omnigenome 0.3.0a1__py3-none-any.whl → 0.3.3a0__py3-none-any.whl

omnigenome/src/dataset/omni_dataset.py

@@ -1,435 +0,0 @@
-# -*- coding: utf-8 -*-
-# file: abstract_dataset.py
-# time: 14:13 06/04/2024
-# 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.
-"""
-Specialized dataset classes for OmniGenome framework.
-
-This module provides specialized dataset classes for various genomic tasks,
-inheriting from the abstract `OmniDataset`. These classes handle data preparation
-for token classification, sequence classification, token regression, and sequence regression,
-integrating with tokenizers and managing metadata.
-"""
-import json
-
-import numpy as np
-import torch
-
-from ..abc.abstract_dataset import OmniDataset
-from ..misc.utils import fprint
-from ... import __name__, __version__
-
-
-class OmniDatasetForTokenClassification(OmniDataset):
-    """
-    Dataset class specifically designed for token classification tasks in genomics.
-    
-    This class extends `OmniDataset` to provide functionalities for preparing input sequences
-    and their corresponding token-level labels. It's designed for tasks where each token
-    in a sequence needs to be classified independently.
-    
-    Attributes:
-        metadata: Dictionary containing dataset metadata including library information
-        label2id: Mapping from label strings to integer IDs
-    """
-
-    def __init__(self, data_source, tokenizer, max_length=None, **kwargs):
-        """
-        Initialize the dataset for token classification.
-
-        Args:
-            data_source: Path to the data file or a list of paths.
-                        Supported formats depend on the `OmniDataset` implementation.
-            tokenizer: The tokenizer instance to use for converting sequences into
-                      tokenized inputs.
-            max_length: The maximum sequence length for tokenization. Sequences longer
-                       than this will be truncated. If None, a default or tokenizer's
-                       max length will be used.
-            **kwargs: Additional keyword arguments to be stored in the dataset's metadata.
-        """
-        super(OmniDatasetForTokenClassification, self).__init__(
-            data_source, tokenizer, max_length, **kwargs
-        )
-        self.metadata.update(
-            {
-                "library_name": __name__,
-                "omnigenome_version": __version__,
-                "task": "genome_token_classification",
-            }
-        )
-
-        for key, value in kwargs.items():
-            self.metadata[key] = value
-
-    def prepare_input(self, instance, **kwargs):
-        """
-        Prepare a single data instance for token classification.
-        
-        This method handles both string sequences and dictionary instances
-        containing sequence and label information. It tokenizes the input
-        sequence and prepares token-level labels for classification.
-
-        Args:
-            instance: A single data instance. Can be a string representing the sequence
-                     or a dictionary with 'seq'/'sequence' and 'labels'/'label' keys.
-            **kwargs: Additional keyword arguments for tokenization, such as 'padding'
-                     and 'truncation'.
-
-        Returns:
-            dict: A dictionary of tokenized inputs, including 'input_ids', 'attention_mask',
-                  and 'labels' (tensor of token-level labels).
-
-        Raises:
-            Exception: If the input instance format is unknown or if a dictionary
-                      instance does not contain a 'seq' or 'sequence' key.
-        """
-        labels = -100
-        if isinstance(instance, str):
-            sequence = instance
-        elif isinstance(instance, dict):
-            sequence = (
-                instance.get("seq", None)
-                if "seq" in instance
-                else instance.get("sequence", None)
-            )
-            label = instance.get("label", None)
-            labels = instance.get("labels", None)
-            labels = labels if labels is not None else label
-            if not sequence:
-                raise Exception(
-                    "The input instance must contain a 'seq' or 'sequence' key."
-                )
-        else:
-            raise Exception("Unknown instance format.")
-
-        tokenized_inputs = self.tokenizer(
-            sequence,
-            padding=kwargs.get("padding", "do_not_pad"),
-            truncation=kwargs.get("truncation", True),
-            max_length=self.max_length,
-            return_tensors="pt",
-        )
-        for col in tokenized_inputs:
-            tokenized_inputs[col] = tokenized_inputs[col].squeeze()
-
-        if labels is not None:
-            if len(set(self.label2id.keys()) | set([str(l) for l in labels])) != len(
-                set(self.label2id.keys())
-            ):
-                fprint(
-                    f"Warning: The labels <{labels}> in the input instance do not match the label2id mapping."
-                )
-            labels = (
-                [-100]
-                + [self.label2id.get(str(l), -100) for l in labels][
-                    : self.max_length - 2
-                ]
-                + [-100]
-            )
-
-        tokenized_inputs["labels"] = torch.tensor(labels)
-        return tokenized_inputs
-
-
-class OmniDatasetForSequenceClassification(OmniDataset):
-    """
-    Dataset class for sequence classification tasks in genomics.
-    
-    This class extends `OmniDataset` to prepare input sequences and their corresponding
-    sequence-level labels. It's designed for tasks where the entire sequence needs
-    to be classified into one of several categories.
-    
-    Attributes:
-        metadata: Dictionary containing dataset metadata including library information
-        label2id: Mapping from label strings to integer IDs
-    """
-
-    def __init__(self, data_source, tokenizer, max_length=None, **kwargs):
-        """
-        Initialize the dataset for sequence classification.
-
-        Args:
-            data_source: Path to the data file or a list of paths.
-                        Supported formats depend on the `OmniDataset` implementation.
-            tokenizer: The tokenizer instance to use for converting sequences into
-                      tokenized inputs.
-            max_length: The maximum sequence length for tokenization. Sequences longer
-                       than this will be truncated. If None, a default or tokenizer's
-                       max length will be used.
-            **kwargs: Additional keyword arguments to be stored in the dataset's metadata.
-        """
-        super(OmniDatasetForSequenceClassification, self).__init__(
-            data_source, tokenizer, max_length, **kwargs
-        )
-
-        self.metadata.update(
-            {
-                "library_name": __name__,
-                "omnigenome_version": __version__,
-                "task": "genome_sequence_classification",
-            }
-        )
-        for key, value in kwargs.items():
-            self.metadata[key] = value
-
-    def prepare_input(self, instance, **kwargs):
-        """
-        Prepare a single data instance for sequence classification.
-        
-        This method handles both string sequences and dictionary instances
-        containing sequence and label information. It tokenizes the input
-        sequence and prepares sequence-level labels for classification.
-
-        Args:
-            instance: A single data instance. Can be a string representing the sequence
-                     or a dictionary with 'seq'/'sequence' and 'labels'/'label' keys.
-            **kwargs: Additional keyword arguments for tokenization, such as 'padding'
-                     and 'truncation'.
-
-        Returns:
-            dict: A dictionary of tokenized inputs, including 'input_ids', 'attention_mask',
-                  and 'labels' (tensor of sequence-level labels).
-
-        Raises:
-            Exception: If the input instance format is unknown or if a dictionary
-                      instance does not contain a 'label' or 'labels' key, or if
-                      the label is not an integer.
-        """
-        labels = -100
-        if isinstance(instance, str):
-            sequence = instance
-        elif isinstance(instance, dict):
-            sequence = (
-                instance.get("seq", None)
-                if "seq" in instance
-                else instance.get("sequence", None)
-            )
-            label = instance.get("label", None)
-            labels = instance.get("labels", None)
-            labels = labels if labels is not None else label
-        else:
-            raise Exception("Unknown instance format.")
-
-        tokenized_inputs = self.tokenizer(
-            sequence,
-            padding=kwargs.get("padding", "do_not_pad"),
-            truncation=kwargs.get("truncation", True),
-            max_length=self.max_length,
-            return_tensors="pt",
-        )
-        for col in tokenized_inputs:
-            tokenized_inputs[col] = tokenized_inputs[col].squeeze()
-
-        if labels is not None:
-            if not isinstance(labels, int):
-                raise Exception(
-                    "The label must be an integer for sequence classification."
-                )
-            labels = self.label2id.get(str(labels), -100)
-
-        tokenized_inputs["labels"] = torch.tensor(labels)
-        return tokenized_inputs
-
-
-class OmniDatasetForTokenRegression(OmniDataset):
-    """
-    Dataset class for token regression tasks in genomics.
-    
-    This class extends `OmniDataset` to prepare input sequences and their corresponding
-    token-level regression targets. It's designed for tasks where each token in a
-    sequence needs to be assigned a continuous value.
-    
-    Attributes:
-        metadata: Dictionary containing dataset metadata including library information
-    """
-
-    def __init__(self, data_source, tokenizer, max_length=None, **kwargs):
-        """
-        Initialize the dataset for token regression.
-
-        Args:
-            data_source: Path to the data file or a list of paths.
-                        Supported formats depend on the `OmniDataset` implementation.
-            tokenizer: The tokenizer instance to use for converting sequences into
-                      tokenized inputs.
-            max_length: The maximum sequence length for tokenization. Sequences longer
-                       than this will be truncated. If None, a default or tokenizer's
-                       max length will be used.
-            **kwargs: Additional keyword arguments to be stored in the dataset's metadata.
-        """
-        super(OmniDatasetForTokenRegression, self).__init__(
-            data_source, tokenizer, max_length, **kwargs
-        )
-
-        self.metadata.update(
-            {
-                "library_name": __name__,
-                "omnigenome_version": __version__,
-                "task": "genome_token_regression",
-            }
-        )
-        for key, value in kwargs.items():
-            self.metadata[key] = value
-
-    def prepare_input(self, instance, **kwargs):
-        """
-        Prepare a single data instance for token regression.
-        
-        This method handles both string sequences and dictionary instances
-        containing sequence and regression target information. It tokenizes
-        the input sequence and prepares token-level regression targets.
-
-        Args:
-            instance: A single data instance. Can be a string representing the sequence
-                     or a dictionary with 'seq'/'sequence' and 'labels'/'label' keys.
-            **kwargs: Additional keyword arguments for tokenization, such as 'padding'
-                     and 'truncation'.
-
-        Returns:
-            dict: A dictionary of tokenized inputs, including 'input_ids', 'attention_mask',
-                  and 'labels' (tensor of token-level regression targets).
-
-        Raises:
-            Exception: If the input instance format is unknown or if a dictionary
-                      instance does not contain a 'seq' or 'sequence' key.
-        """
-        labels = -100
-        if isinstance(instance, str):
-            sequence = instance
-        elif isinstance(instance, dict):
-            sequence = (
-                instance.get("seq", None)
-                if "seq" in instance
-                else instance.get("sequence", None)
-            )
-            label = instance.get("label", None)
-            labels = instance.get("labels", None)
-            labels = labels if labels is not None else label
-            if not sequence:
-                raise Exception(
-                    "The input instance must contain a 'seq' or 'sequence' key."
-                )
-        else:
-            raise Exception("Unknown instance format.")
-
-        tokenized_inputs = self.tokenizer(
-            sequence,
-            padding=kwargs.get("padding", "do_not_pad"),
-            truncation=kwargs.get("truncation", True),
-            max_length=self.max_length,
-            return_tensors="pt",
-        )
-        for col in tokenized_inputs:
-            tokenized_inputs[col] = tokenized_inputs[col].squeeze()
-
-        if labels is not None:
-            # Handle token-level regression labels
-            if isinstance(labels, (list, tuple)):
-                # Ensure labels match sequence length
-                labels = list(labels)[:self.max_length - 2]  # Account for special tokens
-                labels = [-100] + labels + [-100]  # Add padding for special tokens
-            else:
-                # Single value for the entire sequence
-                labels = [-100] + [float(labels)] * (self.max_length - 2) + [-100]
-
-        tokenized_inputs["labels"] = torch.tensor(labels, dtype=torch.float32)
-        return tokenized_inputs
-
-
-class OmniDatasetForSequenceRegression(OmniDataset):
-    """
-    Dataset class for sequence regression tasks in genomics.
-    
-    This class extends `OmniDataset` to prepare input sequences and their corresponding
-    sequence-level regression targets. It's designed for tasks where the entire
-    sequence needs to be assigned a continuous value.
-    
-    Attributes:
-        metadata: Dictionary containing dataset metadata including library information
-    """
-
-    def __init__(self, data_source, tokenizer, max_length=None, **kwargs):
-        """
-        Initialize the dataset for sequence regression.
-
-        Args:
-            data_source: Path to the data file or a list of paths.
-                        Supported formats depend on the `OmniDataset` implementation.
-            tokenizer: The tokenizer instance to use for converting sequences into
-                      tokenized inputs.
-            max_length: The maximum sequence length for tokenization. Sequences longer
-                       than this will be truncated. If None, a default or tokenizer's
-                       max length will be used.
-            **kwargs: Additional keyword arguments to be stored in the dataset's metadata.
-        """
-        super(OmniDatasetForSequenceRegression, self).__init__(
-            data_source, tokenizer, max_length, **kwargs
-        )
-
-        self.metadata.update(
-            {
-                "library_name": __name__,
-                "omnigenome_version": __version__,
-                "task": "genome_sequence_regression",
-            }
-        )
-        for key, value in kwargs.items():
-            self.metadata[key] = value
-
-    def prepare_input(self, instance, **kwargs):
-        """
-        Prepare a single data instance for sequence regression.
-        
-        This method handles both string sequences and dictionary instances
-        containing sequence and regression target information. It tokenizes
-        the input sequence and prepares sequence-level regression targets.
-
-        Args:
-            instance: A single data instance. Can be a string representing the sequence
-                     or a dictionary with 'seq'/'sequence' and 'labels'/'label' keys.
-            **kwargs: Additional keyword arguments for tokenization, such as 'padding'
-                     and 'truncation'.
-
-        Returns:
-            dict: A dictionary of tokenized inputs, including 'input_ids', 'attention_mask',
-                  and 'labels' (tensor of sequence-level regression targets).
-
-        Raises:
-            Exception: If the input instance format is unknown or if a dictionary
-                      instance does not contain a 'label' or 'labels' key.
-        """
-        labels = -100
-        if isinstance(instance, str):
-            sequence = instance
-        elif isinstance(instance, dict):
-            sequence = (
-                instance.get("seq", None)
-                if "seq" in instance
-                else instance.get("sequence", None)
-            )
-            label = instance.get("label", None)
-            labels = instance.get("labels", None)
-            labels = labels if labels is not None else label
-        else:
-            raise Exception("Unknown instance format.")
-
-        tokenized_inputs = self.tokenizer(
-            sequence,
-            padding=kwargs.get("padding", "do_not_pad"),
-            truncation=kwargs.get("truncation", True),
-            max_length=self.max_length,
-            return_tensors="pt",
-        )
-        for col in tokenized_inputs:
-            tokenized_inputs[col] = tokenized_inputs[col].squeeze()
-
-        if labels is not None:
-            # Convert to float for regression
-            labels = float(labels)
-
-        tokenized_inputs["labels"] = torch.tensor(labels, dtype=torch.float32)
-        return tokenized_inputs

omnigenome/src/lora/__init__.py

@@ -1,13 +0,0 @@
-# -*- coding: utf-8 -*-
-# file: __init__.py
-# time: 12:35 11/06/2025
-# author: YANG, HENG <hy345@exeter.ac.uk> (杨恒)
-# homepage: 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.
-"""
-This package contains modules for LoRA (Low-Rank Adaptation) fine-tuning.
-"""
-