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"""Splice Dataset""" |
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from typing import List |
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from functools import partial |
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import datasets |
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import pandas |
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VERSION = datasets.Version("1.0.0") |
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_ENCODING_DICS = {} |
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DESCRIPTION = "Splice dataset." |
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_HOMEPAGE = "https://archive-beta.ics.uci.edu/dataset/69/molecular+biology+splice+junction+gene+sequences" |
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_URLS = ("https://archive-beta.ics.uci.edu/dataset/69/molecular+biology+splice+junction+gene+sequences") |
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_CITATION = """ |
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@misc{misc_molecular_biology_(splice-junction_gene_sequences)_69, |
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title = {{Molecular Biology (Splice-junction Gene Sequences)}}, |
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year = {1992}, |
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howpublished = {UCI Machine Learning Repository}, |
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note = {{DOI}: \\url{10.24432/C5M888}} |
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} |
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""" |
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urls_per_split = { |
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"train": "https://huggingface.co/datasets/mstz/splice/raw/main/splice.data" |
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} |
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features_types_per_config = { |
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"splice": { |
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"position_0": datasets.Value("string"), |
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"position_1": datasets.Value("string"), |
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"position_2": datasets.Value("string"), |
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"position_3": datasets.Value("string"), |
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"position_4": datasets.Value("string"), |
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"position_5": datasets.Value("string"), |
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"position_6": datasets.Value("string"), |
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"position_7": datasets.Value("string"), |
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"position_8": datasets.Value("string"), |
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"position_9": datasets.Value("string"), |
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"position_10": datasets.Value("string"), |
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"position_11": datasets.Value("string"), |
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"position_12": datasets.Value("string"), |
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"position_13": datasets.Value("string"), |
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"position_14": datasets.Value("string"), |
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"position_15": datasets.Value("string"), |
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"position_16": datasets.Value("string"), |
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"position_17": datasets.Value("string"), |
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"position_18": datasets.Value("string"), |
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"position_19": datasets.Value("string"), |
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"position_20": datasets.Value("string"), |
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"position_21": datasets.Value("string"), |
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"position_22": datasets.Value("string"), |
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"position_23": datasets.Value("string"), |
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"position_24": datasets.Value("string"), |
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"position_25": datasets.Value("string"), |
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"position_26": datasets.Value("string"), |
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"position_27": datasets.Value("string"), |
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"position_28": datasets.Value("string"), |
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"position_29": datasets.Value("string"), |
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"position_30": datasets.Value("string"), |
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"position_31": datasets.Value("string"), |
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"position_32": datasets.Value("string"), |
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"position_33": datasets.Value("string"), |
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"position_34": datasets.Value("string"), |
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"position_35": datasets.Value("string"), |
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"position_36": datasets.Value("string"), |
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"position_37": datasets.Value("string"), |
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"position_38": datasets.Value("string"), |
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"position_39": datasets.Value("string"), |
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"position_40": datasets.Value("string"), |
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"position_41": datasets.Value("string"), |
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"position_42": datasets.Value("string"), |
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"position_43": datasets.Value("string"), |
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"position_44": datasets.Value("string"), |
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"position_45": datasets.Value("string"), |
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"position_46": datasets.Value("string"), |
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"position_47": datasets.Value("string"), |
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"position_48": datasets.Value("string"), |
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"position_49": datasets.Value("string"), |
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"position_50": datasets.Value("string"), |
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"position_51": datasets.Value("string"), |
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"position_52": datasets.Value("string"), |
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"position_53": datasets.Value("string"), |
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"position_54": datasets.Value("string"), |
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"position_55": datasets.Value("string"), |
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"position_56": datasets.Value("string"), |
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"position_57": datasets.Value("string"), |
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"position_58": datasets.Value("string"), |
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"position_59": datasets.Value("string"), |
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"class": datasets.ClassLabel(num_classes=3, names=("EI", "IE", "N")) |
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}, |
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"splice_EI": { |
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"position_0": datasets.Value("string"), |
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"position_1": datasets.Value("string"), |
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"position_2": datasets.Value("string"), |
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"position_3": datasets.Value("string"), |
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"position_4": datasets.Value("string"), |
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"position_5": datasets.Value("string"), |
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"position_6": datasets.Value("string"), |
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"position_7": datasets.Value("string"), |
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"position_8": datasets.Value("string"), |
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"position_9": datasets.Value("string"), |
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"position_10": datasets.Value("string"), |
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"position_11": datasets.Value("string"), |
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"position_12": datasets.Value("string"), |
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"position_13": datasets.Value("string"), |
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"position_14": datasets.Value("string"), |
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"position_15": datasets.Value("string"), |
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"position_16": datasets.Value("string"), |
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"position_17": datasets.Value("string"), |
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"position_18": datasets.Value("string"), |
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"position_19": datasets.Value("string"), |
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"position_20": datasets.Value("string"), |
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"position_21": datasets.Value("string"), |
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"position_22": datasets.Value("string"), |
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"position_23": datasets.Value("string"), |
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"position_24": datasets.Value("string"), |
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"position_25": datasets.Value("string"), |
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"position_26": datasets.Value("string"), |
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"position_27": datasets.Value("string"), |
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"position_28": datasets.Value("string"), |
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"position_29": datasets.Value("string"), |
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"position_30": datasets.Value("string"), |
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"position_31": datasets.Value("string"), |
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"position_32": datasets.Value("string"), |
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"position_33": datasets.Value("string"), |
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"position_34": datasets.Value("string"), |
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"position_35": datasets.Value("string"), |
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"position_36": datasets.Value("string"), |
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"position_37": datasets.Value("string"), |
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"position_38": datasets.Value("string"), |
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"position_39": datasets.Value("string"), |
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"position_40": datasets.Value("string"), |
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"position_41": datasets.Value("string"), |
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"position_42": datasets.Value("string"), |
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"position_43": datasets.Value("string"), |
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"position_44": datasets.Value("string"), |
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"position_45": datasets.Value("string"), |
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"position_46": datasets.Value("string"), |
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"position_47": datasets.Value("string"), |
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"position_48": datasets.Value("string"), |
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"position_49": datasets.Value("string"), |
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"position_50": datasets.Value("string"), |
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"position_51": datasets.Value("string"), |
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"position_52": datasets.Value("string"), |
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"position_53": datasets.Value("string"), |
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"position_54": datasets.Value("string"), |
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"position_55": datasets.Value("string"), |
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"position_56": datasets.Value("string"), |
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"position_57": datasets.Value("string"), |
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"position_58": datasets.Value("string"), |
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"position_59": datasets.Value("string"), |
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"is_ei": datasets.ClassLabel(num_classes=2, names=("no", "yes")) |
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}, |
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"splice_IE": { |
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"position_0": datasets.Value("string"), |
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"position_1": datasets.Value("string"), |
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"position_2": datasets.Value("string"), |
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"position_3": datasets.Value("string"), |
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"position_4": datasets.Value("string"), |
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"position_5": datasets.Value("string"), |
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"position_6": datasets.Value("string"), |
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"position_7": datasets.Value("string"), |
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"position_8": datasets.Value("string"), |
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"position_9": datasets.Value("string"), |
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"position_10": datasets.Value("string"), |
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"position_11": datasets.Value("string"), |
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"position_12": datasets.Value("string"), |
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"position_13": datasets.Value("string"), |
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"position_14": datasets.Value("string"), |
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"position_15": datasets.Value("string"), |
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"position_16": datasets.Value("string"), |
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"position_17": datasets.Value("string"), |
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"position_18": datasets.Value("string"), |
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"position_19": datasets.Value("string"), |
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"position_20": datasets.Value("string"), |
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"position_21": datasets.Value("string"), |
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"position_22": datasets.Value("string"), |
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"position_23": datasets.Value("string"), |
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"position_24": datasets.Value("string"), |
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"position_25": datasets.Value("string"), |
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"position_26": datasets.Value("string"), |
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"position_27": datasets.Value("string"), |
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"position_28": datasets.Value("string"), |
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"position_29": datasets.Value("string"), |
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"position_30": datasets.Value("string"), |
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"position_31": datasets.Value("string"), |
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"position_32": datasets.Value("string"), |
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"position_33": datasets.Value("string"), |
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"position_34": datasets.Value("string"), |
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"position_35": datasets.Value("string"), |
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"position_36": datasets.Value("string"), |
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"position_37": datasets.Value("string"), |
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"position_38": datasets.Value("string"), |
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"position_39": datasets.Value("string"), |
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"position_40": datasets.Value("string"), |
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"position_41": datasets.Value("string"), |
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"position_42": datasets.Value("string"), |
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"position_43": datasets.Value("string"), |
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"position_44": datasets.Value("string"), |
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"position_45": datasets.Value("string"), |
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"position_46": datasets.Value("string"), |
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"position_47": datasets.Value("string"), |
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"position_48": datasets.Value("string"), |
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"position_49": datasets.Value("string"), |
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"position_50": datasets.Value("string"), |
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"position_51": datasets.Value("string"), |
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"position_52": datasets.Value("string"), |
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"position_53": datasets.Value("string"), |
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"position_54": datasets.Value("string"), |
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"position_55": datasets.Value("string"), |
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"position_56": datasets.Value("string"), |
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"position_57": datasets.Value("string"), |
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"position_58": datasets.Value("string"), |
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"position_59": datasets.Value("string"), |
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"is_ie": datasets.ClassLabel(num_classes=2, names=("no", "yes")) |
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}, |
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"splice_N": { |
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"position_0": datasets.Value("string"), |
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"position_1": datasets.Value("string"), |
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"position_2": datasets.Value("string"), |
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"position_3": datasets.Value("string"), |
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"position_4": datasets.Value("string"), |
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"position_5": datasets.Value("string"), |
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"position_6": datasets.Value("string"), |
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"position_7": datasets.Value("string"), |
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"position_8": datasets.Value("string"), |
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"position_9": datasets.Value("string"), |
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"position_10": datasets.Value("string"), |
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"position_11": datasets.Value("string"), |
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"position_12": datasets.Value("string"), |
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"position_13": datasets.Value("string"), |
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"position_14": datasets.Value("string"), |
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"position_15": datasets.Value("string"), |
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"position_16": datasets.Value("string"), |
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"position_17": datasets.Value("string"), |
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"position_18": datasets.Value("string"), |
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"position_19": datasets.Value("string"), |
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"position_20": datasets.Value("string"), |
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"position_21": datasets.Value("string"), |
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"position_22": datasets.Value("string"), |
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"position_23": datasets.Value("string"), |
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"position_24": datasets.Value("string"), |
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"position_25": datasets.Value("string"), |
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"position_26": datasets.Value("string"), |
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"position_27": datasets.Value("string"), |
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"position_28": datasets.Value("string"), |
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"position_29": datasets.Value("string"), |
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"position_30": datasets.Value("string"), |
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"position_31": datasets.Value("string"), |
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"position_32": datasets.Value("string"), |
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"position_33": datasets.Value("string"), |
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"position_34": datasets.Value("string"), |
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"position_35": datasets.Value("string"), |
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"position_36": datasets.Value("string"), |
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"position_37": datasets.Value("string"), |
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"position_38": datasets.Value("string"), |
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"position_39": datasets.Value("string"), |
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"position_40": datasets.Value("string"), |
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"position_41": datasets.Value("string"), |
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"position_42": datasets.Value("string"), |
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"position_43": datasets.Value("string"), |
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"position_44": datasets.Value("string"), |
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"position_45": datasets.Value("string"), |
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"position_46": datasets.Value("string"), |
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"position_47": datasets.Value("string"), |
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"position_48": datasets.Value("string"), |
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"position_49": datasets.Value("string"), |
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"position_50": datasets.Value("string"), |
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"position_51": datasets.Value("string"), |
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"position_52": datasets.Value("string"), |
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"position_53": datasets.Value("string"), |
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"position_54": datasets.Value("string"), |
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"position_55": datasets.Value("string"), |
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"position_56": datasets.Value("string"), |
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"position_57": datasets.Value("string"), |
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"position_58": datasets.Value("string"), |
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"position_59": datasets.Value("string"), |
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"is_n": datasets.ClassLabel(num_classes=2, names=("no", "yes")) |
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} |
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} |
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features_per_config = {k: datasets.Features(features_types_per_config[k]) for k in features_types_per_config} |
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class SpliceConfig(datasets.BuilderConfig): |
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def __init__(self, **kwargs): |
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super(SpliceConfig, self).__init__(version=VERSION, **kwargs) |
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self.features = features_per_config[kwargs["name"]] |
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class Splice(datasets.GeneratorBasedBuilder): |
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DEFAULT_CONFIG = "splice1" |
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BUILDER_CONFIGS = [ |
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SpliceConfig(name="splice", |
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description="Splice for multiclass classification."), |
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SpliceConfig(name="splice_IE", |
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description="Splice for binary classification."), |
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SpliceConfig(name="splice_EI", |
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description="Splice for binary classification."), |
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SpliceConfig(name="splice_N", |
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description="Splice for binary classification."), |
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] |
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def _info(self): |
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info = datasets.DatasetInfo(description=DESCRIPTION, citation=_CITATION, homepage=_HOMEPAGE, |
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features=features_per_config[self.config.name]) |
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return info |
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def _split_generators(self, dl_manager: datasets.DownloadManager) -> List[datasets.SplitGenerator]: |
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downloads = dl_manager.download_and_extract(urls_per_split) |
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return [ |
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datasets.SplitGenerator(name=datasets.Split.TRAIN, gen_kwargs={"filepath": downloads["train"]}), |
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] |
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def _generate_examples(self, filepath: str): |
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data = pandas.read_csv(filepath) |
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data = self.preprocess(data) |
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for row_id, row in data.iterrows(): |
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data_row = dict(row) |
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yield row_id, data_row |
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def preprocess(self, data: pandas.DataFrame) -> pandas.DataFrame: |
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if self.config.name == "splice_IE": |
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data["class"] = data["class"].apply(lambda x: 1 if x == "IE" else 0) |
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data = data.rename(columns={"class": "is_ie"}) |
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elif self.config.name == "splice_EI": |
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data["class"] = data["class"].apply(lambda x: 1 if x == "EI" else 0) |
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data = data.rename(columns={"class": "is_ei"}) |
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elif self.config.name == "splice_N": |
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data["class"] = data["class"].apply(lambda x: 1 if x == "N" else 0) |
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data = data.rename(columns={"class": "is_n"}) |
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else: |
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data["class"] = data["class"].apply(lambda x: { |
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"EI": 0, |
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"IE": 1, |
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"N": 2, |
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}[x]) |
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for feature in _ENCODING_DICS: |
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encoding_function = partial(self.encode, feature) |
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data.loc[:, feature] = data[feature].apply(encoding_function) |
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return data[list(features_types_per_config[self.config.name].keys())] |
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def encode(self, feature, value): |
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if feature in _ENCODING_DICS: |
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return _ENCODING_DICS[feature][value] |
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raise ValueError(f"Unknown feature: {feature}") |
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