diff --git a/_modules/mltb2/files.html b/_modules/mltb2/files.html index 553f92a..4eb7909 100644 --- a/_modules/mltb2/files.html +++ b/_modules/mltb2/files.html @@ -201,6 +201,10 @@
if not self._result_dir_path.is_dir():
raise ValueError(f"Faild to create or find result_dir '{self.result_dir}'!")
+
+
@staticmethod
def _get_uuid_from_filename(filename: str) -> Optional[str]:
uuid = None
diff --git a/api-reference/files.html b/api-reference/files.html
index 65a5351..97250aa 100644
--- a/api-reference/files.html
+++ b/api-reference/files.html
@@ -57,6 +57,7 @@
fasttext
files
FileBasedRestartableBatchDataProcessor
+
+
arangodb
", "bs
", "data
", "db
", "fasttext
", "files
", "md
", "openai
", "optuna
", "plot
", "somajo
", "somajo_transformers
", "text
", "transformers
", "MLTB2 Documentation"], "terms": {"arangodb": [0, 15], "b": [0, 5, 13, 15], "data": [0, 1, 4, 6, 9, 14, 15], "db": [0, 9, 15], "fasttext": [0, 15], "file": [0, 1, 3, 5, 8, 15], "md": [0, 15], "openai": [0, 15], "optuna": [0, 15], "plot": [0, 15], "somajo": [0, 12, 15], "somajo_transform": [0, 15], "text": [0, 2, 5, 7, 8, 11, 12, 14, 15], "transform": [0, 12, 15], "util": [1, 4, 6, 14], "modul": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15], "us": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15], "pip": [1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15], "instal": [1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 14], "necessari": [1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15], "depend": [1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15], "thi": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14], "mltb2": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14], "class": [1, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14], "arangobatchdatamanag": 1, "host": [1, 14], "str": [1, 2, 3, 5, 6, 7, 8, 10, 11, 12, 13, 14], "sequenc": [1, 4, 6], "db_name": 1, "usernam": 1, "password": 1, "collection_nam": 1, "attribute_nam": 1, "batch_siz": [1, 6], "int": [1, 5, 6, 7, 8, 9, 10, 12, 13, 14], "20": [1, 9], "aql_overwrit": 1, "none": [1, 2, 3, 4, 5, 6, 8, 10, 11, 13, 14], "sourc": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14], "base": [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14], "abstractbatchdatamanag": [1, 4], "arangoconnectionmanag": 1, "implement": [1, 2, 4, 9, 13], "paramet": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14], "databas": [1, 4], "name": [1, 2, 6, 8], "document": 1, "from": [1, 2, 3, 4, 5, 6, 8, 9, 11, 13], "collect": 1, "ar": [1, 2, 3, 5, 6, 7, 8, 9, 13, 14, 15], "process": [1, 4, 6, 7, 8, 11, 12, 13, 14], "attribut": [1, 2], "i": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15], "check": [1, 9, 13], "alreadi": [1, 7], "If": [1, 2, 3, 5, 6, 8, 10, 11, 12, 13, 14], "present": 1, "avail": [1, 15], "consid": 1, "The": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14], "batch": [1, 4, 6], "size": [1, 6], "aql": 1, "string": [1, 2, 11], "overwrit": 1, "default": [1, 2, 3, 6, 10], "classmethod": [1, 8], "from_config_fil": 1, "config_file_nam": 1, "construct": [1, 8], "config": 1, "must": [1, 9, 13, 15], "contain": [1, 3, 5, 8, 13, 14], "valu": [1, 8, 9, 10, 13], "exampl": [1, 8, 9, 11, 13], "http": [1, 3, 11], "com": [1, 11], "my_ml_databas": 1, "my_usernam": 1, "secret": 1, "my_ml_data_collect": 1, "processing_metadata": 1, "100": [1, 9, 13], "path": [1, 5, 6, 14], "load_batch": [1, 4], "load": [1, 3, 4, 6, 8], "return": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14], "type": [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14], "save_batch": [1, 4, 6], "save": [1, 4, 6, 10], "object": [1, 2, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14], "connect": 1, "manag": [1, 4], "creat": [1, 6, 8, 10], "_arango_client_factori": 1, "arangocli": 1, "an": [1, 4, 5, 8, 9, 11, 12, 14], "client": 1, "_connection_factori": 1, "arango_cli": 1, "standarddatabas": 1, "arangoimportdatamanag": 1, "import": [1, 9, 11], "tool": [1, 2, 3, 5, 8, 9, 10, 11, 12, 13, 14, 15], "fill": 1, "least": [1, 13], "import_datafram": 1, "datafram": [1, 3], "create_collect": 1, "bool": [1, 7, 8, 9, 10, 11, 12, 13, 14], "fals": [1, 7, 8, 10, 11, 12, 13, 14], "panda": [1, 3], "true": [1, 2, 9, 10, 12, 13], "doe": [1, 7, 9, 10, 12], "exist": [1, 6], "rais": [1, 2, 6, 12, 13], "arango": 1, "except": [1, 12], "documentinserterror": 1, "fail": 1, "import_dict": 1, "dict": [1, 2, 5, 6, 8], "ani": [1, 2, 6, 8], "_check_config_kei": 1, "expected_config_kei": 1, "all": [1, 2, 6, 11], "expect": 1, "kei": [1, 8], "arango_collection_backup": 1, "commandlin": 1, "do": [1, 11, 13, 14], "backup": 1, "written": 1, "gzip": 1, "compress": 1, "jsonl": 1, "current": 1, "work": [1, 9], "directori": [1, 3, 6, 14], "run": [1, 4, 8], "col": 1, "h": 1, "get": [1, 5, 8, 11], "command": 1, "line": [1, 2], "help": 1, "beauti": 2, "soup": 2, "html": [2, 3, 13], "specif": [2, 7, 8, 11, 12, 13, 14, 15], "extract_al": 2, "beautifulsoup": 2, "attr": 2, "kwarg": 2, "extract": [2, 11], "specifi": [2, 7, 12], "element": [2, 5], "tag": [2, 13], "addit": 2, "keyword": [2, 8], "argument": [2, 8], "extract_on": 2, "exactli": 2, "one": [2, 4, 10, 11, 13], "function": [2, 4, 6, 8, 9, 10, 13], "expact": 2, "onli": [2, 7, 8, 9, 13], "result": [2, 6, 8, 9], "found": 2, "otherwis": [2, 13], "runtimeerror": 2, "extract_text": 2, "join_str": 2, "ha": [2, 8, 10], "known": 2, "issu": 2, "whitespac": [2, 13], "handl": 2, "join": 2, "part": 2, "per": [2, 7, 9, 12], "space": 2, "html_to_md": 2, "mdformat_opt": 2, "convert": [2, 3, 8, 11], "markdown": [2, 7], "mdformat": 2, "option": [2, 15], "number": [2, 5, 7, 8, 9, 10, 11, 12, 13, 14], "appli": 2, "consecut": 2, "order": 2, "list": [2, 5, 6, 7, 8, 11, 12, 14], "wrap": 2, "paragraph": [2, 7], "word": [2, 11, 12], "mode": 2, "end": [2, 7], "lf": 2, "remove_al": 2, "remov": [2, 6, 7, 13], "done": [2, 4, 9], "place": [2, 11], "noth": 2, "": [2, 9, 10], "soup_to_md": 2, "offer": [3, 5, 9, 11, 12, 13, 14], "follow": [3, 13], "tabular": 3, "set": [3, 5, 8, 9, 11, 14], "biolog": 3, "medic": 3, "domain": 3, "support": [3, 6, 13], "colon": 3, "genom": 3, "pub": 3, "princeton": 3, "edu": 3, "oncologi": 3, "affydata": 3, "index": [3, 15], "prostat": 3, "web": 3, "stanford": 3, "hasti": 3, "casi_fil": 3, "leukemia_big": 3, "leukemia": 3, "after": [3, 6, 13], "internet": 3, "pars": 3, "cach": 3, "determin": [3, 6], "get_and_create_mltb2_data_dir": [3, 6], "_load_colon_data": 3, "label": [3, 10, 14], "also": [3, 8], "see": [3, 8, 9, 15], "_load_colon_label": 3, "seri": 3, "load_colon": 3, "mltb2_base_data_dir": [3, 6], "tupl": [3, 11], "user": [3, 6, 9], "platformdir": [3, 6], "user_data_dir": [3, 6], "load_leukemia_big": 3, "big": 3, "load_prost": 3, "abc": [4, 11], "abstract": [4, 11], "respect": 4, "intend": 4, "conjunct": 4, "batchdataprocessor": 4, "data_manag": 4, "process_batch_callback": 4, "callabl": 4, "A": [4, 5, 8, 9, 15], "callback": 4, "until": [4, 9], "empti": 4, "For": [4, 9, 10, 13, 15], "each": 4, "call": [4, 8, 9, 10, 13], "fasttextlanguageidentif": 5, "identifi": 5, "languag": [5, 11], "__call__": [5, 7, 8, 11, 12, 14], "num_lang": 5, "10": [5, 9], "always_detect_lang": 5, "given": [5, 6, 8, 9, 13], "which": [5, 6, 8, 9, 11, 13, 14], "recogn": 5, "probabl": 5, "should": [5, 9, 11], "alwai": [5, 8, 12], "even": 5, "detect": [5, 13], "0": [5, 9, 10, 13], "more": [5, 9, 10, 13], "than": [5, 12, 13], "so": 5, "guarante": 5, "you": [5, 8, 9, 15], "want": [5, 8, 15], "includ": 5, "case": 5, "when": [5, 8, 15], "veri": 5, "low": 5, "possibl": 5, "af": 5, "al": 5, "am": 5, "arz": 5, "ast": 5, "av": 5, "az": 5, "azb": 5, "ba": 5, "bar": 5, "bcl": 5, "bg": 5, "bh": 5, "bn": 5, "bo": 5, "bpy": 5, "br": 5, "bxr": 5, "ca": 5, "cbk": 5, "ce": 5, "ceb": 5, "ckb": 5, "co": [5, 14], "c": 5, "cv": [5, 9], "cy": 5, "da": [5, 11], "de": [5, 11], "diq": 5, "dsb": 5, "dty": 5, "dv": 5, "el": 5, "eml": 5, "en": 5, "eo": 5, "e": 5, "et": 5, "eu": 5, "fa": 5, "fi": 5, "fr": 5, "frr": 5, 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"uz": 5, "vec": 5, "vep": 5, "vi": 5, "vl": 5, "vo": 5, "wa": [5, 8, 13, 14], "war": 5, "wuu": 5, "xal": 5, "xmf": 5, "yi": 5, "yo": 5, "yue": 5, "zh": 5, "static": [5, 6], "get_model_path_and_download": 5, "model": [5, 8, 9, 14], "download": 5, "need": 5, "full": [5, 6, 8], "provid": [6, 9], "other": [6, 13], "filebasedrestartablebatchdataprocessor": 6, "uuid_nam": 6, "result_dir": 6, "processor": 6, "restart": 6, "back": 6, "uuid": 6, "field": 6, "where": [6, 11], "store": 6, "load_data": 6, "method": [6, 9, 13], "can": [6, 7, 8, 10, 13, 15], "As": [6, 9], "execut": 6, "sever": 6, "time": [6, 10, 13], "parallel": 6, "record": 6, "duplic": [6, 13], "These": [6, 13], "here": [6, 9], "read_batch": 6, "read": 6, "next": 6, "fetch_remote_fil": 6, "dirnam": 6, "filenam": [6, 10], "url": [6, 11], "sha256_checksum": 6, "fetch": 6, "remot": 6, "under": 6, "sha256": 6, "checksum": 6, "ioerror": 6, "wrong": 6, "dir": 6, "exact": 6, "folder": 6, "append": [6, 9], "mdtextsplitt": 7, "max_token": [7, 8, 12], "transformers_token_count": [7, 12], "transformerstokencount": [7, 12, 14], "show_progress_bar": [7, 8, 11, 12, 13, 14], "split": [7, 9, 11, 12, 14], "section": [7, 12], "maximum": [7, 12, 13], "token": [7, 8, 11, 12, 14], "divid": [7, 12], "head": 7, "correspond": 7, "exceed": 7, "singl": [7, 10, 13], "chunk": 7, "larger": [7, 9], "counter": [7, 12, 13], "show": [7, 8, 11, 12, 13, 14], "progressbar": [7, 8, 11, 12, 13, 14], "dure": [7, 8, 11, 12, 13, 14], "md_text": 7, "_chunk_md_by_headlin": 7, "headlin": 7, "chunk_md": 7, "merg": 7, "isol": 7, "subsequ": 7, "without": [7, 8], "content": [7, 8], "openaiazurechat": 8, "api_kei": 8, "api_vers": 8, "azure_endpoint": 8, "openaichat": 8, "interact": 8, "azur": 8, "chat": 8, "from_yaml": 8, "api": [8, 15], "refer": [8, 15], "complet": 8, "quickstart": 8, "start": 8, "gener": [8, 14], "servic": 8, "version": 8, "common": 8, "2023": 8, "05": 8, "15": 8, "endpoint": 8, "create_complet": 8, "prompt": 8, "completion_kwarg": 8, 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"significancerepeatedtrainingprun": 9, "alpha": 9, "float": [9, 11, 13], "1": [9, 14], "n_warmup_step": 9, "baseprun": 9, "pruner": 9, "statist": 9, "signific": 9, "heurist": 9, "decis": 9, "make": [9, 10], "It": [9, 11, 13, 15], "prune": 9, "repeat": 9, "train": [9, 14], "like": 9, "cross": [9, 14], "valid": [9, 14], "test": [9, 14], "t": 9, "our": 9, "experi": 9, "shown": 9, "aplha": 9, "between": [9, 13], "standard": 9, "assum": 9, "adjust": 9, "onc": [9, 13], "hyperparamet": 9, "those": [9, 15], "basi": 9, "intermedi": 9, "epoch": 9, "In": 9, "contrast": 9, "precis": 9, "individu": [9, 15], "fold": [9, 14], "below": 9, "minimalist": 9, "log": 9, "numpi": 9, "np": 9, "sklearn": 9, "dataset": [9, 14], "load_iri": 9, "model_select": 9, "stratifiedkfold": 9, "ensembl": 9, "randomforestclassifi": 9, "metric": 9, "accuracy_scor": 9, "configur": 9, "logger": 9, "debug": 9, "output": [9, 11], "getlogg": 9, "addhandl": 9, "streamhandl": 9, "setlevel": 9, "x": [9, 10, 13], "y": [9, 10, 13], "target": 9, "def": 9, "trial": 9, "min_samples_split": 9, "suggest_int": 9, "2": 9, "n_estim": 9, "validation_result_list": 9, "skf": 9, "n_split": [9, 14], "fold_index": 9, "train_index": 9, "val_index": 9, "enumer": 9, "x_train": 9, "x_val": 9, "y_train": 9, "y_val": 9, "rf": 9, "fit": [9, 13], "y_pred": 9, "predict": 9, "acc": 9, "report": 9, "we": [9, 13], "should_prun": 9, "break": 9, "studi": 9, "create_studi": 9, "storag": 9, "sqlite": 9, "memori": 9, "study_nam": 9, "iris_cv": 9, "direct": 9, "maxim": 9, "load_if_exist": 9, "sampler": 9, "tpesampl": 9, "multivari": 9, "add": 9, "optim": 9, "n_trial": 9, "level": 9, "aggress": 9, "smaller": 9, "stronger": 9, "differ": [9, 10, 13], "two": [9, 10, 11, 13], "distribut": 9, "disabl": 9, "reach": 9, "exce": 9, "step": [9, 10], "frozentri": 9, "judg": 9, "whether": 9, "note": 9, "suppos": 9, "librari": 9, "instead": 9, "interfac": 9, "mechan": 9, "take": 9, "copi": 9, "befor": [9, 13], "modifi": 9, "boolean": 9, "repres": 9, "matplotlib": 10, "boxplot": 10, "titl": 10, "xlabel": 10, "ylabel": 10, "vert": 10, "print": [10, 11], "diagram": 10, "pyplot": 10, "axi": 10, "box": [10, 15], "vertic": 10, "horizont": 10, "boxplot_dict": 10, "values_dict": 10, "form": [10, 13], "dictionari": 10, "save_last_figur": 10, "last": 10, "made": 10, "jupyt": 10, "notebook": 10, "same": 10, "cell": 10, "twin_axes_timeseries_plot": 10, "values_1": 10, "label_1": 10, "values_2": 10, "label_2": 10, "start_timestep_numb": 10, "shift_1": 10, "shift_2": 10, "label_x": 10, "color_1": 10, "tab": 10, "red": 10, "color_2": 10, "blue": 10, "twin": 10, "ax": 10, "timeseri": 10, "curv": 10, "array_lik": 10, "first": [10, 13], "second": 10, "point": 10, "timestep": 10, "shift": 10, "posit": 10, "neg": 10, "color": 10, "jaccardsimilar": 11, "liter": 11, "de_cmc": 11, "en_ptb": 11, "somajobaseclass": 11, "calcul": [11, 13], "jaccard": 11, "similar": 11, "german": 11, "english": 11, "text1": 11, "text2": 11, "get_token_set": 11, "directli": 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\ No newline at end of file