depth: | ||
| n = pydot.Node(name=name, label=name, fontname="Helvetica", fontsize="16") | ||
| if images: | ||
| img = node.group.draw("png") |
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| img = node.group.draw("png") | |
| img = node.group.draw("pdf") |
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Better quality of figures when writing paper and making slides. The figures don't have fuzzy edges when you enlarge them. Additionally, overleaf compiles faster if you include all your figures as pdf.
| @@ -1,27 +1,31 @@ | |||
| from IPython.display import Image, display | |||
| import pydot | |||
| import os | |||
| import numpy as np | |||
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| import numpy as np | |
| import numpy as np | |
| from pathlib import Path |
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| graph.set_fontsize("10") | ||
| if not os.path.exists("./tree"): | ||
| os.makedirs("./tree") |
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Can we change all the use of os to pathlib? pathlib is the more modern way since Python 3.4
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| graph.set_fontsize("10") | |
| if not os.path.exists("./tree"): | |
| os.makedirs("./tree") | |
| graph.set_fontsize("10") | |
| save_dir = Path("./tree") | |
| save_dir.mkdir(exist_ok=True) |
pysidt/plotting.py
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| with open("./tree/" + node.name + ".png", "wb") as f: | ||
| f.write(img) | ||
| n.set_image(os.path.abspath("./tree/" + node.name + ".png")) |
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| with open("./tree/" + node.name + ".png", "wb") as f: | |
| f.write(img) | |
| n.set_image(os.path.abspath("./tree/" + node.name + ".png")) | |
| node_save_path = (save_dir / node.name + ".pdf").resolve() | |
| with open(node_save_path, "wb") as f: | |
| f.write(img) | |
| n.set_image(node_save_path)) |
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| graph.write_dot("./tree/tree.dot") | ||
| graph.write_png("./tree/tree.png") |
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| graph.write_dot("./tree/tree.dot") | |
| graph.write_png("./tree/tree.png") | |
| graph.write_dot(save_dir / "tree.dot") | |
| graph.write_png(save_dir / "tree.png") |
| sidt_val_values = [self.evaluate(d.mol) for d in self.validation_set] | ||
| true_val_values = [d.value for d in self.validation_set] | ||
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| P,N,PP,PN,TP,FN,FP,TN = analyze_binary_classification(sidt_train_values,true_train_values) |
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I'm pretty sure there are metrics functions to compute accuracy, recall, precision, etc. we can just import from sklearn to make the code cleaner. Can you do that?
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| P,N,PP,PN,TP,FN,FP,TN = analyze_binary_classification(sidt_train_values,true_train_values) | |
| P, N, PP, PN, TP, FN, FP, TN = analyze_binary_classification(sidt_train_values, true_train_values) |
| } | ||
| self.best_rule_map = {name:self.nodes[name].rule for name in self.best_tree_nodes} | ||
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| logging.info("# nodes: {}".format(len(self.nodes))) |
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| logging.info("# nodes: {}".format(len(self.nodes))) | |
| logging.info(f"# nodes: {len(self.nodes)}") |
| 2) merges nodes with their parents if they do not result in different predictions | ||
| """ | ||
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| self.datum_truth_map = {datum:[getattr(n,"rule") for n in self.mol_node_maps[datum]["nodes"]] for datum in self.datums} |
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| self.datum_truth_map = {datum:[getattr(n,"rule") for n in self.mol_node_maps[datum]["nodes"]] for datum in self.datums} | |
| self.datum_truth_map = {datum: [getattr(n,"rule") for n in self.mol_node_maps[datum]["nodes"]] for datum in self.datums} |
| """ | ||
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| self.datum_truth_map = {datum:[getattr(n,"rule") for n in self.mol_node_maps[datum]["nodes"]] for datum in self.datums} | ||
| self.datum_node_map = {datum:[n for n in self.mol_node_maps[datum]["nodes"]] for datum in self.datums} |
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| self.datum_node_map = {datum:[n for n in self.mol_node_maps[datum]["nodes"]] for datum in self.datums} | |
| self.datum_node_map = {datum: [n for n in self.mol_node_maps[datum]["nodes"]] for datum in self.datums} |
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| assert len(new) == 0 | ||
| assert len(comp) == 0 | ||
| pnew = new_class_true/Nnew |
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| pnew = new_class_true/Nnew | |
| pnew = new_class_true / Nnew |
hwpang
requested changes
May 7, 2024
| "source": [ | ||
| "data = []\n", | ||
| "for sm in stable_smiles:\n", | ||
| " data.append(Datum(Molecule().from_smiles(sm),True))\n", |
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| " data.append(Datum(Molecule().from_smiles(sm),True))\n", | |
| " data.append(Datum(Molecule().from_smiles(sm), True))\n", |
Can you run black formatter through the notebook too
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Can you also add a pytest for this new type of tree? I don't think it's best practice to only rely on notebook test. The |
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Replaced |
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This adds an SIDT algorithm for Multi-Evaluation binary classification.
It also adds some smaller improvements:
Allows plotting only to specified depth
Saves rules as well as nodes in postpruning
allows specification of an initial set of splits from the root node
An example notebook for unstable Q.OOH classification is provided.