Upload GP-MoLFormer code and pre-trained model

config.json

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+{
+  "architectures": [
+    "MolformerForCausalLM"
+  ],
+  "auto_map": {
+    "AutoConfig": "configuration_molformer.MolformerConfig",
+    "AutoModelForCausalLM": "modeling_molformer.MolformerForCausalLM"
+  },
+  "bos_token_id": 0,
+  "deterministic_eval": false,
+  "embedding_dropout_prob": 0.2,
+  "eos_token_id": 1,
+  "feature_map_kernel": "relu",
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "initializer_range": 0.02,
+  "intermediate_size": 768,
+  "is_decoder": true,
+  "layer_norm_eps": 1e-12,
+  "linear_attention_eps": 1e-06,
+  "max_position_embeddings": 202,
+  "model_type": "molformer",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "num_random_features": 32,
+  "pad_token_id": 2,
+  "tie_word_embeddings": false,
+  "torch_dtype": "float32",
+  "transformers_version": "4.32.1",
+  "use_cache": true,
+  "vocab_size": 2362
+}

configuration_molformer.py

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+# coding=utf-8
+# Copyright 2023 The HuggingFace Inc. team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" Molformer model configuration"""
+
+from collections import OrderedDict
+from typing import Mapping
+
+from transformers.configuration_utils import PretrainedConfig
+from transformers.onnx import OnnxConfig
+from transformers.utils import logging
+
+
+logger = logging.get_logger(__name__)
+
+MOLFORMER_PRETRAINED_CONFIG_ARCHIVE_MAP = {
+    "ibm/GP-MoLFormer-Uniq": "https://huggingface.co/ibm/GP-MoLFormer-Uniq/resolve/main/config.json",
+}
+
+
+class MolformerConfig(PretrainedConfig):
+    r"""
+    This is the configuration class to store the configuration of a [`MolformerModel`]. It is used to instantiate an
+    Molformer model according to the specified arguments, defining the model architecture. Instantiating a
+    configuration with the defaults will yield a similar configuration to that of the Molformer
+    [ibm/MoLFormer-XL-both-10pct](https://huggingface.co/ibm/MoLFormer-XL-both-10pct) architecture.
+
+    Configuration objects inherit from [`PretrainedConfig`] and can be used to control the model outputs. Read the
+    documentation from [`PretrainedConfig`] for more information.
+
+
+    Args:
+        vocab_size (`int`, *optional*, defaults to 2362):
+            Vocabulary size of the Molformer model. Defines the number of different tokens that can be represented by
+            the `inputs_ids` passed when calling [`MolformerModel`] or [`TFMolformerModel`].
+        hidden_size (`int`, *optional*, defaults to 768):
+            Dimension of the encoder layers and the pooler layer.
+        num_hidden_layers (`int`, *optional*, defaults to 12):
+            Number of hidden layers in the Transformer encoder.
+        num_attention_heads (`int`, *optional*, defaults to 12):
+            Number of attention heads for each attention layer in the Transformer encoder.
+        intermediate_size (`int`, *optional*, defaults to 768):
+            Dimension of the "intermediate" (i.e., feed-forward) layer in the Transformer encoder.
+        hidden_act (`str` or `function`, *optional*, defaults to `"gelu"`):
+            The non-linear activation function (function or string) in the encoder and pooler. If string, `"gelu"`,
+            `"relu"`, `"selu"` and `"gelu_new"` are supported.
+        hidden_dropout_prob (`float`, *optional*, defaults to 0.1):
+            The dropout probability for all fully connected layers in the embeddings, encoder, and pooler.
+        embedding_dropout_prob (`float`, *optional*, defaults to 0.2):
+            The dropout probability for the word embeddings.
+        max_position_embeddings (`int`, *optional*, defaults to 202):
+            The maximum sequence length that this model might ever be used with. Typically set this to something large
+            just in case (e.g., 512 or 1024 or 1536).
+        initializer_range (`float`, *optional*, defaults to 0.02):
+            The standard deviation of the truncated_normal_initializer for initializing all weight matrices.
+        layer_norm_eps (`float`, *optional*, defaults to 1e-12):
+            The epsilon used by the layer normalization layers.
+        linear_attention_eps (`float`, *optional*, defaults to 1e-06):
+            The epsilon used by the linear attention layers normalization step.
+        num_random_features (`int`, *optional*, defaults to 32):
+            Random feature map dimension used in linear attention.
+        feature_map_kernel (`str` or `function`, *optional*, defaults to `"relu"`):
+            The non-linear activation function (function or string) in the generalized random features. If string,
+            `"gelu"`, `"relu"`, `"selu"`, and `"gelu_new"` ar supported.
+        deterministic_eval (`bool`, *optional*, defaults to `False`):
+            Whether the random features should only be redrawn when training or not. If `True` and `model.training` is
+            `False`, linear attention random feature weights will be constant, i.e., deterministic.
+        bos_token_id (`int`, *optional*, defaults to 0):
+            Beginning of stream token id.
+        eos_token_id (`int`, *optional*, defaults to 1):
+            End of stream token id.
+        pad_token_id (`int`, *optional*, defaults to 2):
+            The id of the _padding_ token.
+        tie_word_embeddings (`bool`, *optional*, defaults to `False`):
+            Whether to tie weight embeddings
+        is_decoder (`bool`, *optional*, defaults to `True`):
+            Whether the model is used as a decoder or not. If `False`, the model is used as an encoder.
+        use_cache (`bool`, *optional*, defaults to `True`):
+            Whether or not the model should return the last key/values attentions (not used by all models). Only
+            relevant if `config.is_decoder=True`.
+
+    Example:
+
+    ```python
+    >>> from transformers import MolformerModel, MolformerConfig
+
+    >>> # Initializing a Molformer ibm/MoLFormer-XL-both-10pct style configuration
+    >>> configuration = MolformerConfig()
+
+    >>> # Initializing a model from the ibm/MoLFormer-XL-both-10pct style configuration
+    >>> model = MolformerModel(configuration)
+
+    >>> # Accessing the model configuration
+    >>> configuration = model.config
+    ```"""
+    model_type = "molformer"
+
+    def __init__(
+        self,
+        vocab_size=2362,
+        hidden_size=768,
+        num_hidden_layers=12,
+        num_attention_heads=12,
+        intermediate_size=768,
+        hidden_act="gelu",
+        hidden_dropout_prob=0.1,
+        embedding_dropout_prob=0.2,
+        max_position_embeddings=202,
+        initializer_range=0.02,
+        layer_norm_eps=1e-12,
+        linear_attention_eps=1e-6,
+        num_random_features=32,
+        feature_map_kernel="relu",
+        deterministic_eval=False,
+        bos_token_id=0,
+        eos_token_id=1,
+        pad_token_id=2,
+        tie_word_embeddings=False,
+        is_decoder=True,
+        use_cache=True,
+        **kwargs,
+    ):
+        super().__init__(
+            bos_token_id=bos_token_id,
+            eos_token_id=eos_token_id,
+            pad_token_id=pad_token_id,
+            tie_word_embeddings=tie_word_embeddings,
+            **kwargs
+        )
+
+        self.vocab_size = vocab_size
+        self.hidden_size = hidden_size
+        self.num_hidden_layers = num_hidden_layers
+        self.num_attention_heads = num_attention_heads
+        self.hidden_act = hidden_act
+        self.intermediate_size = intermediate_size
+        self.hidden_dropout_prob = hidden_dropout_prob
+        self.embedding_dropout_prob = embedding_dropout_prob
+        self.max_position_embeddings = max_position_embeddings
+        self.initializer_range = initializer_range
+        self.layer_norm_eps = layer_norm_eps
+        self.linear_attention_eps = linear_attention_eps
+        self.num_random_features = num_random_features
+        self.feature_map_kernel = feature_map_kernel
+        self.deterministic_eval = deterministic_eval
+        self.is_decoder = is_decoder
+        self.use_cache = use_cache
+
+
+# Copied from transformers.models.roberta.configuration_roberta.RobertaOnnxConfig with Roberta->Molformer
+class MolformerOnnxConfig(OnnxConfig):
+    @property
+    def inputs(self) -> Mapping[str, Mapping[int, str]]:
+        if self.task == "multiple-choice":
+            dynamic_axis = {0: "batch", 1: "choice", 2: "sequence"}
+        else:
+            dynamic_axis = {0: "batch", 1: "sequence"}
+        return OrderedDict(
+            [
+                ("input_ids", dynamic_axis),
+                ("attention_mask", dynamic_axis),
+            ]
+        )

model.safetensors

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+version https://git-lfs.github.com/spec/v1
+oid sha256:2754f36d8cebc399a54cc486285b81105862159cda42d5af8715d12fd49ebd3c
+size 187248784

modeling_molformer.py

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+# coding=utf-8
+# Copyright 2023 The HuggingFace Inc. team. All rights reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+""" PyTorch Molformer model."""
+
+
+import math
+from typing import Optional, Tuple, Union
+
+import torch
+import torch.utils.checkpoint
+from torch import nn
+from torch.nn import CrossEntropyLoss
+
+from transformers.activations import ACT2FN
+from transformers.modeling_outputs import (
+    BaseModelOutputWithPastAndCrossAttentions,
+    BaseModelOutputWithPoolingAndCrossAttentions,
+    CausalLMOutputWithCrossAttentions,
+)
+from transformers.modeling_utils import PreTrainedModel
+from transformers.pytorch_utils import apply_chunking_to_forward, find_pruneable_heads_and_indices, prune_linear_layer
+from transformers.utils import (
+    add_code_sample_docstrings,
+    add_start_docstrings,
+    add_start_docstrings_to_model_forward,
+    logging,
+    replace_return_docstrings,
+)
+from .configuration_molformer import MolformerConfig
+
+
+logger = logging.get_logger(__name__)
+
+_CHECKPOINT_FOR_DOC = "ibm/GP-MoLFormer-Uniq"
+_CONFIG_FOR_DOC = "MolformerConfig"
+
+MOLFORMER_PRETRAINED_MODEL_ARCHIVE_LIST = [
+    "ibm/GP-MoLFormer-Uniq",
+    # See all MoLFormer models at https://huggingface.co/models?filter=molformer
+]
+
+
+# Copied from transformers.models.esm.modeling_esm.rotate_half
+def rotate_half(x):
+    x1, x2 = x.chunk(2, dim=-1)
+    return torch.cat((-x2, x1), dim=-1)
+
+
+# Copied from transformers.models.llama.modeling_llama.apply_rotary_pos_emb
+def apply_rotary_pos_emb(q, k, cos, sin, position_ids):
+    cos = cos[position_ids].unsqueeze(1)  # [seq_len, dim] -> [batch_size, 1, seq_len, head_dim]
+    sin = sin[position_ids].unsqueeze(1)
+    q_embed = (q * cos) + (rotate_half(q) * sin)
+    k_embed = (k * cos) + (rotate_half(k) * sin)
+    return q_embed, k_embed
+
+
+# Copied from transformers.models.llama.modeling_llama.LlamaRotaryEmbedding with Llama->Molformer
+class MolformerRotaryEmbedding(nn.Module):
+    def __init__(self, dim, max_position_embeddings=2048, base=10000, device=None):
+        super().__init__()
+
+        self.dim = dim
+        self.max_position_embeddings = max_position_embeddings
+        self.base = base
+        inv_freq = 1.0 / (self.base ** (torch.arange(0, self.dim, 2).float().to(device) / self.dim))
+        self.register_buffer("inv_freq", inv_freq, persistent=False)
+
+        # Build here to make `torch.jit.trace` work.
+        self._set_cos_sin_cache(
+            seq_len=max_position_embeddings, device=self.inv_freq.device, dtype=torch.get_default_dtype()
+        )
+
+    def _set_cos_sin_cache(self, seq_len, device, dtype):
+        self.max_seq_len_cached = seq_len
+        t = torch.arange(self.max_seq_len_cached, device=device, dtype=self.inv_freq.dtype)
+
+        freqs = torch.einsum("i,j->ij", t, self.inv_freq)
+        # Different from paper, but it uses a different permutation in order to obtain the same calculation
+        emb = torch.cat((freqs, freqs), dim=-1)
+        self.register_buffer("cos_cached", emb.cos().to(dtype), persistent=False)
+        self.register_buffer("sin_cached", emb.sin().to(dtype), persistent=False)
+
+    def forward(self, x, seq_len=None):
+        # x: [bs, num_attention_heads, seq_len, head_size]
+        if seq_len > self.max_seq_len_cached:
+            self._set_cos_sin_cache(seq_len=seq_len, device=x.device, dtype=x.dtype)
+
+        return (
+            self.cos_cached[:seq_len].to(dtype=x.dtype),
+            self.sin_cached[:seq_len].to(dtype=x.dtype),
+        )
+
+
+class MolformerEmbeddings(nn.Module):
+    """Construct the embeddings from word embeddings."""
+
+    def __init__(self, config):
+        super().__init__()
+        self.word_embeddings = nn.Embedding(config.vocab_size, config.hidden_size, padding_idx=config.pad_token_id)
+        self.dropout = nn.Dropout(config.embedding_dropout_prob)
+
+    def forward(
+        self, input_ids: Optional[torch.LongTensor] = None, inputs_embeds: Optional[torch.FloatTensor] = None
+    ) -> torch.Tensor:
+        if inputs_embeds is None:
+            inputs_embeds = self.word_embeddings(input_ids)
+
+        embeddings = inputs_embeds
+        embeddings = self.dropout(embeddings)
+        return embeddings
+
+
+class MolformerFeatureMap(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.query_size = config.hidden_size // config.num_attention_heads
+        self.num_components = config.num_random_features
+        self.orthogonal_random_weights()
+        if isinstance(config.feature_map_kernel, str):
+            self.kernel = ACT2FN[config.feature_map_kernel]
+        else:
+            self.kernel = config.feature_map_kernel
+        self.deterministic = config.deterministic_eval
+
+    def orthogonal_random_weights(self, device=None):
+        # make sure query size evenly divides feature size (round up)
+        num_batches = math.ceil(self.num_components / self.query_size)
+
+        def orthogonal_batch(size):
+            block = torch.randn(size, size, device=device)
+            norms = torch.linalg.norm(block, dim=1).unsqueeze(0)
+            Q, _ = torch.linalg.qr(block)
+            return Q * norms
+
+        random_weights = torch.cat([orthogonal_batch(self.query_size) for _ in range(num_batches)], dim=1)
+        random_weights = random_weights[:, : self.num_components]
+        self.register_buffer("weight", random_weights)
+
+    def forward(self, query, key, redraw=True):
+        if (not self.deterministic or self.training) and redraw is not False:
+            self.orthogonal_random_weights(query.device)
+        # generalized random fourier features
+        query = torch.matmul(query, self.weight)
+        key = torch.matmul(key, self.weight)
+        return self.kernel(query), self.kernel(key)
+
+
+class MolformerSelfAttention(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        if config.hidden_size % config.num_attention_heads != 0 and not hasattr(config, "embedding_size"):
+            raise ValueError(
+                f"The hidden size ({config.hidden_size}) is not a multiple of the number of attention "
+                f"heads ({config.num_attention_heads})"
+            )
+
+        self.num_attention_heads = config.num_attention_heads
+        self.attention_head_size = int(config.hidden_size / config.num_attention_heads)
+        self.all_head_size = self.num_attention_heads * self.attention_head_size
+
+        self.query = nn.Linear(config.hidden_size, self.all_head_size)
+        self.key = nn.Linear(config.hidden_size, self.all_head_size)
+        self.value = nn.Linear(config.hidden_size, self.all_head_size)
+
+        self.eps = config.linear_attention_eps
+
+        self.rotary_embeddings = MolformerRotaryEmbedding(
+            dim=self.attention_head_size, max_position_embeddings=config.max_position_embeddings
+        )
+        self.feature_map = MolformerFeatureMap(config)
+
+        self.is_decoder = config.is_decoder
+
+    # Copied from transformers.models.bert.modeling_bert.BertSelfAttention.transpose_for_scores
+    def transpose_for_scores(self, x: torch.Tensor) -> torch.Tensor:
+        new_x_shape = x.size()[:-1] + (self.num_attention_heads, self.attention_head_size)
+        x = x.view(new_x_shape)
+        return x.permute(0, 2, 1, 3)
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        encoder_hidden_states: Optional[torch.FloatTensor] = None,
+        encoder_attention_mask: Optional[torch.FloatTensor] = None,
+        past_key_value: Optional[Tuple[Tuple[torch.FloatTensor]]] = None,
+        output_attentions: Optional[bool] = False,
+        use_cache: Optional[bool] = None,
+    ) -> Tuple[torch.Tensor]:
+        query_layer = self.transpose_for_scores(self.query(hidden_states))
+
+        # If this is instantiated as a cross-attention module, the keys
+        # and values come from an encoder; the attention mask needs to be
+        # such that the encoder's padding tokens are not attended to.
+        is_cross_attention = encoder_hidden_states is not None
+
+        if is_cross_attention and past_key_value is not None:
+            # reuse k,v, cross_attentions
+            key_layer = past_key_value[0]
+            value_layer = past_key_value[1]
+            attention_mask = encoder_attention_mask
+        elif is_cross_attention:
+            key_layer = self.transpose_for_scores(self.key(encoder_hidden_states))
+            value_layer = self.transpose_for_scores(self.value(encoder_hidden_states))
+            # save Tuple(torch.Tensor, torch.Tensor) of all cross attention key/value_states.
+            # Further calls to cross_attention layer can then reuse all cross-attention key/value_states
+            past_key_value = (key_layer, value_layer)
+            attention_mask = encoder_attention_mask
+        else:
+            key_layer = self.transpose_for_scores(self.key(hidden_states))
+            value_layer = self.transpose_for_scores(self.value(hidden_states))
+
+            kv_seq_len = key_layer.shape[-2]
+            if past_key_value is not None:
+                kv_seq_len += past_key_value[0].shape[-2]
+
+            cos, sin = self.rotary_embeddings(value_layer, seq_len=kv_seq_len)
+            query_layer, key_layer = apply_rotary_pos_emb(query_layer, key_layer, cos, sin, position_ids)
+            # Apply the feature map to the queries and keys
+            query_layer, key_layer = self.feature_map(query_layer, key_layer, redraw=past_key_value is None)
+
+        if attention_mask is not None:
+            # since we don't use softmax, we need to reconvert this mask to 1/0
+            attention_mask = (attention_mask == 0).to(attention_mask.dtype)
+            # separate original mask from causal mask
+            per_query_attn = attention_mask[:, 0, -1]
+            if self.is_decoder and not is_cross_attention:
+                batch_size, _, seq_length, _ = key_layer.shape
+                per_query_extended = MolformerPreTrainedModel.create_extended_attention_mask_for_decoder(
+                    (batch_size, seq_length), per_query_attn
+                )
+            else:
+                per_query_extended = per_query_attn[:, None, None, :]
+            if not torch.equal(attention_mask, per_query_extended):
+                raise ValueError(
+                    "MolformerSelfAttention does not support arbitrary 3D attention. attention_mask must be 2D (i.e., [batch size, sequence length])"
+                )
+
+            key_layer = key_layer * per_query_attn[:, None, -key_layer.shape[2] :, None]
+
+        if self.is_decoder and not is_cross_attention:
+            # causal linear attention
+            if use_cache:
+                seq_length = key_layer.shape[2]
+                key_value_outer = torch.einsum("bhlr,bhld->bhlrd", key_layer, value_layer)
+                if seq_length > 1:
+                    key_value_outer = key_value_outer.cumsum(dim=2)
+                    key_layer = key_layer.cumsum(dim=2)
+                if past_key_value is not None:
+                    key_layer = key_layer + past_key_value[0][:, :, [-1]]
+                    key_value_outer = key_value_outer + past_key_value[1]
+                    seq_length += past_key_value[0].shape[-2]
+                # NOTE: query and key/value length must match (i.e., square attention matrix)
+                context_layer = torch.einsum("bhlr,bhlrd->bhld", query_layer, key_value_outer)
+                # store running sum of key_layer, key_value_outer, and seq_length -- constant memory!
+                # further calls to uni-directional self-attention can sum previous decoder states with current states
+                past_key_value = (key_layer[:, :, [-1]].expand(-1, -1, seq_length, -1), key_value_outer[:, :, [-1]])
+            else:
+                try:
+                    from fast_transformers.causal_product import causal_dot_product
+                    context_layer = causal_dot_product(query_layer, key_layer, value_layer)
+                except ImportError as e:
+                    logger.warning(f"{e}: Falling back to (slow) pytorch implementation.")
+                    key_value_outer = torch.einsum("bhlr,bhld->bhlrd", key_layer, value_layer)
+                    key_value_outer = key_value_outer.cumsum(dim=2)
+                    context_layer = torch.einsum("bhlr,bhlrd->bhld", query_layer, key_value_outer)
+                key_layer = key_layer.cumsum(dim=2)
+            norm = torch.einsum("bhlr,bhlr->bhl", query_layer, key_layer).unsqueeze(-1).clamp(min=self.eps)
+            context_layer = context_layer / norm
+        else:
+            # linear attention
+            key_value = torch.matmul(key_layer.transpose(-1, -2), value_layer)
+            norm = torch.matmul(query_layer, key_layer.sum(dim=-2).unsqueeze(-1)).clamp(min=self.eps)
+            context_layer = torch.matmul(query_layer, key_value) / norm
+
+        if head_mask is not None:
+            context_layer = context_layer * head_mask
+
+        if output_attentions:
+            logger.warning(
+                "Outputting attentions in linear attention negates the efficiency gains! Only use for visualization/debugging."
+            )
+            attention_scores = torch.matmul(query_layer, key_layer.transpose(-1, -2))
+            if attention_mask is not None:
+                attention_scores = attention_scores * attention_mask
+            attention_probs = nn.functional.normalize(attention_scores, p=1, dim=-1, eps=self.eps)
+            if head_mask is not None:
+                attention_probs = attention_probs * head_mask
+            # recompute context_layer for grad
+            context_layer = torch.matmul(attention_probs, value_layer)
+
+        context_layer = context_layer.permute(0, 2, 1, 3).contiguous()
+        new_context_layer_shape = context_layer.size()[:-2] + (self.all_head_size,)
+        context_layer = context_layer.view(*new_context_layer_shape)
+
+        outputs = (context_layer, attention_probs) if output_attentions else (context_layer,)
+
+        if self.is_decoder:
+            outputs = outputs + (past_key_value,)
+        return outputs
+
+
+# Copied from transformers.models.bert.modeling_bert.BertSelfOutput
+class MolformerSelfOutput(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+
+    def forward(self, hidden_states: torch.Tensor, input_tensor: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.dropout(hidden_states)
+        hidden_states = self.LayerNorm(hidden_states + input_tensor)
+        return hidden_states
+
+
+class MolformerAttention(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.self = MolformerSelfAttention(config)
+        self.output = MolformerSelfOutput(config)
+        self.pruned_heads = set()
+
+    # Copied from transformers.models.bert.modeling_bert.BertAttention.prune_heads
+    def prune_heads(self, heads):
+        if len(heads) == 0:
+            return
+        heads, index = find_pruneable_heads_and_indices(
+            heads, self.self.num_attention_heads, self.self.attention_head_size, self.pruned_heads
+        )
+
+        # Prune linear layers
+        self.self.query = prune_linear_layer(self.self.query, index)
+        self.self.key = prune_linear_layer(self.self.key, index)
+        self.self.value = prune_linear_layer(self.self.value, index)
+        self.output.dense = prune_linear_layer(self.output.dense, index, dim=1)
+
+        # Update hyper params and store pruned heads
+        self.self.num_attention_heads = self.self.num_attention_heads - len(heads)
+        self.self.all_head_size = self.self.attention_head_size * self.self.num_attention_heads
+        self.pruned_heads = self.pruned_heads.union(heads)
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        encoder_hidden_states: Optional[torch.FloatTensor] = None,
+        encoder_attention_mask: Optional[torch.FloatTensor] = None,
+        past_key_value: Optional[Tuple[Tuple[torch.FloatTensor]]] = None,
+        output_attentions: Optional[bool] = False,
+        use_cache: Optional[bool] = None,
+    ) -> Tuple[torch.Tensor]:
+        self_outputs = self.self(
+            hidden_states,
+            attention_mask,
+            position_ids,
+            head_mask,
+            encoder_hidden_states,
+            encoder_attention_mask,
+            past_key_value,
+            output_attentions,
+            use_cache,
+        )
+        attention_output = self.output(self_outputs[0], hidden_states)
+        outputs = (attention_output,) + self_outputs[1:]  # add attentions if we output them
+        return outputs
+
+
+# Copied from transformers.models.bert.modeling_bert.BertIntermediate
+class MolformerIntermediate(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.intermediate_size)
+        if isinstance(config.hidden_act, str):
+            self.intermediate_act_fn = ACT2FN[config.hidden_act]
+        else:
+            self.intermediate_act_fn = config.hidden_act
+
+    def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.intermediate_act_fn(hidden_states)
+        return hidden_states
+
+
+# Copied from transformers.models.bert.modeling_bert.BertOutput
+class MolformerOutput(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.intermediate_size, config.hidden_size)
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.dropout = nn.Dropout(config.hidden_dropout_prob)
+
+    def forward(self, hidden_states: torch.Tensor, input_tensor: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.dropout(hidden_states)
+        hidden_states = self.LayerNorm(hidden_states + input_tensor)
+        return hidden_states
+
+
+class MolformerLayer(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.chunk_size_feed_forward = config.chunk_size_feed_forward
+        self.seq_len_dim = 1
+        self.attention = MolformerAttention(config)
+        self.is_decoder = config.is_decoder
+        self.add_cross_attention = config.add_cross_attention
+        if self.add_cross_attention:
+            if not self.is_decoder:
+                raise ValueError(f"{self} should be used as a decoder model if cross attention is added")
+            self.crossattention = MolformerAttention(config)
+        self.intermediate = MolformerIntermediate(config)
+        self.output = MolformerOutput(config)
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        encoder_hidden_states: Optional[torch.FloatTensor] = None,
+        encoder_attention_mask: Optional[torch.FloatTensor] = None,
+        past_key_value: Optional[Tuple[Tuple[torch.FloatTensor]]] = None,
+        output_attentions: Optional[bool] = False,
+        use_cache: Optional[bool] = None,
+    ) -> Tuple[torch.Tensor]:
+        # decoder uni-directional self-attention cached key/values tuple is at positions 1,2
+        self_attn_past_key_value = past_key_value[:2] if past_key_value is not None else None
+        self_attention_outputs = self.attention(
+            hidden_states,
+            attention_mask,
+            position_ids,
+            head_mask,
+            output_attentions=output_attentions,
+            past_key_value=self_attn_past_key_value,
+            use_cache=use_cache,
+        )
+        attention_output = self_attention_outputs[0]
+
+        # if decoder, the last output is tuple of self-attn cache
+        if self.is_decoder:
+            outputs = self_attention_outputs[1:-1]
+            present_key_value = self_attention_outputs[-1]
+        else:
+            outputs = self_attention_outputs[1:]  # add self attentions if we output attention weights
+
+        cross_attn_present_key_value = None
+        if self.is_decoder and encoder_hidden_states is not None:
+            if not hasattr(self, "crossattention"):
+                raise ValueError(
+                    f"If `encoder_hidden_states` are passed, {self} has to be instantiated with cross-attention layers"
+                    " by setting `config.add_cross_attention=True`"
+                )
+
+            # cross_attn cached key/values tuple is at positions 3,4 of past_key_value tuple
+            cross_attn_past_key_value = past_key_value[-2:] if past_key_value is not None else None
+            cross_attention_outputs = self.crossattention(
+                attention_output,
+                attention_mask,
+                position_ids,
+                head_mask,
+                encoder_hidden_states,
+                encoder_attention_mask,
+                cross_attn_past_key_value,
+                output_attentions,
+                use_cache,
+            )
+            attention_output = cross_attention_outputs[0]
+            outputs = outputs + cross_attention_outputs[1:-1]  # add cross attentions if we output attention weights
+
+            # add cross-attn cache to positions 3,4 of present_key_value tuple
+            cross_attn_present_key_value = cross_attention_outputs[-1]
+            present_key_value = present_key_value + cross_attn_present_key_value
+
+        layer_output = apply_chunking_to_forward(
+            self.feed_forward_chunk, self.chunk_size_feed_forward, self.seq_len_dim, attention_output
+        )
+        outputs = (layer_output,) + outputs
+
+        # if decoder, return the attn key/values as the last output
+        if self.is_decoder:
+            outputs = outputs + (present_key_value,)
+
+        return outputs
+
+    def feed_forward_chunk(self, attention_output):
+        intermediate_output = self.intermediate(attention_output)
+        layer_output = self.output(intermediate_output, attention_output)
+        return layer_output
+
+
+class MolformerEncoder(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+        self.layer = nn.ModuleList([MolformerLayer(config) for _ in range(config.num_hidden_layers)])
+        self.gradient_checkpointing = False
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        encoder_hidden_states: Optional[torch.FloatTensor] = None,
+        encoder_attention_mask: Optional[torch.FloatTensor] = None,
+        past_key_values: Optional[Tuple[Tuple[torch.FloatTensor]]] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = False,
+        output_hidden_states: Optional[bool] = False,
+        return_dict: Optional[bool] = True,
+    ) -> Union[Tuple[torch.Tensor], BaseModelOutputWithPastAndCrossAttentions]:
+        all_hidden_states = () if output_hidden_states else None
+        all_self_attentions = () if output_attentions else None
+        all_cross_attentions = () if output_attentions and self.config.add_cross_attention else None
+
+        if self.gradient_checkpointing and self.training:
+            if use_cache:
+                logger.warning_once(
+                    "`use_cache=True` is incompatible with gradient checkpointing. Setting `use_cache=False`..."
+                )
+                use_cache = False
+
+        next_decoder_cache = () if use_cache else None
+        for i, layer_module in enumerate(self.layer):
+            if output_hidden_states:
+                all_hidden_states = all_hidden_states + (hidden_states,)
+
+            layer_head_mask = head_mask[i] if head_mask is not None else None
+            past_key_value = past_key_values[i] if past_key_values is not None else None
+
+            if self.gradient_checkpointing and self.training:
+
+                def create_custom_forward(module):
+                    def custom_forward(*inputs):
+                        return module(*inputs, past_key_value, output_attentions)
+
+                    return custom_forward
+
+                layer_outputs = torch.utils.checkpoint.checkpoint(
+                    create_custom_forward(layer_module),
+                    hidden_states,
+                    attention_mask,
+                    position_ids,
+                    layer_head_mask,
+                    encoder_hidden_states,
+                    encoder_attention_mask,
+                )
+            else:
+                layer_outputs = layer_module(
+                    hidden_states,
+                    attention_mask,
+                    position_ids,
+                    layer_head_mask,
+                    encoder_hidden_states,
+                    encoder_attention_mask,
+                    past_key_value,
+                    output_attentions,
+                    use_cache,
+                )
+
+            hidden_states = layer_outputs[0]
+            if use_cache:
+                next_decoder_cache += (layer_outputs[-1],)
+            if output_attentions:
+                all_self_attentions = all_self_attentions + (layer_outputs[1],)
+                if self.config.add_cross_attention:
+                    all_cross_attentions = all_cross_attentions + (layer_outputs[2],)
+
+        if output_hidden_states:
+            all_hidden_states = all_hidden_states + (hidden_states,)
+
+        if not return_dict:
+            return tuple(
+                v
+                for v in [
+                    hidden_states,
+                    next_decoder_cache,
+                    all_hidden_states,
+                    all_self_attentions,
+                    all_cross_attentions,
+                ]
+                if v is not None
+            )
+        return BaseModelOutputWithPastAndCrossAttentions(
+            last_hidden_state=hidden_states,
+            past_key_values=next_decoder_cache,
+            hidden_states=all_hidden_states,
+            attentions=all_self_attentions,
+            cross_attentions=all_cross_attentions,
+        )
+
+
+# Copied from transformers.models.bert.modeling_bert.BertPredictionHeadTransform
+class MolformerPredictionHeadTransform(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.dense = nn.Linear(config.hidden_size, config.hidden_size)
+        if isinstance(config.hidden_act, str):
+            self.transform_act_fn = ACT2FN[config.hidden_act]
+        else:
+            self.transform_act_fn = config.hidden_act
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+
+    def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.dense(hidden_states)
+        hidden_states = self.transform_act_fn(hidden_states)
+        hidden_states = self.LayerNorm(hidden_states)
+        return hidden_states
+
+
+class MolformerLMPredictionHead(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.transform = MolformerPredictionHeadTransform(config)
+        self.decoder = nn.Linear(config.hidden_size, config.vocab_size, bias=False)
+
+    def forward(self, hidden_states):
+        hidden_states = self.transform(hidden_states)
+        hidden_states = self.decoder(hidden_states)
+        return hidden_states
+
+
+# Copied from transformers.models.roberta.modeling_roberta.RobertaPreTrainedModel with Roberta->Molformer,roberta->molformer
+class MolformerPreTrainedModel(PreTrainedModel):
+    """
+    An abstract class to handle weights initialization and a simple interface for downloading and loading pretrained
+    models.
+    """
+
+    config_class = MolformerConfig
+    base_model_prefix = "molformer"
+    supports_gradient_checkpointing = True
+    _no_split_modules = ["MolformerEmbeddings", "MolformerSelfAttention"]
+
+    # Copied from transformers.models.bert.modeling_bert.BertPreTrainedModel._init_weights
+    def _init_weights(self, module):
+        """Initialize the weights"""
+        if isinstance(module, nn.Linear):
+            # Slightly different from the TF version which uses truncated_normal for initialization
+            # cf https://github.com/pytorch/pytorch/pull/5617
+            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
+            if module.bias is not None:
+                module.bias.data.zero_()
+        elif isinstance(module, nn.Embedding):
+            module.weight.data.normal_(mean=0.0, std=self.config.initializer_range)
+            if module.padding_idx is not None:
+                module.weight.data[module.padding_idx].zero_()
+        elif isinstance(module, nn.LayerNorm):
+            module.bias.data.zero_()
+            module.weight.data.fill_(1.0)
+
+    def _set_gradient_checkpointing(self, module, value=False):
+        if isinstance(module, MolformerEncoder):
+            module.gradient_checkpointing = value
+
+
+def masked_avg_pool1d(hidden_states, attention_mask, eps=1e-9):
+    attention_mask = attention_mask.unsqueeze(-1).expand_as(hidden_states).float()
+    sum_embeddings = torch.sum(hidden_states * attention_mask, dim=1)
+    sum_mask = torch.clamp(attention_mask.sum(dim=1), min=eps)
+    embedding = sum_embeddings / sum_mask
+    return embedding
+
+
+MOLFORMER_START_DOCSTRING = r"""
+    This model is a PyTorch [torch.nn.Module](https://pytorch.org/docs/stable/nn.html#torch.nn.Module) sub-class. Use
+    it as a regular PyTorch Module and refer to the PyTorch documentation for all matter related to general usage and
+    behavior.
+
+    Parameters:
+        config ([`MolformerConfig`]): Model configuration class with all the parameters of the model.
+            Initializing with a config file does not load the weights associated with the model, only the
+            configuration. Check out the [`~PreTrainedModel.from_pretrained`] method to load the model weights.
+"""
+
+MOLFORMER_INPUTS_DOCSTRING = r"""
+    Args:
+        input_ids (`torch.LongTensor` of shape `({0})`):
+            Indices of input sequence tokens in the vocabulary.
+
+            Indices can be obtained using [`AutoTokenizer`]. See [`PreTrainedTokenizer.encode`] and
+            [`PreTrainedTokenizer.__call__`] for details.
+
+            [What are input IDs?](../glossary#input-ids)
+        attention_mask (`torch.FloatTensor` of shape `({0})`, *optional*):
+            Mask to avoid performing attention on padding token indices. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+
+            [What are attention masks?](../glossary#attention-mask)
+        position_ids (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Indices of positions of each input sequence tokens in the position embeddings. Selected in the range `[0,
+            config.n_positions - 1]`.
+
+            [What are position IDs?](../glossary#position-ids)
+        head_mask (`torch.FloatTensor` of shape `(num_heads,)` or `(num_layers, num_heads)`, *optional*):
+            Mask to nullify selected heads of the self-attention modules. Mask values selected in `[0, 1]`:
+
+            - 1 indicates the head is **not masked**,
+            - 0 indicates the head is **masked**.
+
+        inputs_embeds (`torch.FloatTensor` of shape `({0}, hidden_size)`, *optional*):
+            Optionally, instead of passing `input_ids` you can choose to directly pass an embedded representation. This
+            is useful if you want more control over how to convert *input_ids* indices into associated vectors than the
+            model's internal embedding lookup matrix.
+        output_attentions (`bool`, *optional*):
+            Whether or not to return the attentions tensors of all attention layers. See `attentions` under returned
+            tensors for more detail.
+        output_hidden_states (`bool`, *optional*):
+            Whether or not to return the hidden states of all layers. See `hidden_states` under returned tensors for
+            more detail.
+        return_dict (`bool`, *optional*):
+            Whether or not to return a [`~utils.ModelOutput`] instead of a plain tuple.
+"""
+
+
+@add_start_docstrings(
+    "The bare Molformer Model transformer outputting raw hidden-states without any specific head on top.",
+    MOLFORMER_START_DOCSTRING,
+)
+class MolformerModel(MolformerPreTrainedModel):
+    """
+
+    The model can behave as an encoder (with only self-attention) as well as a decoder, in which case a layer of
+    cross-attention is added between the self-attention layers, following the architecture described in [Attention is
+    all you need](https://arxiv.org/abs/1706.03762) by Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit,
+    Llion Jones, Aidan N. Gomez, Lukasz Kaiser and Illia Polosukhin.
+
+    To behave as an decoder the model needs to be initialized with the `is_decoder` argument of the configuration set
+    to `True`. To be used in a Seq2Seq model, the model needs to initialized with both `is_decoder` argument and
+    `add_cross_attention` set to `True`; an `encoder_hidden_states` is then expected as an input to the forward pass.
+    """
+
+    def __init__(self, config, add_pooling_layer=True):
+        super().__init__(config)
+        self.config = config
+
+        self.embeddings = MolformerEmbeddings(config)
+        self.encoder = MolformerEncoder(config)
+
+        self.LayerNorm = nn.LayerNorm(config.hidden_size, eps=config.layer_norm_eps)
+        self.pooler = masked_avg_pool1d if add_pooling_layer else None
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_input_embeddings(self):
+        return self.embeddings.word_embeddings
+
+    def set_input_embeddings(self, value):
+        self.embeddings.word_embeddings = value
+
+    def _prune_heads(self, heads_to_prune):
+        """
+        Prunes heads of the model. heads_to_prune: dict of {layer_num: list of heads to prune in this layer} See base
+        class PreTrainedModel
+        """
+        for layer, heads in heads_to_prune.items():
+            self.encoder.layer[layer].attention.prune_heads(heads)
+
+    @add_start_docstrings_to_model_forward(MOLFORMER_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @add_code_sample_docstrings(
+        checkpoint=_CHECKPOINT_FOR_DOC,
+        output_type=BaseModelOutputWithPoolingAndCrossAttentions,
+        config_class=_CONFIG_FOR_DOC,
+    )
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        encoder_hidden_states: Optional[torch.FloatTensor] = None,
+        encoder_attention_mask: Optional[torch.FloatTensor] = None,
+        past_key_values: Optional[Tuple[Tuple[torch.FloatTensor]]] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[BaseModelOutputWithPoolingAndCrossAttentions, Tuple[torch.Tensor]]:
+        r"""
+        encoder_hidden_states  (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
+            Sequence of hidden-states at the output of the last layer of the encoder. Used in the cross-attention if
+            the model is configured as a decoder.
+        encoder_attention_mask (`torch.FloatTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Mask to avoid performing attention on the padding token indices of the encoder input. This mask is used in
+            the cross-attention if the model is configured as a decoder. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+        past_key_values (`tuple(tuple(torch.FloatTensor))` of length `config.n_layers` with each tuple having 4 tensors of shape `(batch_size, num_heads, sequence_length - 1, embed_size_per_head)`):
+            Contains precomputed key and value hidden states of the attention blocks. Can be used to speed up decoding.
+            If `past_key_values` are used, the user can optionally input only the last `decoder_input_ids` (those that
+            don't have their past key value states given to this model) of shape `(batch_size, 1)` instead of all
+            `decoder_input_ids` of shape `(batch_size, sequence_length)`.
+        use_cache (`bool`, *optional*):
+            If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding (see
+            `past_key_values`).
+        """
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        if self.config.is_decoder:
+            use_cache = use_cache if use_cache is not None else self.config.use_cache
+        else:
+            use_cache = False
+
+        if input_ids is not None and inputs_embeds is not None:
+            raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
+        elif input_ids is not None:
+            self.warn_if_padding_and_no_attention_mask(input_ids, attention_mask)
+            input_shape = input_ids.size()
+        elif inputs_embeds is not None:
+            input_shape = inputs_embeds.size()[:-1]
+        else:
+            raise ValueError("You have to specify either input_ids or inputs_embeds")
+
+        batch_size, seq_length = input_shape
+        device = input_ids.device if input_ids is not None else inputs_embeds.device
+
+        # past_key_values_length
+        past_key_values_length = past_key_values[0][0].shape[2] if past_key_values is not None else 0
+
+        if position_ids is None:
+            position_ids = torch.arange(
+                past_key_values_length, seq_length + past_key_values_length, dtype=torch.long, device=device
+            )
+            position_ids = position_ids.unsqueeze(0).view(-1, seq_length)
+        else:
+            position_ids = position_ids.view(-1, seq_length).long()
+
+        if attention_mask is None:
+            attention_mask = torch.ones(((batch_size, seq_length + past_key_values_length)), device=device)
+
+        # We can provide a self-attention mask of dimensions [batch_size, from_seq_length, to_seq_length]
+        # ourselves in which case we just need to make it broadcastable to all heads.
+        extended_attention_mask: torch.Tensor = self.get_extended_attention_mask(attention_mask, input_shape)
+
+        # If a 2D or 3D attention mask is provided for the cross-attention
+        # we need to make broadcastable to [batch_size, num_heads, seq_length, seq_length]
+        if self.config.is_decoder and encoder_hidden_states is not None:
+            encoder_batch_size, encoder_sequence_length, _ = encoder_hidden_states.size()
+            encoder_hidden_shape = (encoder_batch_size, encoder_sequence_length)
+            if encoder_attention_mask is None:
+                encoder_attention_mask = torch.ones(encoder_hidden_shape, device=device)
+            encoder_extended_attention_mask = self.invert_attention_mask(encoder_attention_mask)
+        else:
+            encoder_extended_attention_mask = None
+
+        # Prepare head mask if needed
+        # 1.0 in head_mask indicate we keep the head
+        # attention_probs has shape bsz x n_heads x N x N
+        # input head_mask has shape [num_heads] or [num_hidden_layers x num_heads]
+        # and head_mask is converted to shape [num_hidden_layers x batch x num_heads x seq_length x seq_length]
+        head_mask = self.get_head_mask(head_mask, self.config.num_hidden_layers)
+
+        embedding_output = self.embeddings(input_ids=input_ids, inputs_embeds=inputs_embeds)
+
+        encoder_outputs = self.encoder(
+            embedding_output,
+            attention_mask=extended_attention_mask,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            encoder_hidden_states=encoder_hidden_states,
+            encoder_attention_mask=encoder_extended_attention_mask,
+            past_key_values=past_key_values,
+            use_cache=use_cache,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+        sequence_output = encoder_outputs[0]
+        sequence_output = self.LayerNorm(sequence_output)
+        pooled_output = self.pooler(sequence_output, attention_mask) if self.pooler is not None else None
+
+        if not return_dict:
+            return (sequence_output, pooled_output) + encoder_outputs[1:]
+
+        return BaseModelOutputWithPoolingAndCrossAttentions(
+            last_hidden_state=sequence_output,
+            pooler_output=pooled_output,
+            past_key_values=encoder_outputs.past_key_values,
+            hidden_states=encoder_outputs.hidden_states,
+            attentions=encoder_outputs.attentions,
+            cross_attentions=encoder_outputs.cross_attentions,
+        )
+
+
+@add_start_docstrings(
+    """Molformer Model with a `language modeling` head on top for CLM fine-tuning.""", MOLFORMER_START_DOCSTRING
+)
+class MolformerForCausalLM(MolformerPreTrainedModel):
+    _tied_weights_keys = ["lm_head.decoder.weight"]
+
+    # Copied from transformers.models.roberta.modeling_roberta.RobertaForCausalLM.__init__ with Roberta->Molformer,roberta->molformer,LMHeadModel->ForCausalLM,LMHead->LMPredictionHead
+    def __init__(self, config):
+        super().__init__(config)
+
+        if not config.is_decoder:
+            logger.warning("If you want to use `MolformerForCausalLM` as a standalone, add `is_decoder=True.`")
+
+        self.molformer = MolformerModel(config, add_pooling_layer=False)
+        self.lm_head = MolformerLMPredictionHead(config)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_output_embeddings(self):
+        return self.lm_head.decoder
+
+    def set_output_embeddings(self, new_embeddings):
+        self.lm_head.decoder = new_embeddings
+
+    @add_start_docstrings_to_model_forward(MOLFORMER_INPUTS_DOCSTRING.format("batch_size, sequence_length"))
+    @replace_return_docstrings(output_type=CausalLMOutputWithCrossAttentions, config_class=_CONFIG_FOR_DOC)
+    def forward(
+        self,
+        input_ids: Optional[torch.LongTensor] = None,
+        attention_mask: Optional[torch.FloatTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        head_mask: Optional[torch.FloatTensor] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        encoder_hidden_states: Optional[torch.FloatTensor] = None,
+        encoder_attention_mask: Optional[torch.FloatTensor] = None,
+        labels: Optional[torch.LongTensor] = None,
+        past_key_values: Tuple[Tuple[torch.FloatTensor]] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple[torch.Tensor], CausalLMOutputWithCrossAttentions]:
+        r"""
+        encoder_hidden_states  (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
+            Sequence of hidden-states at the output of the last layer of the encoder. Used in the cross-attention if
+            the model is configured as a decoder.
+        encoder_attention_mask (`torch.FloatTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Mask to avoid performing attention on the padding token indices of the encoder input. This mask is used in
+            the cross-attention if the model is configured as a decoder. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+
+        labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Labels for computing the left-to-right language modeling loss (next word prediction). Indices should be in
+            `[-100, 0, ..., config.vocab_size]` (see `input_ids` docstring) Tokens with indices set to `-100` are
+            ignored (masked), the loss is only computed for the tokens with labels in `[0, ..., config.vocab_size]`
+        past_key_values (`tuple(tuple(torch.FloatTensor))` of length `config.n_layers` with each tuple having 4 tensors of shape `(batch_size, num_heads, sequence_length - 1, embed_size_per_head)`):
+            Contains precomputed key and value hidden states of the attention blocks. Can be used to speed up decoding.
+
+            If `past_key_values` are used, the user can optionally input only the last `decoder_input_ids` (those that
+            don't have their past key value states given to this model) of shape `(batch_size, 1)` instead of all
+            `decoder_input_ids` of shape `(batch_size, sequence_length)`.
+        use_cache (`bool`, *optional*):
+            If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding (see
+            `past_key_values`).
+
+        Returns:
+        """
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+        if labels is not None:
+            use_cache = False
+
+        outputs = self.molformer(
+            input_ids,
+            attention_mask=attention_mask,
+            position_ids=position_ids,
+            head_mask=head_mask,
+            inputs_embeds=inputs_embeds,
+            encoder_hidden_states=encoder_hidden_states,
+            encoder_attention_mask=encoder_attention_mask,
+            past_key_values=past_key_values,
+            use_cache=use_cache,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        sequence_output = outputs[0]
+        prediction_scores = self.lm_head(sequence_output)
+
+        lm_loss = None
+        if labels is not None:
+            # move labels to correct device to enable model parallelism
+            labels = labels.to(prediction_scores.device)
+            # we are doing next-token prediction; shift prediction scores and input ids by one
+            shifted_prediction_scores = prediction_scores[:, :-1, :].contiguous()
+            labels = labels[:, 1:].contiguous()
+            loss_fct = CrossEntropyLoss()
+            lm_loss = loss_fct(shifted_prediction_scores.view(-1, self.config.vocab_size), labels.view(-1))
+
+        if not return_dict:
+            output = (prediction_scores,) + outputs[2:]
+            return ((lm_loss,) + output) if lm_loss is not None else output
+
+        return CausalLMOutputWithCrossAttentions(
+            loss=lm_loss,
+            logits=prediction_scores,
+            past_key_values=outputs.past_key_values,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+            cross_attentions=outputs.cross_attentions,
+        )
+
+    # Copied from transformers.models.llama.modeling_llama.LlamaForCausalLM.prepare_inputs_for_generation
+    def prepare_inputs_for_generation(
+        self, input_ids, past_key_values=None, attention_mask=None, inputs_embeds=None, **kwargs
+    ):
+        if past_key_values is not None:
+            past_length = past_key_values[0][0].shape[2]
+
+            # Some generation methods already pass only the last input ID
+            if input_ids.shape[1] > past_length:
+                remove_prefix_length = past_length
+            else:
+                # Default to old behavior: keep only final ID
+                remove_prefix_length = input_ids.shape[1] - 1
+
+            input_ids = input_ids[:, remove_prefix_length:]
+
+        position_ids = kwargs.get("position_ids", None)
+        if attention_mask is not None and position_ids is None:
+            # create position_ids on the fly for batch generation
+            position_ids = attention_mask.long().cumsum(-1) - 1
+            position_ids.masked_fill_(attention_mask == 0, 1)
+            if past_key_values:
+                position_ids = position_ids[:, -input_ids.shape[1] :]
+
+        # if `inputs_embeds` are passed, we only want to use them in the 1st generation step
+        if inputs_embeds is not None and past_key_values is None:
+            model_inputs = {"inputs_embeds": inputs_embeds}
+        else:
+            model_inputs = {"input_ids": input_ids}
+
+        model_inputs.update(
+            {
+                "position_ids": position_ids,
+                "past_key_values": past_key_values,
+                "use_cache": kwargs.get("use_cache"),
+                "attention_mask": attention_mask,
+            }
+        )
+        return model_inputs
+
+    # Copied from transformers.models.bert.modeling_bert.BertLMHeadModel._reorder_cache
+    def _reorder_cache(self, past_key_values, beam_idx):
+        reordered_past = ()
+        for layer_past in past_key_values:
+            reordered_past += (
+                tuple(past_state.index_select(0, beam_idx.to(past_state.device)) for past_state in layer_past),
+            )
+        return reordered_past