geneformer/classifier.py

"""
Geneformer classifier.

**Input data:**

| Cell state classifier:
| Single-cell transcriptomes as Geneformer rank value encodings with cell state labels in Geneformer .dataset format (generated from single-cell RNAseq data by tokenizer.py)

| Gene classifier:
| Dictionary in format {Gene_label: list(genes)} for gene labels and single-cell transcriptomes as Geneformer rank value encodings in Geneformer .dataset format (generated from single-cell RNAseq data by tokenizer.py)

**Usage:**

.. code-block :: python

    >>> from geneformer import Classifier
    >>> cc = Classifier(classifier="cell",  # example of cell state classifier
    ...                 cell_state_dict={"state_key": "disease", "states": "all"},
    ...                 filter_data={"cell_type":["Cardiomyocyte1","Cardiomyocyte2","Cardiomyocyte3"]},
    ...                 training_args=training_args,
    ...                 freeze_layers = 2,
    ...                 num_crossval_splits = 1,
    ...                 forward_batch_size=200,
    ...                 nproc=16)
    >>> cc.prepare_data(input_data_file="path/to/input_data",
    ...                 output_directory="path/to/output_directory",
    ...                 output_prefix="output_prefix")
    >>> all_metrics = cc.validate(model_directory="path/to/model",
    ...                           prepared_input_data_file=f"path/to/output_directory/{output_prefix}_labeled.dataset",
    ...                           id_class_dict_file=f"path/to/output_directory/{output_prefix}_id_class_dict.pkl",
    ...                           output_directory="path/to/output_directory",
    ...                           output_prefix="output_prefix",
    ...                           predict_eval=True)
    >>> cc.plot_conf_mat(conf_mat_dict={"Geneformer": all_metrics["conf_matrix"]},
    ...                  output_directory="path/to/output_directory",
    ...                  output_prefix="output_prefix",
    ...                  custom_class_order=["healthy","disease1","disease2"])
    >>> cc.plot_predictions(predictions_file=f"path/to/output_directory/datestamp_geneformer_cellClassifier_{output_prefix}/ksplit1/predictions.pkl",
    ...                     id_class_dict_file=f"path/to/output_directory/{output_prefix}_id_class_dict.pkl",
    ...                     title="disease",
    ...                     output_directory="path/to/output_directory",
    ...                     output_prefix="output_prefix",
    ...                     custom_class_order=["healthy","disease1","disease2"])
"""

import datetime
import logging
import os
import pickle
import subprocess
from pathlib import Path

import numpy as np
import pandas as pd
import seaborn as sns
from tqdm.auto import tqdm, trange
from transformers import Trainer
from transformers.training_args import TrainingArguments

from . import DataCollatorForCellClassification, DataCollatorForGeneClassification
from . import classifier_utils as cu
from . import evaluation_utils as eu
from . import perturber_utils as pu
from . import TOKEN_DICTIONARY_FILE

sns.set()


logger = logging.getLogger(__name__)


class Classifier:
    valid_option_dict = {
        "classifier": {"cell", "gene"},
        "cell_state_dict": {None, dict},
        "gene_class_dict": {None, dict},
        "filter_data": {None, dict},
        "rare_threshold": {int, float},
        "max_ncells": {None, int},
        "max_ncells_per_class": {None, int},
        "training_args": {None, dict},
        "freeze_layers": {int},
        "num_crossval_splits": {0, 1, 5},
        "split_sizes": {None, dict},
        "no_eval": {bool},
        "stratify_splits_col": {None, str},
        "forward_batch_size": {int},
        "token_dictionary_file": {None, str},
        "nproc": {int},
        "ngpu": {int},
    }

    def __init__(
        self,
        classifier=None,
        cell_state_dict=None,
        gene_class_dict=None,
        filter_data=None,
        rare_threshold=0,
        max_ncells=None,
        max_ncells_per_class=None,
        training_args=None,
        ray_config=None,
        freeze_layers=0,
        num_crossval_splits=1,
        split_sizes={"train": 0.8, "valid": 0.1, "test": 0.1},
        stratify_splits_col=None,
        no_eval=False,
        forward_batch_size=100,
        token_dictionary_file=None,
        nproc=4,
        ngpu=1,
    ):
        """
        Initialize Geneformer classifier.

        **Parameters:**

        classifier : {"cell", "gene"}
            | Whether to fine-tune a cell state or gene classifier.
        cell_state_dict : None, dict
            | Cell states to fine-tune model to distinguish.
            | Two-item dictionary with keys: state_key and states
            | state_key: key specifying name of column in .dataset that defines the states to model
            | states: list of values in the state_key column that specifies the states to model
            | Alternatively, instead of a list of states, can specify "all" to use all states in that state key from input data.
            | Of note, if using "all", states will be defined after data is filtered.
            | Must have at least 2 states to model.
            | For example: {"state_key": "disease",
            |               "states": ["nf", "hcm", "dcm"]}
            |               or
            |               {"state_key": "disease",
            |               "states": "all"}
        gene_class_dict : None, dict
            | Gene classes to fine-tune model to distinguish.
            | Dictionary in format: {Gene_label_A: list(geneA1, geneA2, ...),
            |                        Gene_label_B: list(geneB1, geneB2, ...)}
            | Gene values should be Ensembl IDs.
        filter_data : None, dict
            | Default is to fine-tune with all input data.
            | Otherwise, dictionary specifying .dataset column name and list of values to filter by.
        rare_threshold : float
            | Threshold below which rare cell states should be removed.
            | For example, setting to 0.05 will remove cell states representing
            | < 5% of the total cells from the cell state classifier's possible classes.
        max_ncells : None, int
            | Maximum number of cells to use for fine-tuning.
            | Default is to fine-tune with all input data.
        max_ncells_per_class : None, int
            | Maximum number of cells per cell class to use for fine-tuning.
            | Of note, will be applied after max_ncells above.
            | (Only valid for cell classification.)
        training_args : None, dict
            | Training arguments for fine-tuning.
            | If None, defaults will be inferred for 6 layer Geneformer.
            | Otherwise, will use the Hugging Face defaults:
            | https://huggingface.co/docs/transformers/main_classes/trainer#transformers.TrainingArguments
            | Note: Hyperparameter tuning is highly recommended, rather than using defaults.
        ray_config : None, dict
            | Training argument ranges for tuning hyperparameters with Ray.
        freeze_layers : int
            | Number of layers to freeze from fine-tuning.
            | 0: no layers will be frozen; 2: first two layers will be frozen; etc.
        num_crossval_splits : {0, 1, 5}
            | 0: train on all data without splitting
            | 1: split data into train and eval sets by designated split_sizes["valid"]
            | 5: split data into 5 folds of train and eval sets by designated split_sizes["valid"]
        split_sizes : None, dict
            | Dictionary of proportion of data to hold out for train, validation, and test sets
            | {"train": 0.8, "valid": 0.1, "test": 0.1} if intending 80/10/10 train/valid/test split
        stratify_splits_col : None, str
            | Name of column in .dataset to be used for stratified splitting.
            | Proportion of each class in this column will be the same in the splits as in the original dataset.
        no_eval : bool
            | If True, will skip eval step and use all data for training.
            | Otherwise, will perform eval during training.
        forward_batch_size : int
            | Batch size for forward pass (for evaluation, not training).
        token_dictionary_file : None, str
            | Default is to use token dictionary file from Geneformer
            | Otherwise, will load custom gene token dictionary.
        nproc : int
            | Number of CPU processes to use.
        ngpu : int
            | Number of GPUs available.

        """

        self.classifier = classifier
        if self.classifier == "cell":
            self.model_type = "CellClassifier"
        elif self.classifier == "gene":
            self.model_type = "GeneClassifier"
        self.cell_state_dict = cell_state_dict
        self.gene_class_dict = gene_class_dict
        self.filter_data = filter_data
        self.rare_threshold = rare_threshold
        self.max_ncells = max_ncells
        self.max_ncells_per_class = max_ncells_per_class
        self.training_args = training_args
        self.ray_config = ray_config
        self.freeze_layers = freeze_layers
        self.num_crossval_splits = num_crossval_splits
        self.split_sizes = split_sizes
        self.train_size = self.split_sizes["train"]
        self.valid_size = self.split_sizes["valid"]
        self.oos_test_size = self.split_sizes["test"]
        self.eval_size = self.valid_size / (self.train_size + self.valid_size)
        self.stratify_splits_col = stratify_splits_col
        self.no_eval = no_eval
        self.forward_batch_size = forward_batch_size
        self.token_dictionary_file = token_dictionary_file
        self.nproc = nproc
        self.ngpu = ngpu

        if self.training_args is None:
            logger.warning(
                "Hyperparameter tuning is highly recommended for optimal results. "
                "No training_args provided; using default hyperparameters."
            )

        self.validate_options()

        if self.filter_data is None:
            self.filter_data = dict()

        if self.classifier == "cell":
            if self.cell_state_dict["states"] != "all":
                self.filter_data[
                    self.cell_state_dict["state_key"]
                ] = self.cell_state_dict["states"]

        # load token dictionary (Ensembl IDs:token)
        if self.token_dictionary_file is None:
            self.token_dictionary_file = TOKEN_DICTIONARY_FILE
        with open(self.token_dictionary_file, "rb") as f:
            self.gene_token_dict = pickle.load(f)

        self.token_gene_dict = {v: k for k, v in self.gene_token_dict.items()}

        # filter genes for gene classification for those in token dictionary
        if self.classifier == "gene":
            all_gene_class_values = set(pu.flatten_list(self.gene_class_dict.values()))
            missing_genes = [
                gene
                for gene in all_gene_class_values
                if gene not in self.gene_token_dict.keys()
            ]
            if len(missing_genes) == len(all_gene_class_values):
                logger.error(
                    "None of the provided genes to classify are in token dictionary."
                )
                raise
            elif len(missing_genes) > 0:
                logger.warning(
                    f"Genes to classify {missing_genes} are not in token dictionary."
                )
            self.gene_class_dict = {
                k: set([self.gene_token_dict.get(gene) for gene in v])
                for k, v in self.gene_class_dict.items()
            }
            empty_classes = []
            for k, v in self.gene_class_dict.items():
                if len(v) == 0:
                    empty_classes += [k]
            if len(empty_classes) > 0:
                logger.error(
                    f"Class(es) {empty_classes} did not contain any genes in the token dictionary."
                )
                raise

    def validate_options(self):
        # confirm arguments are within valid options and compatible with each other
        for attr_name, valid_options in self.valid_option_dict.items():
            attr_value = self.__dict__[attr_name]
            if not isinstance(attr_value, (list, dict)):
                if attr_value in valid_options:
                    continue
            valid_type = False
            for option in valid_options:
                if (option in [int, float, list, dict, bool, str]) and isinstance(
                    attr_value, option
                ):
                    valid_type = True
                    break
            if valid_type:
                continue
            logger.error(
                f"Invalid option for {attr_name}. "
                f"Valid options for {attr_name}: {valid_options}"
            )
            raise

        if self.filter_data is not None:
            for key, value in self.filter_data.items():
                if not isinstance(value, list):
                    self.filter_data[key] = [value]
                    logger.warning(
                        "Values in filter_data dict must be lists. "
                        f"Changing {key} value to list ([{value}])."
                    )

        if self.classifier == "cell":
            if set(self.cell_state_dict.keys()) != set(["state_key", "states"]):
                logger.error(
                    "Invalid keys for cell_state_dict. "
                    "The cell_state_dict should have only 2 keys: state_key and states"
                )
                raise

            if self.cell_state_dict["states"] != "all":
                if not isinstance(self.cell_state_dict["states"], list):
                    logger.error(
                        "States in cell_state_dict should be list of states to model."
                    )
                    raise
                if len(self.cell_state_dict["states"]) < 2:
                    logger.error(
                        "States in cell_state_dict should contain at least 2 states to classify."
                    )
                    raise

        if self.classifier == "gene":
            if len(self.gene_class_dict.keys()) < 2:
                logger.error(
                    "Gene_class_dict should contain at least 2 gene classes to classify."
                )
                raise
        if sum(self.split_sizes.values()) != 1:
            logger.error("Train, validation, and test proportions should sum to 1.")
            raise

    def prepare_data(
        self,
        input_data_file,
        output_directory,
        output_prefix,
        split_id_dict=None,
        test_size=None,
        attr_to_split=None,
        attr_to_balance=None,
        max_trials=100,
        pval_threshold=0.1,
    ):
        """
        Prepare data for cell state or gene classification.

        **Parameters**

        input_data_file : Path
            | Path to directory containing .dataset input
        output_directory : Path
            | Path to directory where prepared data will be saved
        output_prefix : str
            | Prefix for output file
        split_id_dict : None, dict
            | Dictionary of IDs for train and test splits
            | Three-item dictionary with keys: attr_key, train, test
            | attr_key: key specifying name of column in .dataset that contains the IDs for the data splits
            | train: list of IDs in the attr_key column to include in the train split
            | test: list of IDs in the attr_key column to include in the test split
            | For example: {"attr_key": "individual",
            |               "train": ["patient1", "patient2", "patient3", "patient4"],
            |               "test": ["patient5", "patient6"]}
        test_size : None, float
            | Proportion of data to be saved separately and held out for test set
            | (e.g. 0.2 if intending hold out 20%)
            | If None, will inherit from split_sizes["test"] from Classifier
            | The training set will be further split to train / validation in self.validate
            | Note: only available for CellClassifiers
        attr_to_split : None, str
            | Key for attribute on which to split data while balancing potential confounders
            | e.g. "patient_id" for splitting by patient while balancing other characteristics
            | Note: only available for CellClassifiers
        attr_to_balance : None, list
            | List of attribute keys on which to balance data while splitting on attr_to_split
            | e.g. ["age", "sex"] for balancing these characteristics while splitting by patient
            | Note: only available for CellClassifiers
        max_trials : None, int
            | Maximum number of trials of random splitting to try to achieve balanced other attributes
            | If no split is found without significant (p<0.05) differences in other attributes, will select best
            | Note: only available for CellClassifiers
        pval_threshold : None, float
            | P-value threshold to use for attribute balancing across splits
            | E.g. if set to 0.1, will accept trial if p >= 0.1 for all attributes in attr_to_balance
        """

        if test_size is None:
            test_size = self.oos_test_size

        # prepare data and labels for classification
        data = pu.load_and_filter(self.filter_data, self.nproc, input_data_file)

        if self.classifier == "cell":
            if "label" in data.features:
                logger.error(
                    "Column name 'label' must be reserved for class IDs. Please rename column."
                )
                raise
        elif self.classifier == "gene":
            if "labels" in data.features:
                logger.error(
                    "Column name 'labels' must be reserved for class IDs. Please rename column."
                )
                raise

        if self.classifier == "cell":
            # remove cell states representing < rare_threshold of cells
            data = cu.remove_rare(
                data, self.rare_threshold, self.cell_state_dict["state_key"], self.nproc
            )
            # downsample max cells and max per class
            data = cu.downsample_and_shuffle(
                data, self.max_ncells, self.max_ncells_per_class, self.cell_state_dict
            )
            # rename cell state column to "label"
            data = cu.rename_cols(data, self.cell_state_dict["state_key"])

        # convert classes to numerical labels and save as id_class_dict
        # of note, will label all genes in gene_class_dict
        # if (cross-)validating, genes will be relabeled in column "labels" for each split
        # at the time of training with Classifier.validate
        data, id_class_dict = cu.label_classes(
            self.classifier, data, self.gene_class_dict, self.nproc
        )

        # save id_class_dict for future reference
        id_class_output_path = (
            Path(output_directory) / f"{output_prefix}_id_class_dict"
        ).with_suffix(".pkl")
        with open(id_class_output_path, "wb") as f:
            pickle.dump(id_class_dict, f)

        if split_id_dict is not None:
            data_dict = dict()
            data_dict["train"] = pu.filter_by_dict(
                data, {split_id_dict["attr_key"]: split_id_dict["train"]}, self.nproc
            )
            data_dict["test"] = pu.filter_by_dict(
                data, {split_id_dict["attr_key"]: split_id_dict["test"]}, self.nproc
            )
            train_data_output_path = (
                Path(output_directory) / f"{output_prefix}_labeled_train"
            ).with_suffix(".dataset")
            test_data_output_path = (
                Path(output_directory) / f"{output_prefix}_labeled_test"
            ).with_suffix(".dataset")
            data_dict["train"].save_to_disk(str(train_data_output_path))
            data_dict["test"].save_to_disk(str(test_data_output_path))
        elif (test_size is not None) and (self.classifier == "cell"):
            if 1 > test_size > 0:
                if attr_to_split is None:
                    data_dict = data.train_test_split(
                        test_size=test_size,
                        stratify_by_column=self.stratify_splits_col,
                        seed=42,
                    )
                    train_data_output_path = (
                        Path(output_directory) / f"{output_prefix}_labeled_train"
                    ).with_suffix(".dataset")
                    test_data_output_path = (
                        Path(output_directory) / f"{output_prefix}_labeled_test"
                    ).with_suffix(".dataset")
                    data_dict["train"].save_to_disk(str(train_data_output_path))
                    data_dict["test"].save_to_disk(str(test_data_output_path))
                else:
                    data_dict, balance_df = cu.balance_attr_splits(
                        data,
                        attr_to_split,
                        attr_to_balance,
                        test_size,
                        max_trials,
                        pval_threshold,
                        self.cell_state_dict["state_key"],
                        self.nproc,
                    )
                    balance_df.to_csv(
                        f"{output_directory}/{output_prefix}_train_test_balance_df.csv"
                    )
                    train_data_output_path = (
                        Path(output_directory) / f"{output_prefix}_labeled_train"
                    ).with_suffix(".dataset")
                    test_data_output_path = (
                        Path(output_directory) / f"{output_prefix}_labeled_test"
                    ).with_suffix(".dataset")
                    data_dict["train"].save_to_disk(str(train_data_output_path))
                    data_dict["test"].save_to_disk(str(test_data_output_path))
            else:
                data_output_path = (
                    Path(output_directory) / f"{output_prefix}_labeled"
                ).with_suffix(".dataset")
                data.save_to_disk(str(data_output_path))
                print(data_output_path)
        else:
            data_output_path = (
                Path(output_directory) / f"{output_prefix}_labeled"
            ).with_suffix(".dataset")
            data.save_to_disk(str(data_output_path))

    def train_all_data(
        self,
        model_directory,
        prepared_input_data_file,
        id_class_dict_file,
        output_directory,
        output_prefix,
        save_eval_output=True,
    ):
        """
        Train cell state or gene classifier using all data.

        **Parameters**

        model_directory : Path
            | Path to directory containing model
        prepared_input_data_file : Path
            | Path to directory containing _labeled.dataset previously prepared by Classifier.prepare_data
        id_class_dict_file : Path
            | Path to _id_class_dict.pkl previously prepared by Classifier.prepare_data
            | (dictionary of format: numerical IDs: class_labels)
        output_directory : Path
            | Path to directory where model and eval data will be saved
        output_prefix : str
            | Prefix for output files
        save_eval_output : bool
            | Whether to save cross-fold eval output
            | Saves as pickle file of dictionary of eval metrics

        **Output**

        Returns trainer after fine-tuning with all data.

        """

        ##### Load data and prepare output directory #####
        # load numerical id to class dictionary (id:class)
        with open(id_class_dict_file, "rb") as f:
            id_class_dict = pickle.load(f)
        class_id_dict = {v: k for k, v in id_class_dict.items()}

        # load previously filtered and prepared data
        data = pu.load_and_filter(None, self.nproc, prepared_input_data_file)
        data = data.shuffle(seed=42)  # reshuffle in case users provide unshuffled data

        # define output directory path
        current_date = datetime.datetime.now()
        datestamp = f"{str(current_date.year)[-2:]}{current_date.month:02d}{current_date.day:02d}"
        if output_directory[-1:] != "/":  # add slash for dir if not present
            output_directory = output_directory + "/"
        output_dir = f"{output_directory}{datestamp}_geneformer_{self.classifier}Classifier_{output_prefix}/"
        subprocess.call(f"mkdir {output_dir}", shell=True)

        # get number of classes for classifier
        num_classes = cu.get_num_classes(id_class_dict)

        if self.classifier == "gene":
            targets = pu.flatten_list(self.gene_class_dict.values())
            labels = pu.flatten_list(
                [
                    [class_id_dict[label]] * len(targets)
                    for label, targets in self.gene_class_dict.items()
                ]
            )
            assert len(targets) == len(labels)
            data = cu.prep_gene_classifier_all_data(
                data, targets, labels, self.max_ncells, self.nproc
            )

        trainer = self.train_classifier(
            model_directory, num_classes, data, None, output_dir
        )

        return trainer

    def validate(
        self,
        model_directory,
        prepared_input_data_file,
        id_class_dict_file,
        output_directory,
        output_prefix,
        split_id_dict=None,
        attr_to_split=None,
        attr_to_balance=None,
        max_trials=100,
        pval_threshold=0.1,
        save_eval_output=True,
        predict_eval=True,
        predict_trainer=False,
        n_hyperopt_trials=0,
    ):
        """
        (Cross-)validate cell state or gene classifier.

        **Parameters**

        model_directory : Path
            | Path to directory containing model
        prepared_input_data_file : Path
            | Path to directory containing _labeled.dataset previously prepared by Classifier.prepare_data
        id_class_dict_file : Path
            | Path to _id_class_dict.pkl previously prepared by Classifier.prepare_data
            | (dictionary of format: numerical IDs: class_labels)
        output_directory : Path
            | Path to directory where model and eval data will be saved
        output_prefix : str
            | Prefix for output files
        split_id_dict : None, dict
            | Dictionary of IDs for train and eval splits
            | Three-item dictionary with keys: attr_key, train, eval
            | attr_key: key specifying name of column in .dataset that contains the IDs for the data splits
            | train: list of IDs in the attr_key column to include in the train split
            | eval: list of IDs in the attr_key column to include in the eval split
            | For example: {"attr_key": "individual",
            |               "train": ["patient1", "patient2", "patient3", "patient4"],
            |               "eval": ["patient5", "patient6"]}
            | Note: only available for CellClassifiers with 1-fold split (self.classifier="cell"; self.num_crossval_splits=1)
        attr_to_split : None, str
            | Key for attribute on which to split data while balancing potential confounders
            | e.g. "patient_id" for splitting by patient while balancing other characteristics
            | Note: only available for CellClassifiers with 1-fold split (self.classifier="cell"; self.num_crossval_splits=1)
        attr_to_balance : None, list
            | List of attribute keys on which to balance data while splitting on attr_to_split
            | e.g. ["age", "sex"] for balancing these characteristics while splitting by patient
        max_trials : None, int
            | Maximum number of trials of random splitting to try to achieve balanced other attribute
            | If no split is found without significant (p < pval_threshold) differences in other attributes, will select best
        pval_threshold : None, float
            | P-value threshold to use for attribute balancing across splits
            | E.g. if set to 0.1, will accept trial if p >= 0.1 for all attributes in attr_to_balance
        save_eval_output : bool
            | Whether to save cross-fold eval output
            | Saves as pickle file of dictionary of eval metrics
        predict_eval : bool
            | Whether or not to save eval predictions
            | Saves as a pickle file of self.evaluate predictions
        predict_trainer : bool
            | Whether or not to save eval predictions from trainer
            | Saves as a pickle file of trainer predictions
        n_hyperopt_trials : int
            | Number of trials to run for hyperparameter optimization
            | If 0, will not optimize hyperparameters
        """
        if self.num_crossval_splits == 0:
            logger.error("num_crossval_splits must be 1 or 5 to validate.")
            raise

        # ensure number of genes in each class is > 5 if validating model
        if self.classifier == "gene":
            insuff_classes = [k for k, v in self.gene_class_dict.items() if len(v) < 5]
            if (self.num_crossval_splits > 0) and (len(insuff_classes) > 0):
                logger.error(
                    f"Insufficient # of members in class(es) {insuff_classes} to (cross-)validate."
                )
                raise

        ##### Load data and prepare output directory #####
        # load numerical id to class dictionary (id:class)
        with open(id_class_dict_file, "rb") as f:
            id_class_dict = pickle.load(f)
        class_id_dict = {v: k for k, v in id_class_dict.items()}

        # load previously filtered and prepared data
        data = pu.load_and_filter(None, self.nproc, prepared_input_data_file)
        data = data.shuffle(seed=42)  # reshuffle in case users provide unshuffled data

        # define output directory path
        current_date = datetime.datetime.now()
        datestamp = f"{str(current_date.year)[-2:]}{current_date.month:02d}{current_date.day:02d}"
        if output_directory[-1:] != "/":  # add slash for dir if not present
            output_directory = output_directory + "/"
        output_dir = f"{output_directory}{datestamp}_geneformer_{self.classifier}Classifier_{output_prefix}/"
        subprocess.call(f"mkdir {output_dir}", shell=True)

        # get number of classes for classifier
        num_classes = cu.get_num_classes(id_class_dict)

        ##### (Cross-)validate the model #####
        results = []
        all_conf_mat = np.zeros((num_classes, num_classes))
        iteration_num = 1
        if self.classifier == "cell":
            for i in trange(self.num_crossval_splits):
                print(
                    f"****** Validation split: {iteration_num}/{self.num_crossval_splits} ******\n"
                )
                ksplit_output_dir = os.path.join(output_dir, f"ksplit{iteration_num}")
                if self.num_crossval_splits == 1:
                    # single 1-eval_size:eval_size split
                    if split_id_dict is not None:
                        data_dict = dict()
                        data_dict["train"] = pu.filter_by_dict(
                            data,
                            {split_id_dict["attr_key"]: split_id_dict["train"]},
                            self.nproc,
                        )
                        data_dict["test"] = pu.filter_by_dict(
                            data,
                            {split_id_dict["attr_key"]: split_id_dict["eval"]},
                            self.nproc,
                        )
                    elif attr_to_split is not None:
                        data_dict, balance_df = cu.balance_attr_splits(
                            data,
                            attr_to_split,
                            attr_to_balance,
                            self.eval_size,
                            max_trials,
                            pval_threshold,
                            self.cell_state_dict["state_key"],
                            self.nproc,
                        )

                        balance_df.to_csv(
                            f"{output_dir}/{output_prefix}_train_valid_balance_df.csv"
                        )
                    else:
                        data_dict = data.train_test_split(
                            test_size=self.eval_size,
                            stratify_by_column=self.stratify_splits_col,
                            seed=42,
                        )
                    train_data = data_dict["train"]
                    eval_data = data_dict["test"]
                else:
                    # 5-fold cross-validate
                    num_cells = len(data)
                    fifth_cells = num_cells * 0.2
                    num_eval = min((self.eval_size * num_cells), fifth_cells)
                    start = i * fifth_cells
                    end = start + num_eval
                    eval_indices = [j for j in range(start, end)]
                    train_indices = [
                        j for j in range(num_cells) if j not in eval_indices
                    ]
                    eval_data = data.select(eval_indices)
                    train_data = data.select(train_indices)
                if n_hyperopt_trials == 0:
                    trainer = self.train_classifier(
                        model_directory,
                        num_classes,
                        train_data,
                        eval_data,
                        ksplit_output_dir,
                        predict_trainer,
                    )
                else:
                    trainer = self.hyperopt_classifier(
                        model_directory,
                        num_classes,
                        train_data,
                        eval_data,
                        ksplit_output_dir,
                        n_trials=n_hyperopt_trials,
                    )
                    if iteration_num == self.num_crossval_splits:
                        return
                    else:
                        iteration_num = iteration_num + 1
                        continue

                result = self.evaluate_model(
                    trainer.model,
                    num_classes,
                    id_class_dict,
                    eval_data,
                    predict_eval,
                    ksplit_output_dir,
                    output_prefix,
                )
                results += [result]
                all_conf_mat = all_conf_mat + result["conf_mat"]
                iteration_num = iteration_num + 1

        elif self.classifier == "gene":
            # set up (cross-)validation splits
            targets = pu.flatten_list(self.gene_class_dict.values())
            labels = pu.flatten_list(
                [
                    [class_id_dict[label]] * len(targets)
                    for label, targets in self.gene_class_dict.items()
                ]
            )
            assert len(targets) == len(labels)
            n_splits = int(1 / (1 - self.train_size))
            skf = cu.StratifiedKFold3(n_splits=n_splits, random_state=0, shuffle=True)
            # (Cross-)validate
            test_ratio = self.oos_test_size / (self.eval_size + self.oos_test_size)
            for train_index, eval_index, test_index in tqdm(
                skf.split(targets, labels, test_ratio)
            ):
                print(
                    f"****** Validation split: {iteration_num}/{self.num_crossval_splits} ******\n"
                )
                ksplit_output_dir = os.path.join(output_dir, f"ksplit{iteration_num}")
                # filter data for examples containing classes for this split
                # subsample to max_ncells and relabel data in column "labels"
                train_data, eval_data = cu.prep_gene_classifier_train_eval_split(
                    data,
                    targets,
                    labels,
                    train_index,
                    eval_index,
                    self.max_ncells,
                    iteration_num,
                    self.nproc,
                )

                if self.oos_test_size > 0:
                    test_data = cu.prep_gene_classifier_split(
                        data,
                        targets,
                        labels,
                        test_index,
                        "test",
                        self.max_ncells,
                        iteration_num,
                        self.nproc,
                    )

                if n_hyperopt_trials == 0:
                    trainer = self.train_classifier(
                        model_directory,
                        num_classes,
                        train_data,
                        eval_data,
                        ksplit_output_dir,
                        predict_trainer,
                    )
                    result = self.evaluate_model(
                        trainer.model,
                        num_classes,
                        id_class_dict,
                        eval_data,
                        predict_eval,
                        ksplit_output_dir,
                        output_prefix,
                    )
                else:
                    trainer = self.hyperopt_classifier(
                        model_directory,
                        num_classes,
                        train_data,
                        eval_data,
                        ksplit_output_dir,
                        n_trials=n_hyperopt_trials,
                    )

                    model = cu.load_best_model(
                        ksplit_output_dir, self.model_type, num_classes
                    )

                    if self.oos_test_size > 0:
                        result = self.evaluate_model(
                            model,
                            num_classes,
                            id_class_dict,
                            test_data,
                            predict_eval,
                            ksplit_output_dir,
                            output_prefix,
                        )
                    else:
                        if iteration_num == self.num_crossval_splits:
                            return
                        else:
                            iteration_num = iteration_num + 1
                            continue
                results += [result]
                all_conf_mat = all_conf_mat + result["conf_mat"]
                # break after 1 or 5 splits, each with train/eval proportions dictated by eval_size
                if iteration_num == self.num_crossval_splits:
                    break
                iteration_num = iteration_num + 1

        all_conf_mat_df = pd.DataFrame(
            all_conf_mat, columns=id_class_dict.values(), index=id_class_dict.values()
        )
        all_metrics = {
            "conf_matrix": all_conf_mat_df,
            "macro_f1": [result["macro_f1"] for result in results],
            "acc": [result["acc"] for result in results],
        }
        all_roc_metrics = None  # roc metrics not reported for multiclass
        if num_classes == 2:
            mean_fpr = np.linspace(0, 1, 100)
            all_tpr = [result["roc_metrics"]["interp_tpr"] for result in results]
            all_roc_auc = [result["roc_metrics"]["auc"] for result in results]
            all_tpr_wt = [result["roc_metrics"]["tpr_wt"] for result in results]
            mean_tpr, roc_auc, roc_auc_sd = eu.get_cross_valid_roc_metrics(
                all_tpr, all_roc_auc, all_tpr_wt
            )
            all_roc_metrics = {
                "mean_tpr": mean_tpr,
                "mean_fpr": mean_fpr,
                "all_roc_auc": all_roc_auc,
                "roc_auc": roc_auc,
                "roc_auc_sd": roc_auc_sd,
            }
        all_metrics["all_roc_metrics"] = all_roc_metrics
        if save_eval_output is True:
            eval_metrics_output_path = (
                Path(output_dir) / f"{output_prefix}_eval_metrics_dict"
            ).with_suffix(".pkl")
            with open(eval_metrics_output_path, "wb") as f:
                pickle.dump(all_metrics, f)

        return all_metrics

    def hyperopt_classifier(
        self,
        model_directory,
        num_classes,
        train_data,
        eval_data,
        output_directory,
        n_trials=100,
    ):
        """
        Fine-tune model for cell state or gene classification.

        **Parameters**

        model_directory : Path
            | Path to directory containing model
        num_classes : int
            | Number of classes for classifier
        train_data : Dataset
            | Loaded training .dataset input
            | For cell classifier, labels in column "label".
            | For gene classifier, labels in column "labels".
        eval_data : None, Dataset
            | (Optional) Loaded evaluation .dataset input
            | For cell classifier, labels in column "label".
            | For gene classifier, labels in column "labels".
        output_directory : Path
            | Path to directory where fine-tuned model will be saved
        n_trials : int
            | Number of trials to run for hyperparameter optimization
        """

        # initiate runtime environment for raytune
        import ray
        from ray import tune
        from ray.tune.search.hyperopt import HyperOptSearch

        ray.shutdown()  # engage new ray session
        ray.init()

        ##### Validate and prepare data #####
        train_data, eval_data = cu.validate_and_clean_cols(
            train_data, eval_data, self.classifier
        )

        if (self.no_eval is True) and (eval_data is not None):
            logger.warning(
                "no_eval set to True; hyperparameter optimization requires eval, proceeding with eval"
            )

        # ensure not overwriting previously saved model
        saved_model_test = os.path.join(output_directory, "pytorch_model.bin")
        if os.path.isfile(saved_model_test) is True:
            logger.error("Model already saved to this designated output directory.")
            raise
        # make output directory
        subprocess.call(f"mkdir {output_directory}", shell=True)

        ##### Load model and training args #####
        model = pu.load_model(self.model_type, num_classes, model_directory, "train")
        def_training_args, def_freeze_layers = cu.get_default_train_args(
            model, self.classifier, train_data, output_directory
        )
        del model

        if self.training_args is not None:
            def_training_args.update(self.training_args)
        logging_steps = round(
            len(train_data) / def_training_args["per_device_train_batch_size"] / 10
        )
        def_training_args["logging_steps"] = logging_steps
        def_training_args["output_dir"] = output_directory
        if eval_data is None:
            def_training_args["evaluation_strategy"] = "no"
            def_training_args["load_best_model_at_end"] = False
        def_training_args.update(
            {"save_strategy": "epoch", "save_total_limit": 1}
        )  # only save last model for each run
        training_args_init = TrainingArguments(**def_training_args)

        ##### Fine-tune the model #####
        # define the data collator
        if self.classifier == "cell":
            data_collator = DataCollatorForCellClassification()
        elif self.classifier == "gene":
            data_collator = DataCollatorForGeneClassification()

        # define function to initiate model
        def model_init():
            model = pu.load_model(
                self.model_type, num_classes, model_directory, "train"
            )

            if self.freeze_layers is not None:
                def_freeze_layers = self.freeze_layers

            if def_freeze_layers > 0:
                modules_to_freeze = model.bert.encoder.layer[:def_freeze_layers]
                for module in modules_to_freeze:
                    for param in module.parameters():
                        param.requires_grad = False

            model = model.to("cuda:0")
            return model

        # create the trainer
        trainer = Trainer(
            model_init=model_init,
            args=training_args_init,
            data_collator=data_collator,
            train_dataset=train_data,
            eval_dataset=eval_data,
            compute_metrics=cu.compute_metrics,
        )

        # specify raytune hyperparameter search space
        if self.ray_config is None:
            logger.warning(
                "No ray_config provided. Proceeding with default, but ranges may need adjustment depending on model."
            )
            def_ray_config = {
                "num_train_epochs": tune.choice([1]),
                "learning_rate": tune.loguniform(1e-6, 1e-3),
                "weight_decay": tune.uniform(0.0, 0.3),
                "lr_scheduler_type": tune.choice(["linear", "cosine", "polynomial"]),
                "warmup_steps": tune.uniform(100, 2000),
                "seed": tune.uniform(0, 100),
                "per_device_train_batch_size": tune.choice(
                    [def_training_args["per_device_train_batch_size"]]
                ),
            }

        hyperopt_search = HyperOptSearch(metric="eval_macro_f1", mode="max")

        # optimize hyperparameters
        trainer.hyperparameter_search(
            direction="maximize",
            backend="ray",
            resources_per_trial={"cpu": int(self.nproc / self.ngpu), "gpu": 1},
            hp_space=lambda _: def_ray_config
            if self.ray_config is None
            else self.ray_config,
            search_alg=hyperopt_search,
            n_trials=n_trials,  # number of trials
            progress_reporter=tune.CLIReporter(
                max_report_frequency=600,
                sort_by_metric=True,
                max_progress_rows=n_trials,
                mode="max",
                metric="eval_macro_f1",
                metric_columns=["loss", "eval_loss", "eval_accuracy", "eval_macro_f1"],
            ),
            local_dir=output_directory,
        )

        return trainer

    def train_classifier(
        self,
        model_directory,
        num_classes,
        train_data,
        eval_data,
        output_directory,
        predict=False,
    ):
        """
        Fine-tune model for cell state or gene classification.

        **Parameters**

        model_directory : Path
            | Path to directory containing model
        num_classes : int
            | Number of classes for classifier
        train_data : Dataset
            | Loaded training .dataset input
            | For cell classifier, labels in column "label".
            | For gene classifier, labels in column "labels".
        eval_data : None, Dataset
            | (Optional) Loaded evaluation .dataset input
            | For cell classifier, labels in column "label".
            | For gene classifier, labels in column "labels".
        output_directory : Path
            | Path to directory where fine-tuned model will be saved
        predict : bool
            | Whether or not to save eval predictions from trainer
        """

        ##### Validate and prepare data #####
        train_data, eval_data = cu.validate_and_clean_cols(
            train_data, eval_data, self.classifier
        )

        if (self.no_eval is True) and (eval_data is not None):
            logger.warning(
                "no_eval set to True; model will be trained without evaluation."
            )
            eval_data = None

        if (self.classifier == "gene") and (predict is True):
            logger.warning(
                "Predictions during training not currently available for gene classifiers; setting predict to False."
            )
            predict = False

        # ensure not overwriting previously saved model
        saved_model_test = os.path.join(output_directory, "pytorch_model.bin")
        if os.path.isfile(saved_model_test) is True:
            logger.error("Model already saved to this designated output directory.")
            raise
        # make output directory
        subprocess.call(f"mkdir {output_directory}", shell=True)

        ##### Load model and training args #####
        model = pu.load_model(self.model_type, num_classes, model_directory, "train")

        def_training_args, def_freeze_layers = cu.get_default_train_args(
            model, self.classifier, train_data, output_directory
        )

        if self.training_args is not None:
            def_training_args.update(self.training_args)
        logging_steps = round(
            len(train_data) / def_training_args["per_device_train_batch_size"] / 10
        )
        def_training_args["logging_steps"] = logging_steps
        def_training_args["output_dir"] = output_directory
        if eval_data is None:
            def_training_args["evaluation_strategy"] = "no"
            def_training_args["load_best_model_at_end"] = False
        training_args_init = TrainingArguments(**def_training_args)

        if self.freeze_layers is not None:
            def_freeze_layers = self.freeze_layers

        if def_freeze_layers > 0:
            modules_to_freeze = model.bert.encoder.layer[:def_freeze_layers]
            for module in modules_to_freeze:
                for param in module.parameters():
                    param.requires_grad = False

        ##### Fine-tune the model #####
        # define the data collator
        if self.classifier == "cell":
            data_collator = DataCollatorForCellClassification()
        elif self.classifier == "gene":
            data_collator = DataCollatorForGeneClassification()

        # create the trainer
        trainer = Trainer(
            model=model,
            args=training_args_init,
            data_collator=data_collator,
            train_dataset=train_data,
            eval_dataset=eval_data,
            compute_metrics=cu.compute_metrics,
        )

        # train the classifier
        trainer.train()
        trainer.save_model(output_directory)
        if predict is True:
            # make eval predictions and save predictions and metrics
            predictions = trainer.predict(eval_data)
            prediction_output_path = f"{output_directory}/predictions.pkl"
            with open(prediction_output_path, "wb") as f:
                pickle.dump(predictions, f)
            trainer.save_metrics("eval", predictions.metrics)
        return trainer

    def evaluate_model(
        self,
        model,
        num_classes,
        id_class_dict,
        eval_data,
        predict=False,
        output_directory=None,
        output_prefix=None,
    ):
        """
        Evaluate the fine-tuned model.

        **Parameters**

        model : nn.Module
            | Loaded fine-tuned model (e.g. trainer.model)
        num_classes : int
            | Number of classes for classifier
        id_class_dict : dict
            | Loaded _id_class_dict.pkl previously prepared by Classifier.prepare_data
            | (dictionary of format: numerical IDs: class_labels)
        eval_data : Dataset
            | Loaded evaluation .dataset input
        predict : bool
            | Whether or not to save eval predictions
        output_directory : Path
            | Path to directory where eval data will be saved
        output_prefix : str
            | Prefix for output files
        """

        ##### Evaluate the model #####
        labels = id_class_dict.keys()
        y_pred, y_true, logits_list = eu.classifier_predict(
            model, self.classifier, eval_data, self.forward_batch_size
        )
        conf_mat, macro_f1, acc, roc_metrics = eu.get_metrics(
            y_pred, y_true, logits_list, num_classes, labels
        )
        if predict is True:
            pred_dict = {
                "pred_ids": y_pred,
                "label_ids": y_true,
                "predictions": logits_list,
            }
            pred_dict_output_path = (
                Path(output_directory) / f"{output_prefix}_pred_dict"
            ).with_suffix(".pkl")
            with open(pred_dict_output_path, "wb") as f:
                pickle.dump(pred_dict, f)
        return {
            "conf_mat": conf_mat,
            "macro_f1": macro_f1,
            "acc": acc,
            "roc_metrics": roc_metrics,
        }

    def evaluate_saved_model(
        self,
        model_directory,
        id_class_dict_file,
        test_data_file,
        output_directory,
        output_prefix,
        predict=True,
    ):
        """
        Evaluate the fine-tuned model.

        **Parameters**

        model_directory : Path
            | Path to directory containing model
        id_class_dict_file : Path
            | Path to _id_class_dict.pkl previously prepared by Classifier.prepare_data
            | (dictionary of format: numerical IDs: class_labels)
        test_data_file : Path
            | Path to directory containing test .dataset
        output_directory : Path
            | Path to directory where eval data will be saved
        output_prefix : str
            | Prefix for output files
        predict : bool
            | Whether or not to save eval predictions
        """

        # load numerical id to class dictionary (id:class)
        with open(id_class_dict_file, "rb") as f:
            id_class_dict = pickle.load(f)

        # get number of classes for classifier
        num_classes = cu.get_num_classes(id_class_dict)

        # load previously filtered and prepared data
        test_data = pu.load_and_filter(None, self.nproc, test_data_file)

        # load previously fine-tuned model
        model = pu.load_model(self.model_type, num_classes, model_directory, "eval")

        # evaluate the model
        result = self.evaluate_model(
            model,
            num_classes,
            id_class_dict,
            test_data,
            predict=predict,
            output_directory=output_directory,
            output_prefix=output_prefix,
        )

        all_conf_mat_df = pd.DataFrame(
            result["conf_mat"],
            columns=id_class_dict.values(),
            index=id_class_dict.values(),
        )
        all_metrics = {
            "conf_matrix": all_conf_mat_df,
            "macro_f1": result["macro_f1"],
            "acc": result["acc"],
        }
        all_roc_metrics = None  # roc metrics not reported for multiclass

        if num_classes == 2:
            mean_fpr = np.linspace(0, 1, 100)
            mean_tpr = result["roc_metrics"]["interp_tpr"]
            all_roc_auc = result["roc_metrics"]["auc"]
            all_roc_metrics = {
                "mean_tpr": mean_tpr,
                "mean_fpr": mean_fpr,
                "all_roc_auc": all_roc_auc,
            }
        all_metrics["all_roc_metrics"] = all_roc_metrics
        test_metrics_output_path = (
            Path(output_directory) / f"{output_prefix}_test_metrics_dict"
        ).with_suffix(".pkl")
        with open(test_metrics_output_path, "wb") as f:
            pickle.dump(all_metrics, f)

        return all_metrics

    def plot_conf_mat(
        self,
        conf_mat_dict,
        output_directory,
        output_prefix,
        custom_class_order=None,
    ):
        """
        Plot confusion matrix results of evaluating the fine-tuned model.

        **Parameters**

        conf_mat_dict : dict
            | Dictionary of model_name : confusion_matrix_DataFrame
            | (all_metrics["conf_matrix"] from self.validate)
        output_directory : Path
            | Path to directory where plots will be saved
        output_prefix : str
            | Prefix for output file
        custom_class_order : None, list
            | List of classes in custom order for plots.
            | Same order will be used for all models.
        """

        for model_name in conf_mat_dict.keys():
            eu.plot_confusion_matrix(
                conf_mat_dict[model_name],
                model_name,
                output_directory,
                output_prefix,
                custom_class_order,
            )

    def plot_roc(
        self,
        roc_metric_dict,
        model_style_dict,
        title,
        output_directory,
        output_prefix,
    ):
        """
        Plot ROC curve results of evaluating the fine-tuned model.

        **Parameters**

        roc_metric_dict : dict
            | Dictionary of model_name : roc_metrics
            | (all_metrics["all_roc_metrics"] from self.validate)
        model_style_dict : dict[dict]
            | Dictionary of model_name : dictionary of style_attribute : style
            | where style includes color and linestyle
            | e.g. {'Model_A': {'color': 'black', 'linestyle': '-'}, 'Model_B': ...}
        title : str
            | Title of plot (e.g. 'Dosage-sensitive vs -insensitive factors')
        output_directory : Path
            | Path to directory where plots will be saved
        output_prefix : str
            | Prefix for output file
        """

        eu.plot_ROC(
            roc_metric_dict, model_style_dict, title, output_directory, output_prefix
        )

    def plot_predictions(
        self,
        predictions_file,
        id_class_dict_file,
        title,
        output_directory,
        output_prefix,
        custom_class_order=None,
        kwargs_dict=None,
    ):
        """
        Plot prediction results of evaluating the fine-tuned model.

        **Parameters**

        predictions_file : path
            | Path of model predictions output to plot
            | (saved output from self.validate if predict_eval=True)
            | (or saved output from self.evaluate_saved_model)
        id_class_dict_file : Path
            | Path to _id_class_dict.pkl previously prepared by Classifier.prepare_data
            | (dictionary of format: numerical IDs: class_labels)
        title : str
            | Title for legend containing class labels.
        output_directory : Path
            | Path to directory where plots will be saved
        output_prefix : str
            | Prefix for output file
        custom_class_order : None, list
            | List of classes in custom order for plots.
            | Same order will be used for all models.
        kwargs_dict : None, dict
            | Dictionary of kwargs to pass to plotting function.
        """
        # load predictions
        with open(predictions_file, "rb") as f:
            predictions = pickle.load(f)

        # load numerical id to class dictionary (id:class)
        with open(id_class_dict_file, "rb") as f:
            id_class_dict = pickle.load(f)

        if isinstance(predictions, dict):
            if all(
                [
                    key in predictions.keys()
                    for key in ["pred_ids", "label_ids", "predictions"]
                ]
            ):
                # format is output from self.evaluate_saved_model
                predictions_logits = np.array(predictions["predictions"])
                true_ids = predictions["label_ids"]
        else:
            # format is output from self.validate if predict_eval=True
            predictions_logits = predictions.predictions
            true_ids = predictions.label_ids

        num_classes = len(id_class_dict.keys())
        num_predict_classes = predictions_logits.shape[1]
        assert num_classes == num_predict_classes
        classes = id_class_dict.values()
        true_labels = [id_class_dict[idx] for idx in true_ids]
        predictions_df = pd.DataFrame(predictions_logits, columns=classes)
        if custom_class_order is not None:
            predictions_df = predictions_df.reindex(columns=custom_class_order)
        predictions_df["true"] = true_labels
        custom_dict = dict(zip(classes, [i for i in range(len(classes))]))
        if custom_class_order is not None:
            custom_dict = dict(
                zip(custom_class_order, [i for i in range(len(custom_class_order))])
            )
        predictions_df = predictions_df.sort_values(
            by=["true"], key=lambda x: x.map(custom_dict)
        )

        eu.plot_predictions(
            predictions_df, title, output_directory, output_prefix, kwargs_dict
        )