Upload folder using huggingface_hub

README.md

@@ -0,0 +1,311 @@
+---
+datasets:
+- multimolecule/gencode
+language: rna
+library_name: multimolecule
+license: agpl-3.0
+mask_token: <mask>
+pipeline_tag: fill-mask
+tags:
+- Biology
+- RNA
+- 3' UTR
+widget:
+- example_title: Human GPI protein p137
+  mask_index: 11
+  mask_index_1based: 12
+  masked_char: A
+  output:
+  - label: AAACCA
+    score: 0.967819
+  - label: AUACCA
+    score: 0.01641
+  - label: AAAGCA
+    score: 0.006732
+  - label: UUACCA
+    score: 0.002422
+  - label: AAAGGA
+    score: 0.000995
+  pipeline_tag: fill-mask
+  sequence_type: 3' UTR
+  task: fill-mask
+  text: UUUUUAAAAGG<mask>UACCAAAUGCCUGCUGCUACCACCCUUUUCAAUUGCUAUGUUU
+---
+
+# 3UTRBERT
+
+Pre-trained model on 3’ untranslated region (3’UTR) using a masked language modeling (MLM) objective.
+
+## Disclaimer
+
+This is an UNOFFICIAL implementation of the [Deciphering 3’ UTR mediated gene regulation using interpretable deep representation learning](https://doi.org/10.1101/2023.09.08.556883) by Yuning Yang, Gen Li, et al.
+
+The OFFICIAL repository of 3UTRBERT is at [yangyn533/3UTRBERT](https://github.com/yangyn533/3UTRBERT).
+
+> [!TIP]
+> The MultiMolecule team has confirmed that the provided model and checkpoints are producing the same intermediate representations as the original implementation.
+
+**The team releasing 3UTRBERT did not write this model card for this model so this model card has been written by the MultiMolecule team.**
+
+## Model Details
+
+3UTRBERT is a [bert](https://huggingface.co/google-bert/bert-base-uncased)-style model pre-trained on a large corpus of 3’ untranslated regions (3’UTRs) in a self-supervised fashion. This means that the model was trained on the raw nucleotides of RNA sequences only, with an automatic process to generate inputs and labels from those texts. Please refer to the [Training Details](#training-details) section for more information on the training process.
+
+### Variants
+
+- **[multimolecule/utrbert-3mer](https://huggingface.co/multimolecule/utrbert-3mer)**: The 3UTRBERT model pre-trained on 3-mer data.
+- **[multimolecule/utrbert-4mer](https://huggingface.co/multimolecule/utrbert-4mer)**: The 3UTRBERT model pre-trained on 4-mer data.
+- **[multimolecule/utrbert-5mer](https://huggingface.co/multimolecule/utrbert-5mer)**: The 3UTRBERT model pre-trained on 5-mer data.
+- **[multimolecule/utrbert-6mer](https://huggingface.co/multimolecule/utrbert-6mer)**: The 3UTRBERT model pre-trained on 6-mer data.
+
+### Model Specification
+
+<table>
+<thead>
+  <tr>
+    <th>Variants</th>
+    <th>Num Layers</th>
+    <th>Hidden Size</th>
+    <th>Num Heads</th>
+    <th>Intermediate Size</th>
+    <th>Num Parameters (M)</th>
+    <th>FLOPs (G)</th>
+    <th>MACs (G)</th>
+    <th>Max Num Tokens</th>
+  </tr>
+</thead>
+<tbody>
+  <tr>
+    <td>3UTRBERT-3mer</td>
+    <td rowspan="4">12</td>
+    <td rowspan="4">768</td>
+    <td rowspan="4">12</td>
+    <td rowspan="4">3072</td>
+    <td>86.14</td>
+    <td rowspan="4">22.36</td>
+    <td rowspan="4">11.17</td>
+    <td rowspan="4">512</td>
+  </tr>
+  <tr>
+    <td>3UTRBERT-4mer</td>
+    <td>86.53</td>
+  </tr>
+  <tr>
+    <td>3UTRBERT-5mer</td>
+    <td>88.45</td>
+  </tr>
+  <tr>
+    <td>3UTRBERT-6mer</td>
+    <td>98.05</td>
+  </tr>
+</tbody>
+</table>
+
+### Links
+
+- **Code**: [multimolecule.utrbert](https://github.com/DLS5-Omics/multimolecule/tree/master/multimolecule/models/utrbert)
+- **Data**: [multimolecule/gencode-human](https://huggingface.co/datasets/multimolecule/gencode-human)
+- **Paper**: [Deciphering 3’ UTR mediated gene regulation using interpretable deep representation learning](https://doi.org/10.1101/2023.09.08.556883)
+- **Developed by**: Yuning Yang, Gen Li, Kuan Pang, Wuxinhao Cao, Xiangtao Li, Zhaolei Zhang
+- **Model type**: [BERT](https://huggingface.co/google-bert/bert-base-uncased) - [FlashAttention](https://huggingface.co/docs/text-generation-inference/en/conceptual/flash_attention)
+- **Original Repository**: [yangyn533/3UTRBERT](https://github.com/yangyn533/3UTRBERT)
+
+## Usage
+
+The model file depends on the [`multimolecule`](https://multimolecule.danling.org) library. You can install it using pip:
+
+```bash
+pip install multimolecule
+```
+
+### Direct Use
+
+#### Masked Language Modeling
+
+> [!WARNING]
+> Default transformers pipeline does not support K-mer tokenization.
+
+You can use this model directly with a pipeline for masked language modeling:
+
+```python
+import multimolecule  # you must import multimolecule to register models
+from transformers import pipeline
+
+predictor = pipeline("fill-mask", model="multimolecule/utrbert-3mer")
+output = predictor("gguc<mask><mask><mask>cugguuagaccagaucugagccu")[1]
+```
+
+### Downstream Use
+
+#### Extract Features
+
+Here is how to use this model to get the features of a given sequence in PyTorch:
+
+```python
+from multimolecule import RnaTokenizer, UtrBertModel
+
+
+tokenizer = RnaTokenizer.from_pretrained("multimolecule/utrbert-3mer")
+model = UtrBertModel.from_pretrained("multimolecule/utrbert-3mer")
+
+text = "UAGCUUAUCAGACUGAUGUUG"
+input = tokenizer(text, return_tensors="pt")
+
+output = model(**input)
+```
+
+#### Sequence Classification / Regression
+
+> [!NOTE]
+> This model is not fine-tuned for any specific task. You will need to fine-tune the model on a downstream task to use it for sequence classification or regression.
+
+Here is how to use this model as backbone to fine-tune for a sequence-level task in PyTorch:
+
+```python
+import torch
+from multimolecule import RnaTokenizer, UtrBertForSequencePrediction
+
+
+tokenizer = RnaTokenizer.from_pretrained("multimolecule/utrbert-3mer")
+model = UtrBertForSequencePrediction.from_pretrained("multimolecule/utrbert-3mer")
+
+text = "UAGCUUAUCAGACUGAUGUUG"
+input = tokenizer(text, return_tensors="pt")
+label = torch.tensor([1])
+
+output = model(**input, labels=label)
+```
+
+#### Token Classification / Regression
+
+> [!NOTE]
+> This model is not fine-tuned for any specific task. You will need to fine-tune the model on a downstream task to use it for token classification or regression.
+
+Here is how to use this model as backbone to fine-tune for a nucleotide-level task in PyTorch:
+
+```python
+import torch
+from multimolecule import RnaTokenizer, UtrBertForTokenPrediction
+
+
+tokenizer = RnaTokenizer.from_pretrained("multimolecule/utrbert-3mer")
+model = UtrBertForTokenPrediction.from_pretrained("multimolecule/utrbert-3mer")
+
+text = "UAGCUUAUCAGACUGAUGUUG"
+input = tokenizer(text, return_tensors="pt")
+label = torch.randint(2, (len(text), ))
+
+output = model(**input, labels=label)
+```
+
+#### Contact Classification / Regression
+
+> [!NOTE]
+> This model is not fine-tuned for any specific task. You will need to fine-tune the model on a downstream task to use it for contact classification or regression.
+
+Here is how to use this model as backbone to fine-tune for a contact-level task in PyTorch:
+
+```python
+import torch
+from multimolecule import RnaTokenizer, UtrBertForContactPrediction
+
+
+tokenizer = RnaTokenizer.from_pretrained("multimolecule/utrbert-3mer")
+model = UtrBertForContactPrediction.from_pretrained("multimolecule/utrbert-3mer")
+
+text = "UAGCUUAUCAGACUGAUGUUG"
+input = tokenizer(text, return_tensors="pt")
+label = torch.randint(2, (len(text), len(text)))
+
+output = model(**input, labels=label)
+```
+
+## Training Details
+
+3UTRBERT used Masked Language Modeling (MLM) as the pre-training objective: taking a sequence, the model randomly masks 15% of the tokens in the input then runs the entire masked sentence through the model and has to predict the masked tokens. This is comparable to the Cloze task in language modeling.
+
+### Training Data
+
+The 3UTRBERT model was pre-trained on human mRNA transcript sequences from [GENCODE](https://gencodegenes.org).
+GENCODE aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. The GENCODE release 40 used by this work contains 61,544 genes, and 246,624 transcripts.
+
+3UTRBERT collected the human mRNA transcript sequences from GENCODE, including 108,573 unique mRNA transcripts. Only the longest transcript of each gene was used in the pre-training process. 3UTRBERT only used the 3’ untranslated regions (3’UTRs) of the mRNA transcripts for pre-training to avoid codon constrains in the CDS region, and to reduce increased complexity of the entire mRNA transcripts. The average length of the 3’UTRs was 1,227 nucleotides, while the median length was 631 nucleotides. Each 3’UTR sequence was cut to non-overlapping patches of 510 nucleotides. The remaining sequences were padded to the same length.
+
+Note [`RnaTokenizer`][multimolecule.RnaTokenizer] will convert "T"s to "U"s for you, you may disable this behaviour by passing `replace_T_with_U=False`.
+
+### Training Procedure
+
+#### Preprocessing
+
+3UTRBERT used masked language modeling (MLM) as the pre-training objective. The masking procedure is similar to the one used in BERT:
+
+- 15% of the tokens are masked.
+- In 80% of the cases, the masked tokens are replaced by `<mask>`.
+- In 10% of the cases, the masked tokens are replaced by a random token (different) from the one they replace.
+- In the 10% remaining cases, the masked tokens are left as is.
+
+Since 3UTRBERT used k-mer tokenizer, it masks the entire k-mer instead of individual nucleotides to avoid information leakage.
+
+For example, if the k-mer is 3, the sequence `"UAGCGUAU"` will be tokenized as `["UAG", "AGC", "GCG", "CGU", "GUA", "UAU"]`. If the nucleotide `"C"` is masked, the adjacent tokens will also be masked, resulting `["UAG", "<mask>", "<mask>", "<mask>", "GUA", "UAU"]`.
+
+#### Pre-training
+
+The model was trained on 4 NVIDIA Quadro RTX 6000 GPUs with 24GiB memories.
+
+- Batch size: 128
+- Steps: 200,000
+- Optimizer: AdamW(β1=0.9, β2=0.98, e=1e-6)
+- Learning rate: 3e-4
+- Learning rate scheduler: Linear
+- Learning rate warm-up: 10,000 steps
+- Weight decay: 0.01
+
+## Citation
+
+```bibtex
+@article {yang2023deciphering,
+	author = {Yang, Yuning and Li, Gen and Pang, Kuan and Cao, Wuxinhao and Li, Xiangtao and Zhang, Zhaolei},
+	title = {Deciphering 3{\textquoteright} UTR mediated gene regulation using interpretable deep representation learning},
+	elocation-id = {2023.09.08.556883},
+	year = {2023},
+	doi = {10.1101/2023.09.08.556883},
+	publisher = {Cold Spring Harbor Laboratory},
+	abstract = {The 3{\textquoteright}untranslated regions (3{\textquoteright}UTRs) of messenger RNAs contain many important cis-regulatory elements that are under functional and evolutionary constraints. We hypothesize that these constraints are similar to grammars and syntaxes in human languages and can be modeled by advanced natural language models such as Transformers, which has been very effective in modeling protein sequence and structures. Here we describe 3UTRBERT, which implements an attention-based language model, i.e., Bidirectional Encoder Representations from Transformers (BERT). 3UTRBERT was pre-trained on aggregated 3{\textquoteright}UTR sequences of human mRNAs in a task-agnostic manner; the pre-trained model was then fine-tuned for specific downstream tasks such as predicting RBP binding sites, m6A RNA modification sites, and predicting RNA sub-cellular localizations. Benchmark results showed that 3UTRBERT generally outperformed other contemporary methods in each of these tasks. We also showed that the self-attention mechanism within 3UTRBERT allows direct visualization of the semantic relationship between sequence elements.Competing Interest StatementThe authors have declared no competing interest.},
+	URL = {https://www.biorxiv.org/content/early/2023/09/12/2023.09.08.556883},
+	eprint = {https://www.biorxiv.org/content/early/2023/09/12/2023.09.08.556883.full.pdf},
+	journal = {bioRxiv}
+}
+```
+
+> [!NOTE]
+> The artifacts distributed in this repository are part of the MultiMolecule project.
+> If you use MultiMolecule in your research, you must cite the MultiMolecule project as follows:
+
+```bibtex
+@software{chen_2024_12638419,
+  author    = {Chen, Zhiyuan and Zhu, Sophia Y.},
+  title     = {MultiMolecule},
+  doi       = {10.5281/zenodo.12638419},
+  publisher = {Zenodo},
+  url       = {https://doi.org/10.5281/zenodo.12638419},
+  year      = 2024,
+  month     = may,
+  day       = 4
+}
+```
+
+## Contact
+
+Please use GitHub issues of [MultiMolecule](https://github.com/DLS5-Omics/multimolecule/issues) for any questions or comments on the model card.
+
+Please contact the authors of the [3UTRBERT paper](https://doi.org/10.1101/2023.09.08.556883) for questions or comments on the paper/model.
+
+## License
+
+This model is licensed under the [GNU Affero General Public License](license.md).
+
+For additional terms and clarifications, please refer to our [License FAQ](license-faq.md).
+
+```spdx
+SPDX-License-Identifier: AGPL-3.0-or-later
+```

config.json

@@ -0,0 +1,52 @@
+{
+  "add_cross_attention": false,
+  "architectures": [
+    "UtrBertForPreTraining"
+  ],
+  "attention_dropout": 0.1,
+  "bos_token_id": 0,
+  "dtype": "float32",
+  "eos_token_id": 2,
+  "eos_token_ids": 0,
+  "finetuning_task": null,
+  "head": null,
+  "hidden_act": "gelu",
+  "hidden_dropout": 0.1,
+  "hidden_size": 768,
+  "id2label": {
+    "0": "LABEL_0",
+    "1": "LABEL_1"
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "is_decoder": false,
+  "label2id": {
+    "LABEL_0": 0,
+    "LABEL_1": 1
+  },
+  "layer_norm_eps": 1e-12,
+  "lm_head": null,
+  "mask_token_id": 4,
+  "max_position_embeddings": 512,
+  "model_type": "utrbert",
+  "nmers": 6,
+  "null_token_id": 5,
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "num_rnn_layer": 1,
+  "output_past": true,
+  "pad_token_id": 0,
+  "position_embedding_type": "absolute",
+  "pruned_heads": {},
+  "rnn": "lstm",
+  "rnn_dropout": 0.0,
+  "rnn_hidden": 768,
+  "split": 10,
+  "torchscript": false,
+  "transformers_version": "5.0.0",
+  "type_vocab_size": 2,
+  "unk_token_id": 3,
+  "use_bfloat16": false,
+  "use_cache": true,
+  "vocab_size": 15631
+}

license-faq.md

@@ -0,0 +1,299 @@
+# License FAQ
+
+This License FAQ (Frequently Asked Questions) clarifies the terms and conditions governing the use of the materials in the MultiMolecule project (the "MultiMolecule") provided by the DanLing Team (also known as DanLing) ("we," "us," or "our").
+This FAQ serves as an addendum to, and is incorporated by reference into, the [GNU Affero General Public License (AGPL)](license.md) (the "License").
+This FAQ and the License together constitute the entire agreement (the "Agreement") between you and us regarding your use of MultiMolecule.
+Capitalized terms used but not defined in this FAQ have the meanings given to them in the AGPL.
+
+## 0. Summary of Key Points
+
+This summary highlights the key aspects of our license.
+For more detailed information, please refer to the corresponding sections below and read the [License](license.md).
+
+<div class="grid cards" markdown>
+
+!!! question "What are source code and object code in MultiMolecule?"
+
+    The Source Code includes all materials necessary to develop, train, evaluate, and run a model, including data, code, configuration, and documentation.
+    The Object Code includes model weight files and compiled code.
+
+    [:octicons-arrow-right-24: What are source code and object code in MultiMolecule?](#1-what-are-source-code-and-object-code-in-multimolecule)
+
+!!! question "Am I required to share my trained model?"
+
+    If you Convey model weight files hosted and distributed by MultiMolecule, you must convey those weight files under the Agreement, along with the Corresponding Source.
+    If you Convey modified versions of such weight files (for example, fine-tuned weights), you must convey those modified weight files under the Agreement, along with the Corresponding Source.
+    These obligations apply regardless of whether you used MultiMolecule, a third-party library, or a customized training pipeline to produce the conveyed weights.
+
+    [:octicons-arrow-right-24: Am I required to share my trained model?](#2-am-i-required-to-share-my-trained-model)
+
+!!! question "Am I required to share the data used for training?"
+
+    If you Convey any model weights covered by Section 2, you must also provide to recipients under the Agreement any training datasets used to train, update, or modify those weights, excluding data used solely for evaluation as clarified in Section 3.
+
+    [:octicons-arrow-right-24: Am I required to share the data used for training?](#3-am-i-required-to-share-the-data-used-for-training)
+
+!!! question "Do I need to acknowledge MultiMolecule?"
+
+    We strongly encourage acknowledgement whenever MultiMolecule contributes to your work.
+    Citation is strongly requested for all research papers and becomes mandatory only as a condition of additional permissions granted in Section 5 or Section 8.
+    Reasonable author attribution in Appropriate Legal Notices is required in certain distributed interactive interfaces.
+
+    [:octicons-arrow-right-24: Do I need to acknowledge MultiMolecule?](#4-do-i-need-to-acknowledge-multimolecule)
+
+!!! question "Can I publish research papers using MultiMolecule?"
+
+    If your manuscript or supplements include MultiMolecule materials (as described in Section 5), then the manuscript and supplements must be distributed under the License unless an additional permission applies.
+    Section 5 and Section 8 grant additional permissions to enable publication in certain venues under manuscript-sharing licenses, subject to Section 6.
+    If you cannot comply with the License and do not qualify for an additional permission, you may not distribute the manuscript or supplements with MultiMolecule materials.
+
+    [:octicons-arrow-right-24: Can I publish research papers using MultiMolecule?](#5-can-i-publish-research-papers-using-multimolecule)
+
+!!! question "Is there any restriction on publishing research papers in certain venues?"
+
+    Yes, there are restrictions on publishing research papers in certain venues under the additional permissions granted by this FAQ.
+    Section 6 limits only additional permissions granted by this FAQ.
+    Section 6 does not restrict publication under the [License](license.md) itself.
+
+    [:octicons-arrow-right-24: Restrictions on Publishing Research Papers in Certain Venues](#6-restrictions-on-publishing-research-papers-in-certain-venues)
+
+!!! question "Can I use MultiMolecule for commercial purposes?"
+
+    Yes, you can use MultiMolecule for commercial purposes under the terms of the Agreement.
+    If you prefer commercial use without the obligations that apply when you Convey covered materials, you must obtain a separate license.
+
+    [:octicons-arrow-right-24: Can I use MultiMolecule for commercial purposes?](#7-can-i-use-multimolecule-for-commercial-purposes)
+
+!!! question "Are there special permissions for MultiMolecule Collaborators?"
+
+    Yes, recognized Collaborators are granted specific additional permissions pursuant to Section 7 of the License.
+    These permissions are subject to the stated conditions and to Section 6.
+
+    [:octicons-arrow-right-24: Are there special permissions for MultiMolecule Collaborators?](#8-are-there-special-permissions-for-multimolecule-collaborators)
+
+</div>
+
+## 1. What are source code and object code in MultiMolecule?
+
+For all materials in the MultiMolecule project, the following definitions clarify and supplement those found in the [License](license.md).
+
+> [!TIP] Scope of materials hosted by MultiMolecule
+> Unless explicitly stated otherwise in the relevant model card, dataset card, file header, directory notice, or accompanying LICENSE/NOTICE, all model weights, datasets, code, configuration, and documentation hosted and distributed by MultiMolecule are provided under the Agreement.
+> If we host any specific item under different terms in the future, we will explicitly label that item, and the stated terms will control for that item.
+
+> [!IMPORTANT] Source Code
+> **Source Code** refers to the preferred form of the licensed materials for making modifications thereto, consistent with Section 1 of the License.
+> It encompasses all materials necessary for developing, training, evaluating and running the models.
+
+Source Code includes, but is not limited to:
+
+- **Data**: The datasets, in the form needed for processing, that are required for training, evaluating, or running the models provided or generated as part of the licensed materials.
+- **Code**: All source code for scripts, programs, libraries (including model architecture and pipeline definitions), and utilities required to process data, train models, perform evaluations, deploy the models, or otherwise operate and modify the licensed materials.
+- **Configuration**: Configuration files, settings parameters, environmental specifications, and any scripts used to control the installation, compilation, training, evaluation, running, or execution processes related to the licensed materials.
+- **Documentation**: Interface definition files, build instructions, manuals, guides, research papers and technical reports distributed by MultiMolecule as part of the licensed materials describing the specific methodologies, architectures and parameters used, and any other technical documentation necessary to understand, install, operate, and modify the licensed materials.
+
+*Providing the Source Code as defined here is necessary to satisfy the requirement to provide the "Corresponding Source" under the Agreement (and where applicable, under the License) when conveying Object Code.*
+
+> [!IMPORTANT] Object Code
+> **Object Code** refers to any form of the licensed materials that is not Source Code.
+
+Object Code primarily includes, but is not limited to:
+
+- **Model Weights**: The numerical parameters representing the learned state of a model after training (e.g., files in SafeTensors, HDF5, or similar formats).
+  This includes all model weights provided or hosted by MultiMolecule except for those stated otherwise.
+  This also includes any fine-tuned model weights derived from model weights provided or hosted by MultiMolecule.
+- **Compiled Code**: Any executable software code not in human-readable source form, like compiled C++ extensions sometimes found in Python packages.
+
+*For model weights treated as Object Code in MultiMolecule, the Corresponding Source includes, at a minimum, the training data and the scripts needed to reproduce the conveyed weights.*
+
+Understanding this distinction helps clarify your obligations under the Agreement.
+For instance, if you Convey Object Code (like model weights), you must also ensure the corresponding Source Code (including the necessary data, code, configuration, and documentation) is available under the terms of the Agreement.
+
+## 2. Am I required to share my trained model?
+
+If you Convey model weights covered by the Agreement, you must convey those weights under the Agreement, along with the Corresponding Source.
+
+As explained in Section 1 of this FAQ, model weights are treated as Object Code in MultiMolecule.
+Whenever you Convey Object Code under the Agreement, you must also provide the Corresponding Source.
+For model weights covered by the Agreement, Corresponding Source includes, at a minimum, the code, training data, configuration, and scripts needed to reproduce, install, run, and modify the conveyed weights, as clarified in Section 1 of this FAQ.
+
+If you modify MultiMolecule and you provide users remote interaction with your modified version through a computer network, you must comply with Section 13 of the License by offering the Corresponding Source of your modified version to those users.
+This Section 13 obligation concerns remote interaction with the modified MultiMolecule Program itself.
+
+Section 3 specifies the training-data requirement.
+
+## 3. Am I required to share the data used for training?
+
+If you Convey model weights covered by the Agreement, you must also provide to recipients under the Agreement any training datasets used to train, update, or modify those weights, excluding data used solely for evaluation as clarified below.
+
+As explained in Section 1 of this FAQ, training datasets are treated as Source Code in MultiMolecule.
+Accordingly, whenever you are required to provide Corresponding Source under the Agreement, the required Corresponding Source includes the training data required to reproduce the conveyed weights, as clarified in Section 1 of this FAQ.
+
+This requirement applies only to data used to train, update, or modify the conveyed model weights.
+Data used solely for evaluation is not required under this provision, provided it was not also used for training.
+
+If the required training data cannot be provided to recipients under the Agreement, you may not Convey the resulting weights under the Agreement.
+
+## 4. Do I need to acknowledge MultiMolecule?
+
+We strongly encourage acknowledgement whenever MultiMolecule contributes to your work.
+This section distinguishes
+
+- (a) what we strongly request as a community norm, and
+- (b) what becomes mandatory as a condition of additional permissions granted by this FAQ.
+
+> [!NOTE]
+> We strongly encourage formal citation in any research paper that uses MultiMolecule.
+> If you publish a paper solely under the [License](license.md), citation is not a condition of license compliance, but it is strongly requested.
+> If you rely on an additional permission in Section 5 or Section 8, formal citation is a condition of that additional permission.
+
+When citation is required under this FAQ (e.g., as a condition of an additional permission in Section 5 or Section 8), it must include, at a minimum, the project name (“MultiMolecule”) and the DOI ([10.5281/zenodo.12638419](https://doi.org/10.5281/zenodo.12638419)).
+If the venue does not support formal citations, the project name and DOI must instead appear in the acknowledgments section.
+
+> [!IMPORTANT]
+> If you Convey a program that incorporates MultiMolecule, you must preserve a reasonable author attribution for MultiMolecule in the Appropriate Legal Notices.
+
+If the Program has an interactive user interface, it must display Appropriate Legal Notices.
+Those notices must include a reasonable author attribution for MultiMolecule, including the project name and a link to the official repository or website.
+
+For command-line programs, this attribution must be shown prominently at startup and be available via `--help`, `--version`, or `--about` where applicable.
+For web services, this attribution must be shown prominently on the main page or another readily accessible location.
+
+For libraries or non-interactive components, this attribution must be shown prominently in the documentation and, if the component provides any interactive interface, in that interface.
+
+## 5. Can I publish research papers using MultiMolecule?
+
+> [!IMPORTANT]
+> As clarified in Section 1, Documentation is part of Source Code in MultiMolecule.
+> Accordingly, if your manuscript or supplements include MultiMolecule materials (i.e., contain or reproduce MultiMolecule code, weights, datasets, documentation text, figures, or other MultiMolecule materials), then the manuscript and supplements are treated as Documentation distributed with those MultiMolecule materials.
+> This requirement concerns manuscripts and supplements that include MultiMolecule materials, not separate and independent works that are merely distributed alongside MultiMolecule.
+> Therefore, absent an additional permission, the manuscript and supplements that include MultiMolecule materials must be distributed under the License to the extent the manuscript or supplements contain or reproduce MultiMolecule materials, as part of the same distribution of those MultiMolecule materials.
+> If you cannot comply with the License, you may not distribute the manuscript or supplements with MultiMolecule materials under the Agreement.
+
+This section grants additional permissions under Section 7 of the License for specific publication scenarios in which authors prefer to release manuscripts under manuscript-sharing licenses.
+For avoidance of doubt, the additional permissions in this Section 5 apply only to the manuscript text and other documentary materials.
+They do not alter the License that governs any MultiMolecule code, model weights, or datasets that you Convey, which remain under the Agreement unless explicitly stated otherwise.
+
+
+> [!IMPORTANT]
+> If you rely on any additional permission in this Section 5, formal citation as described in Section 4 is a condition of that additional permission.
+> Any additional permission granted in this Section 5 remains subject to Section 6.
+
+> [!TIP] Diamond Open Access
+> Diamond open access venues are permitted under the additional permissions below.
+
+You may publish manuscripts that Convey MultiMolecule materials in fully open access journals, conferences, or platforms that do not charge fees to either authors or readers.
+
+The public version of the manuscript must be made available under a license that permits sharing of manuscripts.
+You may use one of the following licenses.
+
+- GNU Free Documentation License (GFDL)
+- Creative Commons licenses
+- OSI-approved licenses
+
+This permission is granted as an additional permission under Section 7 of the [License](license.md).
+
+> [!WARNING] Non-Profit
+> Certain non-profit venues are permitted under the additional permissions below.
+
+You may publish manuscripts that Convey MultiMolecule materials in certain non-profit journals, conferences, or platforms.
+
+This includes the following venues.
+
+- eLife
+
+This permission is granted as an additional permission under Section 7 of the [License](license.md).
+
+> [!CAUTION] Closed-Access / Author-Fee
+> Closed-access or author-fee venues often make compliance impossible.
+
+We do not endorse publishing MultiMolecule materials in closed-access or author-fee venues.
+
+If a venue’s terms would prevent you from complying with the License for any MultiMolecule materials you Convey in connection with the publication, you must obtain a separate written license agreement from us prior to submission or publication.
+Such an agreement may involve conditions such as co-authorship or financial contributions to the project.
+
+## 6. Restrictions on Publishing Research Papers in Certain Venues
+
+> [!IMPORTANT]
+> This section limits only additional permissions granted by this FAQ.
+> This section does not restrict publication under the [License](license.md) itself.
+> If you Convey MultiMolecule materials as part of a publication and you comply with the License for those materials, Section 6 does not apply.
+
+Accordingly, Section 6 constrains only the additional permissions in Section 5 and Section 8.
+Section 6 also constrains any separate written license agreement that incorporates or references this FAQ, unless that separate agreement expressly states otherwise in writing.
+
+We believe that free and open access to research is a cornerstone of the machine learning community.
+Inspired by the [Statement on Nature Machine Intelligence](https://openaccess.engineering.oregonstate.edu), and by the ongoing culture of [zero-cost open access](https://diamasproject.eu), we hold that research should be universally accessible without barriers to authors or readers.
+
+The following publication venues adopt closed-access or author-fee models that contradict these fundamental values.
+We view such practices as a regressive step in the evolution of machine learning research dissemination, one that undermines community efforts to foster open collaboration and knowledge sharing.
+
+- Nature Machine Intelligence
+
+Notwithstanding Sections 5 and 8, none of the additional permissions granted by this FAQ authorize submission or publication of a manuscript that Conveys MultiMolecule materials in the venues listed above.
+You may submit or publish such a manuscript in the venues listed above only if you have a separate written license agreement from us that expressly permits publication notwithstanding this Section 6.
+
+We strongly discourage publishing work that Conveys MultiMolecule materials in the venues listed above.
+
+## 7. Can I use MultiMolecule for commercial purposes?
+
+Yes.
+You may use MultiMolecule for commercial purposes, provided you comply with the Agreement.
+
+If you Convey modified MultiMolecule materials, you must provide the Corresponding Source and related artifacts required by the License and this FAQ.
+
+Where applicable, this includes training data as clarified in Section 3 and model weights as clarified in Section 2.
+
+If you prefer commercial use without making such materials available under the License, you must obtain a separate written license agreement from us.
+Please contact [license@danling.org](mailto:license@danling.org) for details.
+
+## 8. Are there special permissions for MultiMolecule Collaborators?
+
+Yes.
+If you are recognized as a Collaborator by the DanLing Team, you are entitled to the following additional permissions granted under Section 7 of the [License](license.md).
+
+> [!TIP] Internal network use waiver
+> Notwithstanding Section 13 of the License, Collaborators receive a waiver of the obligation to offer Corresponding Source to users interacting remotely through a computer network with a modified version of MultiMolecule, provided that the interaction is solely for internal research and development within the Collaborator’s team.
+> This waiver does not apply to external users, public deployments, or Conveyance.
+
+> [!TIP] Expanded permission for publishing papers
+> Collaborators may publish manuscripts that Convey MultiMolecule materials in any peer-reviewed scientific venue, including journals and conference proceedings, regardless of access model or author fees.
+> This expanded permission is granted as an additional permission under Section 7 of the [License](license.md).
+> This expanded permission remains subject to Section 6 of this FAQ.
+> This expanded permission affects only the licensing of the manuscript and supplementary documentation, and does not alter the License that governs any MultiMolecule materials you Convey.
+> As a condition of this expanded permission, you must comply with the acknowledgement and citation requirements in Section 4.
+
+> [!IMPORTANT] Source release timing related to publications
+> This additional permission concerns the timing of *public release* of publication-related modifications.
+> It does not delay any obligation under the License to provide Corresponding Source to recipients upon Conveyance, or to remote users upon network interaction under Section 13.
+> If your modifications are utilized in research described in a manuscript, you must make the Corresponding Source for those publication-related modifications publicly available upon the first of the following events.
+>
+> - The manuscript’s formal acceptance for publication in a peer-reviewed venue.
+> - 366 days have passed since the manuscript was first posted on a public preprint server.
+>
+> You must make the public release immediately upon the first applicable trigger event.
+> If modifications are Conveyed or made available for remote interaction through a computer network in ways not tied to a publication or preprint, the standard timing rules of the License apply.
+
+> [!NOTE] General conditions for Collaborator permissions
+> These permissions are granted only to active, invited Collaborators recognized by the DanLing Team.
+> These permissions are non-transferable and non-sublicensable.
+> All other provisions of the License and this FAQ remain in full force and effect unless explicitly modified above.
+> The DanLing Team may grant additional case-specific permissions through written communication.
+
+## 9. How can I use MultiMolecule if my organization forbids the use of code under the AGPL License?
+
+Certain organizations, such as [Google](https://opensource.google/documentation/reference/using/agpl-policy), prohibit the use of AGPL-licensed code.
+If you are affiliated with an organization that disallows the use of AGPL-licensed software, you must obtain a separate license from us to use MultiMolecule.
+
+To request a separate license, please contact us at [license@danling.org](mailto:license@danling.org).
+
+## 10. Do we make updates to this FAQ?
+
+> [!TIP] "In Short"
+> Yes, we will update this FAQ as necessary to stay compliant with relevant laws.
+
+We may update this license FAQ from time to time.
+The updated version will be indicated by an updated 'Last Revised Time' at the bottom of this license FAQ.
+If we make any material changes, we will notify you by posting the new license FAQ on this page.
+We are unable to notify you directly as we do not collect any contact information from you.
+We encourage you to review this license FAQ frequently to stay informed of how you can use our data, models, code, configuration, and documentation.

license.md

@@ -0,0 +1,661 @@
+# GNU AFFERO GENERAL PUBLIC LICENSE
+
+Version 3, 19 November 2007
+
+Copyright (C) 2007 Free Software Foundation, Inc.
+<https://fsf.org/>
+
+Everyone is permitted to copy and distribute verbatim copies of this
+license document, but changing it is not allowed.
+
+## Preamble
+
+The GNU Affero General Public License is a free, copyleft license for
+software and other kinds of works, specifically designed to ensure
+cooperation with the community in the case of network server software.
+
+The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works. By contrast,
+our General Public Licenses are intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains
+free software for all its users.
+
+When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+Developers that use our General Public Licenses protect your rights
+with two steps: (1) assert copyright on the software, and (2) offer
+you this License which gives you legal permission to copy, distribute
+and/or modify the software.
+
+A secondary benefit of defending all users' freedom is that
+improvements made in alternate versions of the program, if they
+receive widespread use, become available for other developers to
+incorporate. Many developers of free software are heartened and
+encouraged by the resulting cooperation. However, in the case of
+software used on network servers, this result may fail to come about.
+The GNU General Public License permits making a modified version and
+letting the public access it on a server without ever releasing its
+source code to the public.
+
+The GNU Affero General Public License is designed specifically to
+ensure that, in such cases, the modified source code becomes available
+to the community. It requires the operator of a network server to
+provide the source code of the modified version running there to the
+users of that server. Therefore, public use of a modified version, on
+a publicly accessible server, gives the public access to the source
+code of the modified version.
+
+An older license, called the Affero General Public License and
+published by Affero, was designed to accomplish similar goals. This is
+a different license, not a version of the Affero GPL, but Affero has
+released a new version of the Affero GPL which permits relicensing
+under this license.
+
+The precise terms and conditions for copying, distribution and
+modification follow.
+
+## TERMS AND CONDITIONS
+
+### 0. Definitions.
+
+"This License" refers to version 3 of the GNU Affero General Public
+License.
+
+"Copyright" also means copyright-like laws that apply to other kinds
+of works, such as semiconductor masks.
+
+"The Program" refers to any copyrightable work licensed under this
+License. Each licensee is addressed as "you". "Licensees" and
+"recipients" may be individuals or organizations.
+
+To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of
+an exact copy. The resulting work is called a "modified version" of
+the earlier work or a work "based on" the earlier work.
+
+A "covered work" means either the unmodified Program or a work based
+on the Program.
+
+To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy. Propagation includes copying,
+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.
+
+To "convey" a work means any kind of propagation that enables other
+parties to make or receive copies. Mere interaction with a user
+through a computer network, with no transfer of a copy, is not
+conveying.
+
+An interactive user interface displays "Appropriate Legal Notices" to
+the extent that it includes a convenient and prominently visible
+feature that (1) displays an appropriate copyright notice, and (2)
+tells the user that there is no warranty for the work (except to the
+extent that warranties are provided), that licensees may convey the
+work under this License, and how to view a copy of this License. If
+the interface presents a list of user commands or options, such as a
+menu, a prominent item in the list meets this criterion.
+
+### 1. Source Code.
+
+The "source code" for a work means the preferred form of the work for
+making modifications to it. "Object code" means any non-source form of
+a work.
+
+A "Standard Interface" means an interface that either is an official
+standard defined by a recognized standards body, or, in the case of
+interfaces specified for a particular programming language, one that
+is widely used among developers working in that language.
+
+The "System Libraries" of an executable work include anything, other
+than the work as a whole, that (a) is included in the normal form of
+packaging a Major Component, but which is not part of that Major
+Component, and (b) serves only to enable use of the work with that
+Major Component, or to implement a Standard Interface for which an
+implementation is available to the public in source code form. A
+"Major Component", in this context, means a major essential component
+(kernel, window system, and so on) of the specific operating system
+(if any) on which the executable work runs, or a compiler used to
+produce the work, or an object code interpreter used to run it.
+
+The "Corresponding Source" for a work in object code form means all
+the source code needed to generate, install, and (for an executable
+work) run the object code and to modify the work, including scripts to
+control those activities. However, it does not include the work's
+System Libraries, or general-purpose tools or generally available free
+programs which are used unmodified in performing those activities but
+which are not part of the work. For example, Corresponding Source
+includes interface definition files associated with source files for
+the work, and the source code for shared libraries and dynamically
+linked subprograms that the work is specifically designed to require,
+such as by intimate data communication or control flow between those
+subprograms and other parts of the work.
+
+The Corresponding Source need not include anything that users can
+regenerate automatically from other parts of the Corresponding Source.
+
+The Corresponding Source for a work in source code form is that same
+work.
+
+### 2. Basic Permissions.
+
+All rights granted under this License are granted for the term of
+copyright on the Program, and are irrevocable provided the stated
+conditions are met. This License explicitly affirms your unlimited
+permission to run the unmodified Program. The output from running a
+covered work is covered by this License only if the output, given its
+content, constitutes a covered work. This License acknowledges your
+rights of fair use or other equivalent, as provided by copyright law.
+
+You may make, run and propagate covered works that you do not convey,
+without conditions so long as your license otherwise remains in force.
+You may convey covered works to others for the sole purpose of having
+them make modifications exclusively for you, or provide you with
+facilities for running those works, provided that you comply with the
+terms of this License in conveying all material for which you do not
+control copyright. Those thus making or running the covered works for
+you must do so exclusively on your behalf, under your direction and
+control, on terms that prohibit them from making any copies of your
+copyrighted material outside their relationship with you.
+
+Conveying under any other circumstances is permitted solely under the
+conditions stated below. Sublicensing is not allowed; section 10 makes
+it unnecessary.
+
+### 3. Protecting Users' Legal Rights From Anti-Circumvention Law.
+
+No covered work shall be deemed part of an effective technological
+measure under any applicable law fulfilling obligations under article
+11 of the WIPO copyright treaty adopted on 20 December 1996, or
+similar laws prohibiting or restricting circumvention of such
+measures.
+
+When you convey a covered work, you waive any legal power to forbid
+circumvention of technological measures to the extent such
+circumvention is effected by exercising rights under this License with
+respect to the covered work, and you disclaim any intention to limit
+operation or modification of the work as a means of enforcing, against
+the work's users, your or third parties' legal rights to forbid
+circumvention of technological measures.
+
+### 4. Conveying Verbatim Copies.
+
+You may convey verbatim copies of the Program's source code as you
+receive it, in any medium, provided that you conspicuously and
+appropriately publish on each copy an appropriate copyright notice;
+keep intact all notices stating that this License and any
+non-permissive terms added in accord with section 7 apply to the code;
+keep intact all notices of the absence of any warranty; and give all
+recipients a copy of this License along with the Program.
+
+You may charge any price or no price for each copy that you convey,
+and you may offer support or warranty protection for a fee.
+
+### 5. Conveying Modified Source Versions.
+
+You may convey a work based on the Program, or the modifications to
+produce it from the Program, in the form of source code under the
+terms of section 4, provided that you also meet all of these
+conditions:
+
+- a) The work must carry prominent notices stating that you modified
+  it, and giving a relevant date.
+- b) The work must carry prominent notices stating that it is
+  released under this License and any conditions added under
+  section 7. This requirement modifies the requirement in section 4
+  to "keep intact all notices".
+- c) You must license the entire work, as a whole, under this
+  License to anyone who comes into possession of a copy. This
+  License will therefore apply, along with any applicable section 7
+  additional terms, to the whole of the work, and all its parts,
+  regardless of how they are packaged. This License gives no
+  permission to license the work in any other way, but it does not
+  invalidate such permission if you have separately received it.
+- d) If the work has interactive user interfaces, each must display
+  Appropriate Legal Notices; however, if the Program has interactive
+  interfaces that do not display Appropriate Legal Notices, your
+  work need not make them do so.
+
+A compilation of a covered work with other separate and independent
+works, which are not by their nature extensions of the covered work,
+and which are not combined with it such as to form a larger program,
+in or on a volume of a storage or distribution medium, is called an
+"aggregate" if the compilation and its resulting copyright are not
+used to limit the access or legal rights of the compilation's users
+beyond what the individual works permit. Inclusion of a covered work
+in an aggregate does not cause this License to apply to the other
+parts of the aggregate.
+
+### 6. Conveying Non-Source Forms.
+
+You may convey a covered work in object code form under the terms of
+sections 4 and 5, provided that you also convey the machine-readable
+Corresponding Source under the terms of this License, in one of these
+ways:
+
+- a) Convey the object code in, or embodied in, a physical product
+  (including a physical distribution medium), accompanied by the
+  Corresponding Source fixed on a durable physical medium
+  customarily used for software interchange.
+- b) Convey the object code in, or embodied in, a physical product
+  (including a physical distribution medium), accompanied by a
+  written offer, valid for at least three years and valid for as
+  long as you offer spare parts or customer support for that product
+  model, to give anyone who possesses the object code either (1) a
+  copy of the Corresponding Source for all the software in the
+  product that is covered by this License, on a durable physical
+  medium customarily used for software interchange, for a price no
+  more than your reasonable cost of physically performing this
+  conveying of source, or (2) access to copy the Corresponding
+  Source from a network server at no charge.
+- c) Convey individual copies of the object code with a copy of the
+  written offer to provide the Corresponding Source. This
+  alternative is allowed only occasionally and noncommercially, and
+  only if you received the object code with such an offer, in accord
+  with subsection 6b.
+- d) Convey the object code by offering access from a designated
+  place (gratis or for a charge), and offer equivalent access to the
+  Corresponding Source in the same way through the same place at no
+  further charge. You need not require recipients to copy the
+  Corresponding Source along with the object code. If the place to
+  copy the object code is a network server, the Corresponding Source
+  may be on a different server (operated by you or a third party)
+  that supports equivalent copying facilities, provided you maintain
+  clear directions next to the object code saying where to find the
+  Corresponding Source. Regardless of what server hosts the
+  Corresponding Source, you remain obligated to ensure that it is
+  available for as long as needed to satisfy these requirements.
+- e) Convey the object code using peer-to-peer transmission,
+  provided you inform other peers where the object code and
+  Corresponding Source of the work are being offered to the general
+  public at no charge under subsection 6d.
+
+A separable portion of the object code, whose source code is excluded
+from the Corresponding Source as a System Library, need not be
+included in conveying the object code work.
+
+A "User Product" is either (1) a "consumer product", which means any
+tangible personal property which is normally used for personal,
+family, or household purposes, or (2) anything designed or sold for
+incorporation into a dwelling. In determining whether a product is a
+consumer product, doubtful cases shall be resolved in favor of
+coverage. For a particular product received by a particular user,
+"normally used" refers to a typical or common use of that class of
+product, regardless of the status of the particular user or of the way
+in which the particular user actually uses, or expects or is expected
+to use, the product. A product is a consumer product regardless of
+whether the product has substantial commercial, industrial or
+non-consumer uses, unless such uses represent the only significant
+mode of use of the product.
+
+"Installation Information" for a User Product means any methods,
+procedures, authorization keys, or other information required to
+install and execute modified versions of a covered work in that User
+Product from a modified version of its Corresponding Source. The
+information must suffice to ensure that the continued functioning of
+the modified object code is in no case prevented or interfered with
+solely because modification has been made.
+
+If you convey an object code work under this section in, or with, or
+specifically for use in, a User Product, and the conveying occurs as
+part of a transaction in which the right of possession and use of the
+User Product is transferred to the recipient in perpetuity or for a
+fixed term (regardless of how the transaction is characterized), the
+Corresponding Source conveyed under this section must be accompanied
+by the Installation Information. But this requirement does not apply
+if neither you nor any third party retains the ability to install
+modified object code on the User Product (for example, the work has
+been installed in ROM).
+
+The requirement to provide Installation Information does not include a
+requirement to continue to provide support service, warranty, or
+updates for a work that has been modified or installed by the
+recipient, or for the User Product in which it has been modified or
+installed. Access to a network may be denied when the modification
+itself materially and adversely affects the operation of the network
+or violates the rules and protocols for communication across the
+network.
+
+Corresponding Source conveyed, and Installation Information provided,
+in accord with this section must be in a format that is publicly
+documented (and with an implementation available to the public in
+source code form), and must require no special password or key for
+unpacking, reading or copying.
+
+### 7. Additional Terms.
+
+"Additional permissions" are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions.
+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
+that they are valid under applicable law. If additional permissions
+apply only to part of the Program, that part may be used separately
+under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.
+
+When you convey a copy of a covered work, you may at your option
+remove any additional permissions from that copy, or from any part of
+it. (Additional permissions may be written to require their own
+removal in certain cases when you modify the work.) You may place
+additional permissions on material, added by you to a covered work,
+for which you have or can give appropriate copyright permission.
+
+Notwithstanding any other provision of this License, for material you
+add to a covered work, you may (if authorized by the copyright holders
+of that material) supplement the terms of this License with terms:
+
+- a) Disclaiming warranty or limiting liability differently from the
+  terms of sections 15 and 16 of this License; or
+- b) Requiring preservation of specified reasonable legal notices or
+  author attributions in that material or in the Appropriate Legal
+  Notices displayed by works containing it; or
+- c) Prohibiting misrepresentation of the origin of that material,
+  or requiring that modified versions of such material be marked in
+  reasonable ways as different from the original version; or
+- d) Limiting the use for publicity purposes of names of licensors
+  or authors of the material; or
+- e) Declining to grant rights under trademark law for use of some
+  trade names, trademarks, or service marks; or
+- f) Requiring indemnification of licensors and authors of that
+  material by anyone who conveys the material (or modified versions
+  of it) with contractual assumptions of liability to the recipient,
+  for any liability that these contractual assumptions directly
+  impose on those licensors and authors.
+
+All other non-permissive additional terms are considered "further
+restrictions" within the meaning of section 10. If the Program as you
+received it, or any part of it, contains a notice stating that it is
+governed by this License along with a term that is a further
+restriction, you may remove that term. If a license document contains
+a further restriction but permits relicensing or conveying under this
+License, you may add to a covered work material governed by the terms
+of that license document, provided that the further restriction does
+not survive such relicensing or conveying.
+
+If you add terms to a covered work in accord with this section, you
+must place, in the relevant source files, a statement of the
+additional terms that apply to those files, or a notice indicating
+where to find the applicable terms.
+
+Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions; the
+above requirements apply either way.
+
+### 8. Termination.
+
+You may not propagate or modify a covered work except as expressly
+provided under this License. Any attempt otherwise to propagate or
+modify it is void, and will automatically terminate your rights under
+this License (including any patent licenses granted under the third
+paragraph of section 11).
+
+However, if you cease all violation of this License, then your license
+from a particular copyright holder is reinstated (a) provisionally,
+unless and until the copyright holder explicitly and finally
+terminates your license, and (b) permanently, if the copyright holder
+fails to notify you of the violation by some reasonable means prior to
+60 days after the cessation.
+
+Moreover, your license from a particular copyright holder is
+reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
+copyright holder, and you cure the violation prior to 30 days after
+your receipt of the notice.
+
+Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License. If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.
+
+### 9. Acceptance Not Required for Having Copies.
+
+You are not required to accept this License in order to receive or run
+a copy of the Program. Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance. However,
+nothing other than this License grants you permission to propagate or
+modify any covered work. These actions infringe copyright if you do
+not accept this License. Therefore, by modifying or propagating a
+covered work, you indicate your acceptance of this License to do so.
+
+### 10. Automatic Licensing of Downstream Recipients.
+
+Each time you convey a covered work, the recipient automatically
+receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License. You are not responsible
+for enforcing compliance by third parties with this License.
+
+An "entity transaction" is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations. If propagation of a covered
+work results from an entity transaction, each party to that
+transaction who receives a copy of the work also receives whatever
+licenses to the work the party's predecessor in interest had or could
+give under the previous paragraph, plus a right to possession of the
+Corresponding Source of the work from the predecessor in interest, if
+the predecessor has it or can get it with reasonable efforts.
+
+You may not impose any further restrictions on the exercise of the
+rights granted or affirmed under this License. For example, you may
+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that
+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+
+### 11. Patents.
+
+A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The
+work thus licensed is called the contributor's "contributor version".
+
+A contributor's "essential patent claims" are all patent claims owned
+or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
+by this License, of making, using, or selling its contributor version,
+but do not include claims that would be infringed only as a
+consequence of further modification of the contributor version. For
+purposes of this definition, "control" includes the right to grant
+patent sublicenses in a manner consistent with the requirements of
+this License.
+
+Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to
+make, use, sell, offer for sale, import and otherwise run, modify and
+propagate the contents of its contributor version.
+
+In the following three paragraphs, a "patent license" is any express
+agreement or commitment, however denominated, not to enforce a patent
+(such as an express permission to practice a patent or covenant not to
+sue for patent infringement). To "grant" such a patent license to a
+party means to make such an agreement or commitment not to enforce a
+patent against the party.
+
+If you convey a covered work, knowingly relying on a patent license,
+and the Corresponding Source of the work is not available for anyone
+to copy, free of charge and under the terms of this License, through a
+publicly available network server or other readily accessible means,
+then you must either (1) cause the Corresponding Source to be so
+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients. "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.
+
+If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+
+A patent license is "discriminatory" if it does not include within the
+scope of its coverage, prohibits the exercise of, or is conditioned on
+the non-exercise of one or more of the rights that are specifically
+granted under this License. You may not convey a covered work if you
+are a party to an arrangement with a third party that is in the
+business of distributing software, under which you make payment to the
+third party based on the extent of your activity of conveying the
+work, and under which the third party grants, to any of the parties
+who would receive the covered work from you, a discriminatory patent
+license (a) in connection with copies of the covered work conveyed by
+you (or copies made from those copies), or (b) primarily for and in
+connection with specific products or compilations that contain the
+covered work, unless you entered into that arrangement, or that patent
+license was granted, prior to 28 March 2007.
+
+Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+### 12. No Surrender of Others' Freedom.
+
+If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under
+this License and any other pertinent obligations, then as a
+consequence you may not convey it at all. For example, if you agree to
+terms that obligate you to collect a royalty for further conveying
+from those to whom you convey the Program, the only way you could
+satisfy both those terms and this License would be to refrain entirely
+from conveying the Program.
+
+### 13. Remote Network Interaction; Use with the GNU General Public License.
+
+Notwithstanding any other provision of this License, if you modify the
+Program, your modified version must prominently offer all users
+interacting with it remotely through a computer network (if your
+version supports such interaction) an opportunity to receive the
+Corresponding Source of your version by providing access to the
+Corresponding Source from a network server at no charge, through some
+standard or customary means of facilitating copying of software. This
+Corresponding Source shall include the Corresponding Source for any
+work covered by version 3 of the GNU General Public License that is
+incorporated pursuant to the following paragraph.
+
+Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the work with which it is combined will remain governed by version
+3 of the GNU General Public License.
+
+### 14. Revised Versions of this License.
+
+The Free Software Foundation may publish revised and/or new versions
+of the GNU Affero General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies that a certain numbered version of the GNU Affero General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU Affero General Public License, you may choose any version ever
+published by the Free Software Foundation.
+
+If the Program specifies that a proxy can decide which future versions
+of the GNU Affero General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+### 15. Disclaimer of Warranty.
+
+THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT
+WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND
+PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE
+DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR
+CORRECTION.
+
+### 16. Limitation of Liability.
+
+IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR
+CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES
+ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT
+NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR
+LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM
+TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER
+PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
+
+### 17. Interpretation of Sections 15 and 16.
+
+If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+END OF TERMS AND CONDITIONS
+
+## How to Apply These Terms to Your New Programs
+
+If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these
+terms.
+
+To do so, attach the following notices to the program. It is safest to
+attach them to the start of each source file to most effectively state
+the exclusion of warranty; and each file should have at least the
+"copyright" line and a pointer to where the full notice is found.
+
+        <one line to give the program's name and a brief idea of what it does.>
+        Copyright (C) <year>  <name of author>
+
+        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 (at your option) 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 <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper
+mail.
+
+If your software can interact with users remotely through a computer
+network, you should also make sure that it provides a way for users to
+get its source. For example, if your program is a web application, its
+interface could display a "Source" link that leads users to an archive
+of the code. There are many ways you could offer source, and different
+solutions will be better for different programs; see section 13 for
+the specific requirements.
+
+You should also get your employer (if you work as a programmer) or
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary. For more information on this, and how to apply and follow
+the GNU AGPL, see <https://www.gnu.org/licenses/>.
+

model.safetensors

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:924959c9f14bb98941f95c5d9286bc585f942d51e0a1def3bb3d9c62194d073a
+size 442657492

tokenizer_config.json

@@ -0,0 +1,72 @@
+{
+  "added_tokens_decoder": {
+    "0": {
+      "content": "<pad>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "1": {
+      "content": "<cls>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "2": {
+      "content": "<eos>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "3": {
+      "content": "<unk>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "4": {
+      "content": "<mask>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "5": {
+      "content": "<null>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    }
+  },
+  "additional_special_tokens": [
+    "<null>"
+  ],
+  "backend": "custom",
+  "bos_token": "<cls>",
+  "clean_up_tokenization_spaces": true,
+  "cls_token": "<cls>",
+  "codon": false,
+  "eos_token": "<eos>",
+  "extra_special_tokens": [
+    "<null>"
+  ],
+  "mask_token": "<mask>",
+  "model_max_length": 510,
+  "nmers": 6,
+  "pad_token": "<pad>",
+  "replace_T_with_U": true,
+  "sep_token": "<eos>",
+  "tokenizer_class": "RnaTokenizer",
+  "unk_token": "<unk>"
+}