fusion-bench 0.2.5__py3-none-any.whl → 0.2.7__py3-none-any.whl

fusion_bench/compat/method/__init__.py

@@ -21,6 +21,7 @@ class AlgorithmFactory:
         "clip_task_wise_adamerging": ".adamerging.clip_task_wise_adamerging.CLIPTaskWiseAdaMergingAlgorithm",
         "clip_layer_wise_adamerging": ".adamerging.clip_layer_wise_adamerging.CLIPLayerWiseAdaMergingAlgorithm",
         "singular_projection_merging": "fusion_bench.method.smile_upscaling.singular_projection_merging.SingularProjectionMergingAlgorithm",
+        "clip_layer_wise_adamerging_surgery": ".surgery.clip_layer_wise_adamerging_surgery.CLIPLayerWiseAdaMergingSurgeryAlgorithm",
         # plug-and-play model merging methods
         "clip_concrete_task_arithmetic": ".concrete_subspace.clip_concrete_task_arithmetic.ConcreteTaskArithmeticAlgorithmForCLIP",
         "clip_concrete_task_wise_adamerging": ".concrete_subspace.clip_concrete_adamerging.ConcreteTaskWiseAdaMergingForCLIP",
@@ -29,6 +30,7 @@ class AlgorithmFactory:
         "clip_weight_ensembling_moe": ".we_moe.clip_we_moe.CLIPWeightEnsemblingMoEAlgorithm",
         "sparse_clip_weight_ensembling_moe": "fusion_bench.method.SparseCLIPWeightEnsemblingMoEAlgorithm",
         "smile_mistral_upscaling": ".smile_upscaling.smile_mistral_upscaling.SmileMistralUpscalingAlgorithm",
+        "rankone_moe": ".rankone_moe.clip_rankone_moe.CLIPRankOneMoEAlgorithm",
     }
 
     @staticmethod

fusion_bench/compat/method/base_algorithm.py

@@ -1,8 +1,11 @@
 from abc import ABC, abstractmethod
-from typing import Optional
+from typing import Optional, TYPE_CHECKING
 
 from omegaconf import DictConfig
 
+if TYPE_CHECKING:
+    from fusion_bench.programs.base_program import BaseHydraProgram
+
 __all__ = ["ModelFusionAlgorithm"]
 
 
@@ -18,6 +21,9 @@ class ModelFusionAlgorithm(ABC):
         config (DictConfig): Configuration for the algorithm.
     """
 
+    _program: "BaseHydraProgram" = None
+    """A reference to the program that is running the algorithm."""
+
     def __init__(self, algorithm_config: Optional[DictConfig] = None):
         """
         Initialize the model fusion algorithm with the given configuration.
@@ -26,7 +32,6 @@ class ModelFusionAlgorithm(ABC):
             algorithm_config (Optional[DictConfig]): Configuration for the algorithm. Defaults to an empty configuration if not provided.
                 Get access to the configuration using `self.config`.
         """
-        super().__init__()
         if algorithm_config is None:
             algorithm_config = DictConfig({})
         self.config = algorithm_config

fusion_bench/compat/modelpool/__init__.py

@@ -1,4 +1,6 @@
 # flake8: noqa F401
+import warnings
+
 from omegaconf import DictConfig
 
 from fusion_bench.modelpool.huggingface_gpt2_classification import (
@@ -9,7 +11,6 @@ from fusion_bench.modelpool.PeftModelForSeq2SeqLM import PeftModelForSeq2SeqLMPo
 from .AutoModelForSeq2SeqLM import AutoModelForSeq2SeqLMPool
 from .base_pool import DictModelPool, ListModelPool, ModelPool, to_modelpool
 from .huggingface_clip_vision import HuggingFaceClipVisionPool
-import warnings
 
 
 class ModelPoolFactory:
@@ -21,7 +22,7 @@ class ModelPoolFactory:
     """
 
     _modelpool = {
-        "NYUv2ModelPool": ".nyuv2_modelpool.NYUv2ModelPool",
+        "NYUv2ModelPool": "fusion_bench.modelpool.nyuv2_modelpool.NYUv2ModelPool",
         "huggingface_clip_vision": HuggingFaceClipVisionPool,
         "HF_GPT2ForSequenceClassification": GPT2ForSequenceClassificationPool,
         "AutoModelPool": ".huggingface_automodel.AutoModelPool",

fusion_bench/compat/taskpool/__init__.py

@@ -20,7 +20,7 @@ class TaskPoolFactory:
         "dummy": DummyTaskPool,
         "clip_vit_classification": ".clip_image_classification.CLIPImageClassificationTaskPool",
         "FlanT5GLUETextGenerationTaskPool": ".flan_t5_glue_text_generation.FlanT5GLUETextGenerationTaskPool",
-        "NYUv2TaskPool": ".nyuv2_taskpool.NYUv2TaskPool",
+        "NYUv2TaskPool": "fusion_bench.taskpool.nyuv2_taskpool.NYUv2TaskPool",
     }
 
     @staticmethod

fusion_bench/dataset/arc_agi/__init__.py

@@ -1 +1,6 @@
-from .arc_agi import load_tokenized_arc_agi_dataset
+from .arc_agi import (
+    load_tokenized_arc_agi_dataset,
+    load_tokenized_arc_agi_dataset_for_ttt,
+    process_task,
+    process_task_for_ttt,
+)

fusion_bench/dataset/arc_agi/arc.py

@@ -7,6 +7,7 @@ Task: a class to represent a task (task.test_example and task.train_examples are
 read_from_single_file: a function to read challenge problems and solutions from a single file
 make_submission: a function to create a submission file
 """
+
 import dataclasses
 import glob
 import json
@@ -15,7 +16,6 @@ from typing import List, Optional
 
 import numpy as np
 
-
 Grid = np.ndarray
 
 
@@ -66,7 +66,9 @@ class Example:
     def __eq__(self, other: object) -> bool:
         if not isinstance(other, Example):
             return NotImplemented
-        return np.array_equal(self.input, other.input) and np.array_equal(self.output, other.output)
+        return np.array_equal(self.input, other.input) and np.array_equal(
+            self.output, other.output
+        )
 
     @classmethod
     def deserialize(cls, data: dict, test: bool = False) -> "Example":
@@ -150,7 +152,16 @@ class Task:
         tasks = []
         for test_data in data["test"]:
             task = cls.deserialize(
-                {"train": data["train"], "test": [test_data], "name": data.get("name", "")},
+                {
+                    "train": data["train"],
+                    "test": [test_data],
+                    "name": data.get("name", ""),
+                },
+                {
+                    "train": data["train"],
+                    "test": [test_data],
+                    "name": data.get("name", ""),
+                },
                 test=test,
             )
             tasks.append(task)
@@ -245,7 +256,9 @@ def make_submission(
     """
     Make a submission
     """
-    assert len(tasks) == len(predictions), "Number of tasks and predictions should be the same"
+    assert len(tasks) == len(
+        predictions
+    ), "Number of tasks and predictions should be the same"
 
     # sort by task_name alphabetically to ensure order of subtasks
     indices = np.argsort([task.name for task in tasks])
@@ -259,8 +272,12 @@ def make_submission(
         if task_name not in submissions:
             submissions[task_name] = []
 
-        assert len(prediction) == number_of_attempts, "Number of attempts should be the same"
-        attempts = {f"attempt_{j+1}": to_list(pred) for j, pred in enumerate(prediction)}
+        assert (
+            len(prediction) == number_of_attempts
+        ), "Number of attempts should be the same"
+        attempts = {
+            f"attempt_{j+1}": to_list(pred) for j, pred in enumerate(prediction)
+        }
         while len(submissions[task_name]) <= task_no:
             submissions[task_name].append({"attempt_1": [[0]], "attempt_2": [[0]]})
 
@@ -277,7 +294,9 @@ if __name__ == "__main__":
     arc_path = "/kaggle/input/arc-prize-2024/"
     tasks = read_tasks_from_single_file(arc_path + "arc-agi_training_challenges.json")
     print(tasks[0])
-    tasks = read_tasks_from_single_file(arc_path + "arc-agi_evaluation_challenges.json", test=True)
+    tasks = read_tasks_from_single_file(
+        arc_path + "arc-agi_evaluation_challenges.json", test=True
+    )
     print(tasks[0])
 
     tasks = read_tasks_from_single_file(

fusion_bench/dataset/arc_agi/arc_agi.py

@@ -5,15 +5,16 @@ import sys
 from multiprocessing import Pool
 from typing import Any, Dict, List, Literal, Optional
 
-import fusion_bench
 import numpy as np
 from datasets import Dataset, DatasetDict, load_dataset, load_from_disk
 from lightning.fabric.utilities import rank_zero_only
 from tqdm.auto import tqdm
 from typing_extensions import TYPE_CHECKING
 
+import fusion_bench
+
 from .arc import Example, Task
-from .preprocess import get_augmenters, process_task
+from .preprocess import get_augmenters, process_task, process_task_for_ttt
 
 if TYPE_CHECKING:
     from transformers import PreTrainedTokenizer
@@ -65,7 +66,7 @@ def _join_list(lists: List[List[Any]]) -> List[Any]:
     return ans
 
 
-def _to_task(
+def _to_tasks(
     train_data: List[Dict[str, Any]],
     test_data: List[Dict[str, Any]],
     name: str,
@@ -87,7 +88,7 @@ def _to_task(
     return tasks
 
 
-def _tokenizer_tasks(
+def tokenizer_tasks_for_ttt(
     tasks: List[Task],
     tokenizer: "PreTrainedTokenizer",
     use_data_augmentation: bool = True,
@@ -106,7 +107,7 @@ def _tokenizer_tasks(
 
     formatter = _get_formatter("new")
     processor = functools.partial(
-        process_task,
+        process_task_for_ttt,
         augmenters=augmenters_to_apply,
         formatter=formatter,
         tokenizer=tokenizer,
@@ -133,7 +134,34 @@ def _tokenizer_tasks(
     return dataset
 
 
-def load_tokenized_arc_agi_dataset(
+def tokenizer_tasks(
+    tasks: List[Task],
+    tokenizer: "PreTrainedTokenizer",
+):
+    formatter = _get_formatter("new")
+    processor = functools.partial(
+        process_task, formatter=formatter, tokenizer=tokenizer
+    )
+
+    # with Pool(multiprocessing.cpu_count()) as p:
+    #     data = p.map(processor, tasks)
+    data = _join_list(
+        [
+            processor(task)
+            for task in tqdm(
+                tasks,
+                desc="Processing tasks",
+                dynamic_ncols=True,
+                leave=False,
+                disable=not rank_zero_only.rank == 0,
+            )
+        ]
+    )
+    dataset = Dataset.from_list(data)
+    return dataset
+
+
+def load_tokenized_arc_agi_dataset_for_ttt(
     tokenizer: Optional["PreTrainedTokenizer"],
     path: str = "dataartist/arc-agi",
     split: Optional[str] = None,
@@ -144,47 +172,47 @@ def load_tokenized_arc_agi_dataset(
     max_num_tasks: Optional[int] = None,
 ):
     # regularize split
-    if split.lower() == "train":
-        split = "training"
-    if split.lower() == "test":
-        split = "evaluation"
+    split = split.lower() if split is not None else split
 
     # load cached dataset if available
     if cache_path is not None and fusion_bench.utils.path.path_is_dir_and_not_empty(
         cache_path
     ):
         datasets = load_from_disk(cache_path)
-        if split is None:
-            return datasets
-        else:
+        if split is None and split in datasets.column_names:
             return datasets[split]
+        else:
+            return datasets
     else:
         assert (
             tokenizer is not None
         ), "Cached dataset not found. Need tokenizer to process the raw data."
 
     # load raw dataset
-    datasets = load_dataset(path, split=split)
+    datasets = load_dataset(path)
+    datasets = DatasetDict(
+        {"train": datasets["training"], "test": datasets["evaluation"]}
+    )
     if split is None:
-        converted_datasets = {
+        converted_datasets: Dict[str, List[Task]] = {
             "train": _join_list(
                 [
-                    _to_task(
+                    _to_tasks(
                         task["train"],
                         task["test"],
                         task["id"],
                     )
-                    for task in datasets["training"]
+                    for task in datasets["train"]
                 ]
             ),
             "test": _join_list(
                 [
-                    _to_task(
+                    _to_tasks(
                         task["train"],
                         task["test"],
                         task["id"],
                     )
-                    for task in datasets["evaluation"]
+                    for task in datasets["test"]
                 ]
             ),
         }
@@ -195,7 +223,7 @@ def load_tokenized_arc_agi_dataset(
                 for split in converted_datasets
             }
         converted_datasets = {
-            split: _tokenizer_tasks(
+            split: tokenizer_tasks_for_ttt(
                 converted_datasets[split],
                 tokenizer,
                 use_data_augmentation,
@@ -210,25 +238,128 @@ def load_tokenized_arc_agi_dataset(
             )
         }
         converted_datasets = DatasetDict(converted_datasets)
-    else:
+    else:  # split is not None
         converted_datasets = _join_list(
             [
-                _to_task(
+                _to_tasks(
                     task["train"],
                     task["test"],
                     task["id"],
                 )
-                for task in datasets
+                for task in datasets[split]
             ]
         )
         if max_num_tasks is not None:
             # limit the number of tasks, useful for debugging
             converted_datasets = converted_datasets[:max_num_tasks]
-        converted_datasets = _tokenizer_tasks(
+        converted_datasets = tokenizer_tasks_for_ttt(
             converted_datasets, tokenizer, use_data_augmentation, permute_n, seed
         )
 
-    if cache_path is not None:
+    if cache_path is not None and rank_zero_only.rank == 0:
+        os.makedirs(cache_path, exist_ok=True)
+        converted_datasets.save_to_disk(cache_path)
+    return converted_datasets
+
+
+def load_tokenized_arc_agi_dataset(
+    tokenizer: Optional["PreTrainedTokenizer"],
+    path: str = "dataartist/arc-agi",
+    split: Optional[str] = None,
+    cache_path: Optional[str] = None,
+    max_num_tasks: Optional[int] = None,
+):
+    """
+    Loads and tokenizes the ARC-AGI dataset.
+
+    Args:
+        tokenizer (Optional[PreTrainedTokenizer]): The tokenizer to use for tokenizing the dataset.
+        path (str, optional): The path to the dataset. Defaults to "dataartist/arc-agi".
+        split (Optional[str], optional): The dataset split to load (e.g., "train", "test"). Defaults to None.
+        cache_path (Optional[str], optional): The path to cache the processed dataset. Defaults to None.
+        max_num_tasks (Optional[int], optional): The maximum number of tasks to load. Useful for debugging. Defaults to None.
+
+    Returns:
+        DatasetDict or Dataset: The tokenized dataset, either as a DatasetDict if split is None, or as a Dataset if a specific split is specified.
+    """
+    # regularize split
+    split = split.lower() if split is not None else split
+
+    # load cached dataset if available
+    if cache_path is not None and fusion_bench.utils.path.path_is_dir_and_not_empty(
+        cache_path
+    ):
+        datasets = load_from_disk(cache_path)
+        if split is None and split in datasets.column_names:
+            return datasets[split]
+        else:
+            return datasets
+    else:
+        assert (
+            tokenizer is not None
+        ), "Cached dataset not found. Need tokenizer to process the raw data."
+
+    # load raw dataset
+    datasets = load_dataset(path)
+    datasets = DatasetDict(
+        {"train": datasets["training"], "test": datasets["evaluation"]}
+    )
+    if split is None:
+        converted_datasets: Dict[str, List[Task]] = {
+            "train": _join_list(
+                [
+                    _to_tasks(
+                        task["train"],
+                        task["test"],
+                        task["id"],
+                    )
+                    for task in datasets["train"]
+                ]
+            ),
+            "test": _join_list(
+                [
+                    _to_tasks(
+                        task["train"],
+                        task["test"],
+                        task["id"],
+                    )
+                    for task in datasets["test"]
+                ]
+            ),
+        }
+        if max_num_tasks is not None:
+            # limit the number of tasks, useful for debugging
+            converted_datasets = {
+                split: converted_datasets[split][:max_num_tasks]
+                for split in converted_datasets
+            }
+        converted_datasets = {
+            split: tokenizer_tasks(converted_datasets[split], tokenizer)
+            for split in tqdm(
+                converted_datasets,
+                desc="Processing splits",
+                dynamic_ncols=True,
+                disable=not rank_zero_only.rank == 0,
+            )
+        }
+        converted_datasets = DatasetDict(converted_datasets)
+    else:  # split is not None
+        converted_datasets = _join_list(
+            [
+                _to_tasks(
+                    task["train"],
+                    task["test"],
+                    task["id"],
+                )
+                for task in datasets[split]
+            ]
+        )
+        if max_num_tasks is not None:
+            # limit the number of tasks, useful for debugging
+            converted_datasets = converted_datasets[:max_num_tasks]
+        converted_datasets = tokenizer_tasks(converted_datasets, tokenizer)
+
+    if cache_path is not None and rank_zero_only.rank == 0:
         os.makedirs(cache_path, exist_ok=True)
         converted_datasets.save_to_disk(cache_path)
     return converted_datasets

fusion_bench/dataset/arc_agi/np_cache.py

@@ -6,7 +6,6 @@ from typing import Callable, Optional, TypeVar, cast
 import numpy as np
 from xxhash import xxh3_64_hexdigest
 
-
 __all__ = ["np_lru_cache"]
 
 TCallable = TypeVar("TCallable", bound=Callable)

fusion_bench/dataset/arc_agi/preprocess.py

@@ -112,19 +112,41 @@ def get_augmenters(
 def format_and_filter(
     formatter: MessageRepresenter,
     tokenizer: "PreTrainedTokenizer",
-    task,
+    task: Task,
 ):
+    """
+    Formats and filters a task for model input.
+
+    Args:
+        formatter (MessageRepresenter): The formatter to encode the task.
+        tokenizer (PreTrainedTokenizer): The tokenizer to tokenize the conversation.
+        task: The task to be formatted and filtered.
+
+    Returns:
+        Dict[str, Any]: A dictionary containing the formatted data with keys:
+            - "input_ids": The tokenized input IDs.
+            - "attention_mask": The attention mask for the input IDs.
+            - "labels": The labels for the input IDs.
+            - "task_id": The task ID.
+            - "num_prompt_tokens": The number of prompt tokens.
+            - "num_output_tokens": The number of output tokens.
+    """
+    task_id = task.name
     task = formatter.encode(task)
     conversation = task[0] + [task[1]]
     assert conversation[-1]["role"] == "assistant", "Last message should be assistant"
     prompt_tokens = tokenizer.apply_chat_template(
         conversation[:-1], tokenize=True, add_generation_prompt=True
     )
-    output_tokens = tokenizer.encode(conversation[-1]["content"] + tokenizer.eos_token)
+    generation_tokens = tokenizer.apply_chat_template(conversation, tokenize=True)
+    output_tokens = generation_tokens[len(prompt_tokens) :]
     data = {
         "input_ids": prompt_tokens + output_tokens,
         "attention_mask": [1] * len(prompt_tokens) + [1] * len(output_tokens),
-        "labels": [-100] * len(prompt_tokens) + output_tokens,
+        "labels": prompt_tokens + output_tokens,
+        "task_id": task_id,
+        "num_prompt_tokens": len(prompt_tokens),
+        "num_output_tokens": len(output_tokens),
     }
     return data
 
@@ -136,6 +158,19 @@ def get_test_time_train_data(
     permute_n: int = 1,
     seed: int = 0,
 ) -> List[Task]:
+    """
+    Generates augmented training data for test-time training.
+
+    Args:
+        original_task (Task): The original task containing training examples.
+        augmenters (List[Augmenter]): A list of augmenters to apply to the tasks.
+        n (int, optional): The number of examples to leave out for testing. Defaults to 1.
+        permute_n (int, optional): The number of times to permute the augmented tasks. Defaults to 1.
+        seed (int, optional): The random seed for reproducibility. Defaults to 0.
+
+    Returns:
+        List[Task]: A list of augmented tasks.
+    """
     rng = np.random.RandomState(seed)
     train_examples = original_task.train_examples.copy()
     initial_tasks = []
@@ -150,7 +185,7 @@ def get_test_time_train_data(
         for comb in combs:
             initial_tasks.append(
                 Task(
-                    name="",
+                    name=original_task.name,
                     train_examples=[examples[j] for j in comb],
                     test_example=examples[i],
                 )
@@ -183,7 +218,6 @@ def get_test_time_train_data(
             color_and_permute_augmented_tasks.append(new_task)
 
     augmented_tasks = color_and_permute_augmented_tasks + augmented_tasks
-
     augmented_tasks = list(set(augmented_tasks))
 
     return augmented_tasks
@@ -193,13 +227,12 @@ def get_formatted_data(
     task: Task,
     augmenters: List[Augmenter],
     formatter: MessageRepresenter,
-    tokenizer,
+    tokenizer: "PreTrainedTokenizer",
     leave_n: int = 1,
     permute_n: int = 1,
     seed: int = 0,
     max_tokens: int = 8192,
 ):
-
     train_data = get_test_time_train_data(
         task, augmenters, n=leave_n, permute_n=permute_n, seed=seed
     )
@@ -213,11 +246,11 @@ def get_formatted_data(
     return formatted_data
 
 
-def process_task(
+def process_task_for_ttt(
     task: Task,
     augmenters: List[Augmenter],
     formatter: MessageRepresenter,
-    tokenizer,
+    tokenizer: "PreTrainedTokenizer",
     permute_n: int = 1,
     Nmax: int = 250,
     seed: int = 0,
@@ -254,3 +287,12 @@ def process_task(
         train = train[:Nmax]
 
     return train
+
+
+def process_task(
+    task: Task,
+    formatter: MessageRepresenter,
+    tokenizer: "PreTrainedTokenizer",
+):
+    formatted = format_and_filter(formatter, tokenizer, task)
+    return [formatted]

fusion_bench/dataset/llama/__init__.py

@@ -0,0 +1 @@
+from . import collate