omnigenome 0.3.0a1__py3-none-any.whl → 1.0.0b0__py3-none-any.whl

omnigenome/utility/dataset_hub/dataset_hub.py

@@ -1,178 +0,0 @@
-# -*- coding: utf-8 -*-
-# File: dataset_hub.py
-# Time: 02:22 20/06/2025
-# Author: YANG, HENG <hy345@exeter.ac.uk> (杨恒)
-# Website: https://yangheng95.github.io
-# GitHub: https://github.com/yangheng95
-# HuggingFace: https://huggingface.co/yangheng
-# Google Scholar: https://scholar.google.com/citations?user=NPq5a_0AAAAJ&hl=en
-# Copyright (C) 2019-2025. All rights reserved.
-"""
-Dataset Hub Module
-
-This module provides utilities for loading benchmark datasets from the OmniGenome hub.
-It handles automatic downloading, configuration loading, and dataset initialization
-for various genomic benchmarks.
-"""
-
-import os
-import warnings
-
-import findfile
-from typing_extensions import Union
-
-from ... import OmniTokenizer, download_benchmark
-from ...src.misc.utils import load_module_from_path, fprint
-
-
-def load_benchmark_datasets(
-    benchmark: str,
-    tokenizer: Union["OmniTokenizer", str] = None,
-    **kwargs: dict,
-):
-    """
-    Load benchmark datasets from the OmniGenome hub.
-    
-    This function automatically downloads benchmark datasets if they don't exist locally,
-    loads their configurations, and initializes train/validation/test datasets with
-    the specified tokenizer.
-    
-    Args:
-        benchmark (str): Name or path of the benchmark to load. If the benchmark
-            doesn't exist locally, it will be downloaded from the hub.
-        tokenizer (Union[OmniTokenizer, str], optional): Tokenizer to use for
-            dataset preprocessing. Can be an OmniTokenizer instance or a string
-            identifier for a pre-trained tokenizer. If None, the tokenizer will
-            be loaded from the benchmark configuration.
-        **kwargs: Additional keyword arguments to override benchmark configuration.
-            These will be passed to the dataset classes and tokenizer initialization.
-    
-    Returns:
-        dict: Dictionary containing datasets for each benchmark task, with keys
-            being benchmark names and values being dictionaries with 'train',
-            'valid', and 'test' datasets.
-    
-    Raises:
-        FileNotFoundError: If the benchmark cannot be found or downloaded.
-        ValueError: If the benchmark configuration is invalid.
-        ImportError: If required dependencies are not available.
-    
-    Example:
-        >>> from omnigenome import OmniSingleNucleotideTokenizer
-        >>> tokenizer = OmniSingleNucleotideTokenizer.from_pretrained("model_name")
-        >>> datasets = load_benchmark_datasets("RGB", tokenizer, max_length=512)
-        >>> print(f"Loaded {len(datasets)} benchmark tasks")
-        >>> for task_name, task_datasets in datasets.items():
-        ...     print(f"{task_name}: {len(task_datasets['train'])} train samples")
-    
-    Note:
-        - The function automatically handles U/T conversion and other preprocessing
-          based on the benchmark configuration.
-        - If a tokenizer string is provided, it will be loaded with the benchmark's
-          trust_remote_code setting.
-        - The function supports multiple seeds for robust evaluation.
-        - Long sequences can be dropped or truncated based on configuration.
-    """
-    if not os.path.exists(benchmark):
-        fprint(
-            "Benchmark:",
-            benchmark,
-            "does not exist. Search online for available benchmarks.",
-        )
-        benchmark = download_benchmark(benchmark)
-        
-    # Import benchmark list
-    bench_metadata = load_module_from_path(
-        f"bench_metadata", f"{benchmark}/metadata.py"
-    )
-    datasets = {}
-    for _, bench in enumerate(bench_metadata.bench_list):
-
-        bench_config_path = findfile.find_file(
-            benchmark, f"{benchmark}.{bench}.config".split(".")
-        )
-        config = load_module_from_path("config", bench_config_path)
-        bench_config = config.bench_config
-        fprint(f"Loaded config for {bench} from {bench_config_path}")
-        fprint(bench_config)
-        _kwargs = kwargs.copy()
-
-        # Init Tokenizer and Model
-        if isinstance(tokenizer, str):
-            tokenizer = OmniTokenizer.from_pretrained(
-                tokenizer,
-                trust_remote_code=bench_config.get("trust_remote_code", True),
-                **bench_config,
-            )
-
-        for key, value in _kwargs.items():
-            if key in bench_config:
-                fprint(
-                    "Override", key, "with", value, "according to the input kwargs"
-                )
-                bench_config.update({key: value})
-
-            else:
-                warnings.warn(
-                    f"kwarg: {key} not found in bench_config while setting {key} = {value}"
-                )
-                bench_config.update({key: value})
-
-        for key, value in bench_config.items():
-            if key in bench_config and key in _kwargs:
-                _kwargs.pop(key)
-
-        if not isinstance(bench_config["seeds"], list):
-            bench_config["seeds"] = [bench_config["seeds"]]
-
-        # Init Trainer
-        dataset_cls = bench_config["dataset_cls"]
-
-        max_length = bench_config["max_length"]
-
-        train_set = dataset_cls(
-            data_source=bench_config["train_file"],
-            tokenizer=tokenizer,
-            label2id=bench_config["label2id"],
-            max_length=max_length,
-            structure_in=bench_config.get("structure_in", False),
-            max_examples=bench_config.get("max_examples", None),
-            shuffle=bench_config.get("shuffle", True),
-            drop_long_seq=bench_config.get("drop_long_seq", False),
-            **_kwargs,
-        )
-        test_set = dataset_cls(
-            data_source=bench_config["test_file"],
-            tokenizer=tokenizer,
-            label2id=bench_config["label2id"],
-            max_length=max_length,
-            structure_in=bench_config.get("structure_in", False),
-            max_examples=bench_config.get("max_examples", None),
-            shuffle=False,
-            drop_long_seq=bench_config.get("drop_long_seq", False),
-            **_kwargs,
-        )
-        valid_set = dataset_cls(
-            data_source=bench_config["valid_file"],
-            tokenizer=tokenizer,
-            label2id=bench_config["label2id"],
-            max_length=max_length,
-            structure_in=bench_config.get("structure_in", False),
-            max_examples=bench_config.get("max_examples", None),
-            shuffle=False,
-            drop_long_seq=bench_config.get("drop_long_seq", False),
-            **_kwargs,
-        )
-
-        dataset = {
-            "train": train_set,
-            "test": test_set,
-            "valid": valid_set,
-        }
-
-        fprint(f"Loaded dataset for {bench} with {len(train_set)} train samples, "
-              f"{len(test_set)} test samples and {len(valid_set)} valid samples.")
-
-        datasets[bench] = dataset
-
-    return datasets

omnigenome/utility/ensemble.py

@@ -1,324 +0,0 @@
-# -*- coding: utf-8 -*-
-# file: ensemble.py
-# time: 21:39 24/04/2024
-# author: YANG, HENG <hy345@exeter.ac.uk> (杨恒)
-# github: https://github.com/yangheng95
-# huggingface: https://huggingface.co/yangheng
-# google scholar: https://scholar.google.com/citations?user=NPq5a_0AAAAJ&hl=en
-# Copyright (C) 2019-2024. All Rights Reserved.
-from typing import List
-
-import numpy as np
-
-
-class VoteEnsemblePredictor:
-    """
-    An ensemble predictor that combines predictions from multiple models using voting.
-    
-    This class implements ensemble methods for combining predictions from multiple
-    models or checkpoints. It supports both weighted and unweighted voting, and
-    provides various aggregation methods for different data types (numeric and string).
-    
-    Attributes:
-        checkpoints: List of checkpoint names
-        predictors: Dictionary of initialized predictors
-        weights: List of weights for each predictor
-        numeric_agg_func: Function for aggregating numeric predictions
-        str_agg: Function for aggregating string predictions
-        numeric_agg_methods: Dictionary of available numeric aggregation methods
-        str_agg_methods: Dictionary of available string aggregation methods
-        
-    Example:
-        >>> from omnigenome.utility import VoteEnsemblePredictor
-        >>> predictors = {
-        ...     "model1": predictor1,
-        ...     "model2": predictor2,
-        ...     "model3": predictor3
-        ... }
-        >>> weights = {"model1": 1.0, "model2": 0.8, "model3": 0.6}
-        >>> ensemble = VoteEnsemblePredictor(predictors, weights, numeric_agg="average")
-        >>> result = ensemble.predict("ACGUAGGUAUCGUAGA")
-        >>> print(result)
-        {'prediction': 0.85}
-    """
-
-    def __init__(
-        self,
-        predictors: [List, dict],
-        weights: [List, dict] = None,
-        numeric_agg="average",
-        str_agg="max_vote",
-    ):
-        """
-        Initialize the VoteEnsemblePredictor.
-        
-        Args:
-            predictors (List or dict): A list of checkpoints, or a dictionary of initialized predictors
-            weights (List or dict, optional): A list of weights for each predictor, or a dictionary of weights for each predictor
-            numeric_agg (str, optional): The aggregation method for numeric data. Options are 'average', 'mean', 'max', 'min',
-                                        'median', 'mode', and 'sum'. Defaults to 'average'
-            str_agg (str, optional): The aggregation method for string data. Options are 'max_vote', 'min_vote', 'vote', and 'mode'. Defaults to 'max_vote'
-                                        
-        Raises:
-            AssertionError: If predictors and weights have different lengths or types
-            AssertionError: If predictors list is empty
-            AssertionError: If unsupported aggregation methods are provided
-        """
-        if weights is not None:
-            assert len(predictors) == len(
-                weights
-            ), "Checkpoints and weights should have the same length"
-            assert type(predictors) == type(
-                weights
-            ), "Checkpoints and weights should have the same type"
-
-        assert len(predictors) > 0, "Checkpoints should not be empty"
-
-        self.numeric_agg_methods = {
-            "average": np.mean,
-            "mean": np.mean,
-            "max": np.max,
-            "min": np.min,
-            "median": np.median,
-            "mode": lambda x: max(set(x), key=x.count),
-            "sum": np.sum,
-        }
-        self.str_agg_methods = {
-            "max_vote": lambda x: max(set(x), key=x.count),
-            "min_vote": lambda x: min(set(x), key=x.count),
-            "vote": lambda x: max(set(x), key=x.count),
-            "mode": lambda x: max(set(x), key=x.count),
-        }
-        assert (
-            numeric_agg in self.numeric_agg_methods
-        ), "numeric_agg should be either: " + str(self.numeric_agg_methods.keys())
-        assert (
-            str_agg in self.str_agg_methods
-        ), "str_agg should be either max or vote" + str(self.str_agg_methods.keys())
-
-        self.numeric_agg_func = numeric_agg
-        self.str_agg = self.str_agg_methods[str_agg]
-
-        if isinstance(predictors, dict):
-            self.checkpoints = list(predictors.keys())
-            self.predictors = predictors
-            self.weights = (
-                list(weights.values()) if weights else [1] * len(self.checkpoints)
-            )
-        else:
-            raise NotImplementedError(
-                "Only support dict type for checkpoints and weights"
-            )
-
-    def numeric_agg(self, result: list):
-        """
-        Aggregate a list of numeric values.
-        
-        Args:
-            result (list): A list of numeric values to aggregate
-            
-        Returns:
-            The aggregated value using the specified numeric aggregation method
-            
-        Example:
-            >>> ensemble = VoteEnsemblePredictor(predictors, numeric_agg="average")
-            >>> result = ensemble.numeric_agg([0.8, 0.9, 0.7])
-            >>> print(result)
-            0.8
-        """
-        res = np.stack([np.array(x) for x in result])
-        return self.numeric_agg_methods[self.numeric_agg_func](res, axis=0)
-
-    def __ensemble(self, result: dict):
-        """
-        Aggregate prediction results by calling the appropriate aggregation method.
-        
-        This method determines the type of result and calls the appropriate
-        aggregation method (numeric or string).
-        
-        Args:
-            result (dict): A dictionary containing the prediction results
-            
-        Returns:
-            The aggregated prediction result
-        """
-        if isinstance(result, dict):
-            return self.__dict_aggregate(result)
-        elif isinstance(result, list):
-            return self.__list_aggregate(result)
-        else:
-            return result
-
-    def __dict_aggregate(self, result: dict):
-        """
-        Recursively aggregate a dictionary of prediction results.
-        
-        This method recursively processes nested dictionaries and applies
-        appropriate aggregation methods to each level.
-        
-        Args:
-            result (dict): A dictionary containing the prediction results
-            
-        Returns:
-            dict: The aggregated prediction result
-        """
-        ensemble_result = {}
-        for k, v in result.items():
-            if isinstance(result[k], list):
-                ensemble_result[k] = self.__list_aggregate(result[k])
-            elif isinstance(result[k], dict):
-                ensemble_result[k] = self.__dict_aggregate(result[k])
-            else:
-                ensemble_result[k] = result[k]
-        return ensemble_result
-
-    def __list_aggregate(self, result: list):
-        """
-        Aggregate a list of prediction results.
-        
-        This method handles different types of list elements and applies
-        appropriate aggregation methods based on the data type.
-        
-        Args:
-            result (list): A list of prediction results to aggregate
-            
-        Returns:
-            The aggregated result
-            
-        Raises:
-            AssertionError: If all elements in the list are not of the same type
-        """
-        if not isinstance(result, list):
-            result = [result]
-
-        assert all(
-            isinstance(x, (type(result[0]))) for x in result
-        ), "all type of result should be the same"
-
-        if isinstance(result[0], list):
-            for i, k in enumerate(result):
-                result[i] = self.__list_aggregate(k)
-            # start to aggregate
-            try:
-                new_result = self.numeric_agg(result)
-            except Exception as e:
-                try:
-                    new_result = self.str_agg(result)
-                except Exception as e:
-                    new_result = result
-            return [new_result]
-
-        elif isinstance(result[0], dict):
-            for k in result:
-                result[k] = self.__dict_aggregate(result[k])
-            return result
-
-        # start to aggregate
-        try:
-            new_result = self.numeric_agg(result)
-        except Exception as e:
-            try:
-                new_result = self.str_agg(result)
-            except Exception as e:
-                new_result = result
-
-        return new_result
-
-    def predict(self, text, ignore_error=False, print_result=False):
-        """
-        Predicts on a single text and returns the ensemble result.
-        
-        This method combines predictions from all predictors in the ensemble
-        using the specified weights and aggregation methods.
-        
-        Args:
-            text (str): The text to perform prediction on
-            ignore_error (bool, optional): Whether to ignore any errors that occur during prediction. Defaults to False
-            print_result (bool, optional): Whether to print the prediction result. Defaults to False
-            
-        Returns:
-            dict: The ensemble prediction result
-            
-        Example:
-            >>> result = ensemble.predict("ACGUAGGUAUCGUAGA", ignore_error=True)
-            >>> print(result)
-            {'prediction': 0.85, 'confidence': 0.92}
-        """
-        # Initialize an empty dictionary to store the prediction result
-        result = {}
-        # Loop through each checkpoint and predictor in the ensemble
-        for ckpt, predictor in self.predictors.items():
-            # Perform prediction on the text using the predictor
-            raw_result = predictor.inference(
-                text, ignore_error=ignore_error, print_result=print_result
-            )
-            # For each key-value pair in the raw result dictionary
-            for key, value in raw_result.items():
-                # If the key is not already in the result dictionary
-                if key not in result:
-                    # Initialize an empty list for the key
-                    result[key] = []
-                # Append the value to the list the number of times specified by the corresponding weight
-                for _ in range(self.weights[self.checkpoints.index(ckpt)]):
-                    result[key].append(value)
-        # Return the ensemble result by aggregating the values in the result dictionary
-        return self.__ensemble(result)
-
-    def batch_predict(self, texts, ignore_error=False, print_result=False):
-        """
-        Predicts on a batch of texts using the ensemble of predictors.
-        
-        This method processes multiple texts efficiently by combining predictions
-        from all predictors in the ensemble for each text in the batch.
-        
-        Args:
-            texts (list): A list of strings to predict on
-            ignore_error (bool, optional): Boolean indicating whether to ignore errors or raise exceptions when prediction fails. Defaults to False
-            print_result (bool, optional): Boolean indicating whether to print the raw results for each predictor. Defaults to False
-            
-        Returns:
-            list: A list of dictionaries, each dictionary containing the aggregated results of the corresponding text in the input list
-            
-        Example:
-            >>> texts = ["ACGUAGGUAUCGUAGA", "GGCTAGCTA", "TATCGCTA"]
-            >>> results = ensemble.batch_predict(texts, ignore_error=True)
-            >>> print(len(results))
-            3
-        """
-        batch_raw_results = []
-        for ckpt, predictor in self.predictors.items():
-            if hasattr(predictor, "inference"):
-                raw_results = predictor.inference(
-                    texts,
-                    ignore_error=ignore_error,
-                    print_result=print_result,
-                    merge_results=False,
-                )
-            else:
-                raw_results = predictor.inference(
-                    texts, ignore_error=ignore_error, print_result=print_result
-                )
-            batch_raw_results.append(raw_results)
-
-        batch_results = []
-        for raw_result in batch_raw_results:
-            for i, result in enumerate(raw_result):
-                if i >= len(batch_results):
-                    batch_results.append({})
-                for key, value in result.items():
-                    if key not in batch_results[i]:
-                        batch_results[i][key] = []
-                    for _ in range(self.weights[self.checkpoints.index(ckpt)]):
-                        batch_results[i][key].append(value)
-
-        ensemble_results = []
-        for result in batch_results:
-            ensemble_results.append(self.__ensemble(result))
-        return ensemble_results
-
-    # def batch_predict(self, texts, ignore_error=False, print_result=False):
-    #     batch_results = []
-    #     for text in tqdm.tqdm(texts, desc='Batch predict: '):
-    #         result = self.predict(text, ignore_error=ignore_error, print_result=print_result)
-    #         batch_results.append(result)
-    #     return batch_results