add runner

Signed-off-by: Zhiyuan Chen <[email protected]>

.codespell-whitelist.txt

@@ -1,3 +1,4 @@
+datas
 ser
 marz
 manuel

multimolecule/__init__.py

@@ -14,6 +14,7 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
+from .apis import evaluate, inference, train
 from .data import Dataset
 from .models import (
     AutoModelForContactPrediction,
@@ -130,14 +131,20 @@
     TokenKMerHead,
     TokenPredictionHead,
 )
+from .runners import MultiMoleculeConfig, MultiMoleculeRunner
 from .tasks import Task, TaskLevel, TaskType
 from .tokenisers import Alphabet, DnaTokenizer, DotBracketTokenizer, ProteinTokenizer, RnaTokenizer, Tokenizer
 from .utils import count_parameters
 
 __all__ = [
+    "train",
+    "evaluate",
+    "inference",
     "modeling_auto",
     "modeling_outputs",
     "Dataset",
+    "MultiMoleculeConfig",
+    "MultiMoleculeRunner",
     "PreTrainedConfig",
     "HeadConfig",
     "BaseHeadConfig",

multimolecule/apis/__init__.py

@@ -0,0 +1,19 @@
+# MultiMolecule
+# Copyright (C) 2024-Present  MultiMolecule
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+from .run import evaluate, inference, train
+
+__all__ = ["train", "evaluate", "inference"]

multimolecule/apis/run.py

@@ -0,0 +1,110 @@
+# MultiMolecule
+# Copyright (C) 2024-Present  MultiMolecule
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+import atexit
+import os
+import warnings
+from typing import Type
+
+import danling as dl
+import torch
+
+from multimolecule.runners import MultiMoleculeConfig, MultiMoleculeRunner
+
+try:
+    import nni
+except ImportError:
+    nni = None
+
+
+def train(
+    config: MultiMoleculeConfig = None,  # type: ignore
+    runner_cls: Type[MultiMoleculeRunner] = MultiMoleculeRunner,
+):
+    if config is None:
+        config = MultiMoleculeConfig()
+    config = config.parse(default_config="config", no_default_config_action="warn")
+    config.interpolate(unsafe_eval=True)
+    if config.allow_tf32:
+        torch.backends.cudnn.allow_tf32 = True
+        torch.backends.cuda.matmul.allow_tf32 = True
+    if config.reduced_precision_reduction:
+        torch.backends.cuda.matmul.allow_fp16_reduced_precision_reduction = True
+        torch.backends.cuda.matmul.allow_bf16_reduced_precision_reduction = True
+    if config.get("nni", False):
+        if nni is None:
+            raise ValueError("Unable to retrieve nni parameters, since nni is not installed.")
+        config.merge(nni.get_next_parameter())
+    with dl.debug(config.get("debug", False)):
+        runner = runner_cls(config)
+        atexit.register(runner.print_result)
+        atexit.register(runner.save_result)
+        atexit.register(runner.save_checkpoint)
+        result = runner.train()
+        return result
+
+
+def evaluate(
+    config: MultiMoleculeConfig = None,  # type: ignore
+    runner_cls: Type[MultiMoleculeRunner] = MultiMoleculeRunner,
+):
+    if config is None:
+        config = MultiMoleculeConfig.empty()
+    config = config.parse(default_config="config", no_default_config_action="warn")
+    config.interpolate(unsafe_eval=True)
+    if config.allow_tf32:
+        torch.backends.cudnn.allow_tf32 = True
+        torch.backends.cuda.matmul.allow_tf32 = True
+    if config.reduced_precision_reduction:
+        torch.backends.cuda.matmul.allow_fp16_reduced_precision_reduction = True
+        torch.backends.cuda.matmul.allow_bf16_reduced_precision_reduction = True
+    if "checkpoint" not in config or not isinstance(config.checkpoint, str):
+        raise RuntimeError("Please specify `checkpoint` to run evaluate")
+    for name, data in config.datas.items():
+        if "eval" not in data or not isinstance(data.eval, str):
+            raise RuntimeError(f"Please specify `eval` to run evaluate in datas.{name}")
+    runner = runner_cls(config)
+    result = runner.evaluate_epoch("eval")
+    print(result)
+    return result
+
+
+def inference(
+    config: MultiMoleculeConfig = None,  # type: ignore
+    runner_cls: Type[MultiMoleculeRunner] = MultiMoleculeRunner,
+):
+    if config is None:
+        config = MultiMoleculeConfig.empty()
+    config = config.parse(default_config="config", no_default_config_action="warn")
+    config.interpolate(unsafe_eval=True)
+    if config.allow_tf32:
+        torch.backends.cudnn.allow_tf32 = True
+        torch.backends.cuda.matmul.allow_tf32 = True
+    if config.reduced_precision_reduction:
+        torch.backends.cuda.matmul.allow_fp16_reduced_precision_reduction = True
+        torch.backends.cuda.matmul.allow_bf16_reduced_precision_reduction = True
+    if "checkpoint" not in config or not isinstance(config.checkpoint, str):
+        raise RuntimeError("Please specify `checkpoint` to run infer.")
+    for name, data in config.datas.items():
+        if "inf" not in data or not isinstance(data.inf, str):
+            raise RuntimeError(f"Please specify `inf` to run infer in datas.{name}")
+    if "result_path" not in config or not isinstance(config.result_path, str):
+        config.result_path = os.path.join(os.getcwd(), "result.json")
+        warnings.warn("`result_path` is not specified, default to `result.json`.", RuntimeWarning, stacklevel=2)
+    runner = runner_cls(config)
+    result = runner.inference()
+    runner.save(result, config.result_path)
+    return result

multimolecule/data/dataset.py

@@ -17,7 +17,6 @@
 from __future__ import annotations
 
 from collections.abc import Iterable, Mapping, Sequence
-from functools import cached_property
 from typing import Any, List
 from warnings import warn
 
@@ -232,7 +231,7 @@ def post(
             self.update(self.map(self.map_discrete))
         self.set_transform(self.transform)
 
-    @cached_property
+    @property
     def tasks(self) -> NestedDict:
         return self.infer_tasks()
 

multimolecule/models/calm/configuration_calm.py

@@ -130,5 +130,5 @@ def __init__(
         self.use_cache = use_cache
         self.emb_layer_norm_before = emb_layer_norm_before
         self.token_dropout = token_dropout
-        self.head = HeadConfig(**head if head is not None else {})
-        self.lm_head = MaskedLMHeadConfig(**lm_head if lm_head is not None else {})
+        self.head = HeadConfig(**head) if head is not None else None
+        self.lm_head = MaskedLMHeadConfig(**lm_head) if lm_head is not None else None

multimolecule/models/configuration_utils.py

@@ -30,7 +30,7 @@ class PreTrainedConfig(PretrainedConfig):
     Base class for all model configuration classes.
     """
 
-    head: HeadConfig
+    head: HeadConfig | None
 
     hidden_size: int
 

multimolecule/models/ernierna/configuration_ernierna.py

@@ -113,5 +113,5 @@ def __init__(
         self.pairwise_alpha = pairwise_alpha
         self.is_decoder = is_decoder
         self.use_cache = use_cache
-        self.head = HeadConfig(**head if head is not None else {})
-        self.lm_head = MaskedLMHeadConfig(**lm_head if lm_head is not None else {})
+        self.head = HeadConfig(**head) if head is not None else None
+        self.lm_head = MaskedLMHeadConfig(**lm_head) if lm_head is not None else None

multimolecule/models/ernierna/modeling_ernierna.py

@@ -1232,7 +1232,7 @@ def __init__(self, config: ErnieRnaConfig, head_config: HeadConfig | None = None
         super().__init__()
         if head_config is None:
             head_config = config.head
-        self.config = head_config
+        self.config = head_config  # type: HeadConfig # type: ignore[assignment]
         self.bos_token_id = config.bos_token_id
         self.eos_token_id = config.eos_token_id
         self.pad_token_id = config.pad_token_id

multimolecule/models/rinalmo/configuration_rinalmo.py

@@ -128,6 +128,6 @@ def __init__(
         self.use_cache = use_cache
         self.learnable_beta = learnable_beta
         self.token_dropout = token_dropout
-        self.head = HeadConfig(**head if head is not None else {})
-        self.lm_head = MaskedLMHeadConfig(**lm_head if lm_head is not None else {})
+        self.head = HeadConfig(**head) if head is not None else None
+        self.lm_head = MaskedLMHeadConfig(**lm_head) if lm_head is not None else None
         self.emb_layer_norm_before = emb_layer_norm_before

multimolecule/models/rnabert/configuration_rnabert.py

@@ -115,5 +115,5 @@ def __init__(
         self.position_embedding_type = position_embedding_type
         self.is_decoder = is_decoder
         self.use_cache = use_cache
-        self.head = HeadConfig(**head if head is not None else {})
-        self.lm_head = MaskedLMHeadConfig(**lm_head if lm_head is not None else {})
+        self.head = HeadConfig(**head) if head is not None else None
+        self.lm_head = MaskedLMHeadConfig(**lm_head) if lm_head is not None else None

multimolecule/models/rnaernie/configuration_rnaernie.py

@@ -111,5 +111,5 @@ def __init__(
         self.position_embedding_type = position_embedding_type
         self.is_decoder = is_decoder
         self.use_cache = use_cache
-        self.head = HeadConfig(**head if head is not None else {})
-        self.lm_head = MaskedLMHeadConfig(**lm_head if lm_head is not None else {})
+        self.head = HeadConfig(**head) if head is not None else None
+        self.lm_head = MaskedLMHeadConfig(**lm_head) if lm_head is not None else None

multimolecule/models/rnafm/configuration_rnafm.py

@@ -134,5 +134,5 @@ def __init__(
         self.use_cache = use_cache
         self.emb_layer_norm_before = emb_layer_norm_before
         self.token_dropout = token_dropout
-        self.head = HeadConfig(**head if head is not None else {})
-        self.lm_head = MaskedLMHeadConfig(**lm_head if lm_head is not None else {})
+        self.head = HeadConfig(**head) if head is not None else None
+        self.lm_head = MaskedLMHeadConfig(**lm_head) if lm_head is not None else None

multimolecule/models/rnamsm/configuration_rnamsm.py

@@ -119,5 +119,5 @@ def __init__(
         self.attention_type = attention_type
         self.embed_positions_msa = embed_positions_msa
         self.attention_bias = attention_bias
-        self.head = HeadConfig(**head if head is not None else {})
-        self.lm_head = MaskedLMHeadConfig(**lm_head if lm_head is not None else {})
+        self.head = HeadConfig(**head) if head is not None else None
+        self.lm_head = MaskedLMHeadConfig(**lm_head) if lm_head is not None else None

multimolecule/models/splicebert/configuration_splicebert.py

@@ -111,5 +111,5 @@ def __init__(
         self.position_embedding_type = position_embedding_type
         self.is_decoder = is_decoder
         self.use_cache = use_cache
-        self.head = HeadConfig(**head if head is not None else {})
-        self.lm_head = MaskedLMHeadConfig(**lm_head if lm_head is not None else {})
+        self.head = HeadConfig(**head) if head is not None else None
+        self.lm_head = MaskedLMHeadConfig(**lm_head) if lm_head is not None else None

multimolecule/models/utrbert/configuration_utrbert.py

@@ -128,5 +128,5 @@ def __init__(
         self.position_embedding_type = position_embedding_type
         self.is_decoder = is_decoder
         self.use_cache = use_cache
-        self.head = HeadConfig(**head if head is not None else {})
-        self.lm_head = MaskedLMHeadConfig(**lm_head if lm_head is not None else {})
+        self.head = HeadConfig(**head) if head is not None else None
+        self.lm_head = MaskedLMHeadConfig(**lm_head) if lm_head is not None else None

multimolecule/models/utrlm/configuration_utrlm.py

@@ -130,7 +130,7 @@ def __init__(
         self.use_cache = use_cache
         self.emb_layer_norm_before = emb_layer_norm_before
         self.token_dropout = token_dropout
-        self.head = HeadConfig(**head if head is not None else {})
-        self.lm_head = MaskedLMHeadConfig(**lm_head if lm_head is not None else {})
+        self.head = HeadConfig(**head) if head is not None else None
+        self.lm_head = MaskedLMHeadConfig(**lm_head) if lm_head is not None else None
         self.ss_head = HeadConfig(**ss_head) if ss_head is not None else None
         self.mfe_head = HeadConfig(**mfe_head) if mfe_head is not None else None

multimolecule/module/__init__.py

@@ -14,7 +14,7 @@
 # You should have received a copy of the GNU Affero General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-from .criterions import Criterion
+from .criterions import Criterion, CriterionRegistry
 from .embeddings import PositionEmbeddingRegistry, PositionEmbeddingRegistryHF, RotaryEmbedding, SinusoidalEmbedding
 from .heads import (
     BaseHeadConfig,
@@ -38,8 +38,13 @@
     TokenKMerHead,
     TokenPredictionHead,
 )
+from .model import MultiMoleculeModel
+from .registry import ModelRegistry
 
 __all__ = [
+    "ModelRegistry",
+    "MultiMoleculeModel",
+    "CriterionRegistry",
     "Criterion",
     "PositionEmbeddingRegistry",
     "PositionEmbeddingRegistryHF",

multimolecule/module/backbones/__init__.py

@@ -0,0 +1,21 @@
+# MultiMolecule
+# Copyright (C) 2024-Present  MultiMolecule
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+from .registry import BackboneRegistry
+from .sequence import SequenceBackbone
+from .sequences import SequenceRegistry
+
+__all__ = ["BackboneRegistry", "SequenceRegistry", "SequenceBackbone"]

multimolecule/module/backbones/registry.py

@@ -0,0 +1,21 @@
+# MultiMolecule
+# Copyright (C) 2024-Present  MultiMolecule
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+from __future__ import annotations
+
+from chanfig import Registry
+
+BackboneRegistry = Registry()

multimolecule/module/backbones/sequence.py

@@ -0,0 +1,46 @@
+# MultiMolecule
+# Copyright (C) 2024-Present  MultiMolecule
+
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+from __future__ import annotations
+
+import torch
+from chanfig import FlatDict
+from danling import NestedTensor
+from torch import Tensor, nn
+
+from .registry import BackboneRegistry
+from .sequences import SequenceRegistry
+
+
+@BackboneRegistry.register("sequence", default=True)
+class SequenceBackbone(nn.Module):
+    def __init__(self, sequence) -> None:
+        super().__init__()
+        self.sequence = SequenceRegistry.build(**sequence)
+        self.sequence_dropout = nn.Dropout(sequence.pop("dropout", 0), inplace=True)
+        self.config = self.sequence.config
+        self.out_channels = self.config.hidden_size
+
+    def forward(self, sequence: NestedTensor | Tensor, *args, **kwargs) -> tuple[FlatDict, FlatDict]:
+        attentions = None
+        input_ids, attention_mask = sequence.tensor, sequence.mask
+        sequence_output = self.sequence(input_ids.int(), attention_mask)
+        sequence_output["pooler_output"] = self.sequence_dropout(sequence_output["pooler_output"])
+        sequence_output["last_hidden_state"] = self.sequence_dropout(sequence_output["last_hidden_state"])
+        if "attentions" in sequence_output:
+            attentions = torch.stack(sequence_output["attentions"], dim=1).detach()
+
+        return sequence_output, attentions