multimolecule/aparent

1---2library_name: multimolecule3license: agpl-3.04pipeline: polyadenylation5pipeline_tag: other6tags:7- Biology8- RNA9- 3' UTR10- rna11widget:12- example_title: microRNA 2113  pipeline_tag: polyadenylation14  sequence_type: ncRNA15  task: polyadenylation16  text: UAGCUUAUCAGACUGAUGUUGA17- example_title: microRNA 146a18  pipeline_tag: polyadenylation19  sequence_type: ncRNA20  task: polyadenylation21  text: UGAGAACUGAAUUCCAUGGGUU22- example_title: microRNA 15523  pipeline_tag: polyadenylation24  sequence_type: ncRNA25  task: polyadenylation26  text: UUAAUGCUAAUCGUGAUAGGGGUU27- example_title: RNA component of mitochondrial RNA processing endoribonuclease28  pipeline_tag: polyadenylation29  sequence_type: ncRNA30  task: polyadenylation31  text: GGUUCGUGCUGAAGGCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCUCAUUCUCAGCGCGGCUGUAAAAAAAAA32- example_title: 7SK small nuclear RNA33  pipeline_tag: polyadenylation34  sequence_type: ncRNA35  task: polyadenylation36  text: GGAUGUGAGGGCGAUCUGGCUGCGACAUCUGUCACCCCAUUGAUCGCCAGGGUUGAUUCGGCUGAUCUGGCUGGCUAGGCGGGUGUCCCCUUCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGCGCUCGGUCGAAGAGGACGACCAUCCCCGAUAGAGGAGGACCGGUCUUCGGUCAAGGGUAUACGAGUAGCUGCGCUCCCCUGCUAGAACCUCCAAACAAGCUCUCAAGGUCCAUUUGUAGGAGAACGUAGGGUAGUCAAGCUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGCAUGUGGCAGUCUGCCUUUCUUUU37- example_title: telomerase RNA component38  pipeline_tag: polyadenylation39  sequence_type: ncRNA40  task: polyadenylation41  text: GGGUUGCGGAGGGUGGGCCUGGGAGGGGUGGUGGCCAUUUUUUGUCUAACCCUAACUGAGAAGGGCGUAGGCGCCGUGCUUUUGCUCCCCGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGAAAAGCCUCGGCCUGCCGCCUUCCACCGUUCAUUCUAGAGCAAACAAAAAAUGUCAGCUGCUGGCCCGUUCGCCCCUCCCGGGGACCUGCGGCGGGUCGCCUGCCCAGCCCCCGAACCCCGCCUGGAGGCCGCGGUCGGCCCGGGGCUUCUCCGGAGGCACCCACUGCCACCGCGAAGAGUUGGGCUCUGUCAGCCGCGGGUCUCUCGGGGGCGAGGGCGAGGUUCAGGCCUUUCAGGCCGCAGGAAGAGGAACGGAGCGAGUCCCCGCGCGCGGCGCGAUUCCCUGAGCUGUGGGACGUGCACCCAGGACUCGGCUCACACAUGC42- example_title: vault RNA 2-143  pipeline_tag: polyadenylation44  sequence_type: ncRNA45  task: polyadenylation46  text: CGGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUUAUGCAA47- example_title: brain cytoplasmic RNA 148  pipeline_tag: polyadenylation49  sequence_type: ncRNA50  task: polyadenylation51  text: GGCCGGGCGCGGUGGCUCACGCCUGUAAUCCCAGCUCUCAGGGAGGCUAAGAGGCGGGAGGAUAGCUUGAGCCCAGGAGUUCGAGACCUGCCUGGGCAAUAUAGCGAGACCCCGUUCUCCAGAAAAAGGAAAAAAAAAAACAAAAGACAAAAAAAAAAUAAGCGUAACUUCCCUCAAAGCAACAACCCCCCCCCCCCUUU52- example_title: HIV-1 TAR-WT53  pipeline_tag: polyadenylation54  sequence_type: ncRNA55  task: polyadenylation56  text: GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACC57- example_title: prion protein (Kanno blood group)58  pipeline_tag: polyadenylation59  sequence_type: mRNA60  task: polyadenylation61  text: AUGGCGAACCUUGGCUGCUGGAUGCUGGUUCUCUUUGUGGCCACAUGGAGUGACCUGGGCCUCUGC62- example_title: interleukin 1063  pipeline_tag: polyadenylation64  sequence_type: mRNA65  task: polyadenylation66  text: AUGCACAGCUCAGCACUGCUCUGUUGCCUGGUCCUCCUGACUGGGGUGAGGGCC67- example_title: Zaire ebolavirus68  pipeline_tag: polyadenylation69  sequence_type: mRNA70  task: polyadenylation71  text: AAUGUUCAAACACUUUGUGAAGCUCUGUUAGCUGAUGGUCUUGCUAAAGCAUUUCCUAGCAAUAUGAUGGUAGUCACAGAGCGUGAGCAAAAAGAAAGCUUAUUGCAUCAAGCAUCAUGGCACCACACAAGUGAUGAUUUUGGUGAGCAUGCCACAGUUAGAGGGAGUAGCUUUGUAACUGAUUUAGAGAAAUACAAUCUUGCAUUUAGAUAUGAGUUUACAGCACCUUUUAUAGAAUAUUGUAACCGUUGCUAUGGUGUUAAGAAUGUUUUUAAUUGGAUGCAUUAUACAAUCCCACAGUGUUAU72- example_title: SARS coronavirus73  pipeline_tag: polyadenylation74  sequence_type: mRNA75  task: polyadenylation76  text: AUGUUUAUUUUCUUAUUAUUUCUUACUCUCACUAGUGGUAGUGACCUUGACCGGUGCACCACUUUUGAUGAUGUUCAAGCUCCUAAUUACACUCAACAUACUUCAUCUAUGAGGGGGGUUUACUAUCCUGAUGAAAUUUUUAGAUCAGACACUCUUUAUUUAACUCAGGAUUUAUUUCUUCCAUUUUAUUCUAAUGUUACAGGGUUUCAUACUAUUAAUCAUACGUUUGACAACCCUGUCAUACCUUUUAAGGAUGGUAUUUAUUUUGCUGCCACAGAGAAAUCAAAUGUUGUCCGUGGUUGGGUUUUUGGUUCUACCAUGAACAACAAGUCACAGUCGGUGAUUAUUAUUAACAAUUCUACUAAUGUUGUUAUACGAGCAUGUAACUUUGAAUUGUGUGACAACCCUUUCUUUGCUGUUUCUAAACCCAUGGGUACACAGACACAUACUAUGAUAUUCGAUAAUGCAUUUAAAUGCACUUUCGAGUACAUAUCU77- example_title: insulin78  pipeline_tag: polyadenylation79  sequence_type: mRNA80  task: polyadenylation81  text: AUGGCCCUGUGGAUGCGCCUCCUGCCCCUGCUGGCGCUGCUGGCCCUCUGGGGACCUGACCCAGCCGCAGCCUUUGUGAACCAACACCUGUGCGGCUCACACCUGGUGGAAGCUCUCUACCUAGUGUGCGGGGAACGAGGCUUCUUCUACACACCCAAGACCCGCCGGGAGGCAGAGGACCUGCAGGUGGGGCAGGUGGAGCUGGGCGGGGGCCCUGGUGCAGGCAGCCUGCAGCCCUUGGCCCUGGAGGGGUCCCUGCAGAAGCGUGGCAUUGUGGAACAAUGCUGUACCAGCAUCUGCUCCCUCUACCAGCUGGAGAACUACUGCAACUAG82- example_title: cyclin dependent kinase inhibitor 2A83  pipeline_tag: polyadenylation84  sequence_type: mRNA85  task: polyadenylation86  text: AUGGAGCCGGCGGCGGGGAGCAGCAUGGAGCCUUCGGCUGACUGGCUGGCCACGGCCGCGGCCCGGGGUCGGGUAGAGGAGGUGCGGGCGCUGCUGGAGGCGGGGGCGCUGCCCAACGCACCGAAUAGUUACGGUCGGAGGCCGAUCCAGGUCAUGAUGAUGGGCAGCGCCCGAGUGGCGGAGCUGCUGCUGCUCCACGGCGCGGAGCCCAACUGCGCCGACCCCGCCACUCUCACCCGACCCGUGCACGACGCUGCCCGGGAGGGCUUCCUGGACACGCUGGUGGUGCUGCACCGGGCCGGGGCGCGGCUGGACGUGCGCGAUGCCUGGGGCCGUCUGCCCGUGGACCUGGCUGAGGAGCUGGGCCAUCGCGAUGUCGCACGGUACCUGCGCGCGGCUGCGGGGGGCACCAGAGGCAGUAACCAUGCCCGCAUAGAUGCCGCGGAAGGUCCCUCAGACAUCCCCGAUUGA87- example_title: human papillomavirus type 16 E688  pipeline_tag: polyadenylation89  sequence_type: mRNA90  task: polyadenylation91  text: AUGCACCAAAAGAGAACUGCAAUGUUUCAGGACCCACAGGAGCGACCCAGAAAGUUACCACAGUUAUGCACAGAGCUGCAAACAACUAUACAUGAUAUAAUAUUAGAAUGUGUGUACUGCAAGCAACAGUUACUGCGACGUGAGGUAUAUGACUUUGCUUUUCGGGAUUUAUGCAUAGUAUAUAGAGAUGGGAAUCCAUAUGCUGUAUGUGAUAAAUGUUUAAAGUUUUAUUCUAAAAUUAGUGAGUAUAGACAUUAUUGUUAUAGUUUGUAUGGAACAACAUUAGAACAGCAAUACAACAAACCGUUGUGUGAUUUGUUAAUUAGGUGUAUUAACUGUCAAAAGCCACUGUGUCCUGAAGAAAAGCAAAGACAUCUGGACAAAAAGCAAAGAUUCCAUAAUAUAAGGGGUCGGUGGACCGGUCGAUGUAUGUCUUGUUGCAGAUCAUCAAGAACACGUAGAGAAACCCAGCUGUAA92- example_title: NRAS proto-oncogene93  pipeline_tag: polyadenylation94  sequence_type: 5' UTR95  task: polyadenylation96  text: GGGGCCGGAAGUGCCGCUCCUUGGUGGGGGCUGUUCAUGGCGGUUCCGGGGUCUCCAACAUUUUUCCCGGCUGUGGUCCUAAAUCUGUCCAAAGCAGAGGCAGUGGAGCUUGAGGUUCUUGCUGGUGUGAA97- example_title: amyloid beta precursor protein98  pipeline_tag: polyadenylation99  sequence_type: 5' UTR100  task: polyadenylation101  text: GUCAGUUUCCUCGGCAGCGGUAGGCGAGAGCACGCGGAGGAGCGUGCGCGGGGGCCCCGGGAGACGGCGGCGGUGGCGGCGCGGGCAGAGCAAGGACGCGGCGGAUCCCACUCGCACAGCAGCGCACUCGGUGCCCCGCGCAGGGUCGCG102- example_title: RUNX family transcription factor 1103  pipeline_tag: polyadenylation104  sequence_type: 5' UTR105  task: polyadenylation106  text: ACUUCUUUGGGCCUCAUAAACAACCACAGAACCACAAGUUGGGUAGCCUGGCAGUGUCAGAAGUCUGAACCCAGCAUAGUGGUCAGCAGGCAGGACGAAUCACACUGAAUGCAAACCACAGGGUUUCGCAGCGUGGUAAAAGAAAUCAUUGAGUCCCCCGCCUUCAGAAGAGGGUGCAUUUUCAGGAGGAAGCG107- example_title: fragile X messenger ribonucleoprotein 1108  pipeline_tag: polyadenylation109  sequence_type: 5' UTR110  task: polyadenylation111  text: CUCAGUCAGGCGCUCAGCUCCGUUUCGGUUUCACUUCCGGUGGAGGGCCGCCUCUGAGCGGGCGGCGGGCCGACGGCGAGCGCGGGCGGCGGCGGUGACGGAGGCGCCGCUGCCAGGGGGCGUGCGGCAGCGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCUGGGCCUCGAGCGCCCGCAGCCCACCUCUCGGGGGCGGGCUCCCGGCGCUAGCAGGGCUGAAGAGAAG112- example_title: MYC proto-oncogene113  pipeline_tag: polyadenylation114  sequence_type: 5' UTR115  task: polyadenylation116  text: AACUCGCUGUAGUAAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGCCGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCUGAUCCCCCAGCCAGCGGUCCGCAACCCUUGCCGCAUCCACGAAACUUUGCCCAUAGCAGCGGGCGGGCACUUUGCACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCUAUUCUGCCCAUUUGGGGACACUUCCCCGCCGCUGCCAGGACCCGCUUCUCUGAAAGGCUCUCCUUGCAGCUGCUUAGACG117- example_title: activating transcription factor 4118  pipeline_tag: polyadenylation119  sequence_type: 5' UTR120  task: polyadenylation121  text: CAUUUCUACUUUGCCCGCCCACAGAUGUAGUUUUCUCUGCGCGUGUGCGUUUUCCCUCCUCCCCGCCCUCAGGGUCCACGGCCACCAUGGCGUAUUAGGGGCAGCAGUGCCUGCGGCAGCAUUGGCCUUUGCAGCGGCGGCAGCAGCACCAGGCUCUGCAGCGGCAACCCCCAGCGGCUUAAGCCAUGGCGCUUCUCACGGCAUUCAGCAGCAGCGUUGCUGUAACCGACAAAGACACCUUCGAAUUAAGCACAUUCCUCGAUUCCAGCAAAGCACCGCAAC122- example_title: Human GPI protein p137123  pipeline_tag: polyadenylation124  sequence_type: 3' UTR125  task: polyadenylation126  text: UUUUUAAAAGGAAAAGAUACCAAAUGCCUGCUGCUACCACCCUUUUCAAUUGCUAUGUUUUGAAAGGCACCAGUAUGUGUUUUAGAUUGAUUUAAAUGUUUCAUUUAAAUCACGGACAGUAGUUUCAGUUCUGAUGGUAUAAGCAAAACAAAUAAAACGUUUAUAAAAGUUGUAUCUUGAAACACUGGUGUUCAACAGCUAGCAGCUUAUGUGAUUCACCCCAUGCCACGUUAGUGUCACAAAUUUUAUGGUUUAUCUCCAGCAACAUUUCUCUAGUACUUGCACUUAUUAUCUGAAUUC127- example_title: nucleophosmin 1128  pipeline_tag: polyadenylation129  sequence_type: 3' UTR130  task: polyadenylation131  text: GAAAAUAGUUUAAACAAUUUGUUAAAAAAUUUUCCGUCUUAUUUCAUUUCUGUAACAGUUGAUAUCUGGCUGUCCUUUUUAUAAUGCAGAGUGAGAACUUUCCCUACCGUGUUUGAUAAAUGUUGUCCAGGUUCUAUUGCCAAGAAUGUGUUGUCCAAAAUGCCUGUUUAGUUUUUAAAGAUGGAACUCCACCCUUUGCUUGGUUUUAAGUAUGUAUGGAAUGUUAUGAUAGGACAUAGUAGUAGCGGUGGUCAGACAUGGAAAUGGUGGGGAGACAAAAAUAUACAUGUGAAAUAAAACUCAGUAUUUUAAUAAAGUAGCACGGUUUCUAUUGA132- example_title: superoxide dismutase 1133  pipeline_tag: polyadenylation134  sequence_type: 3' UTR135  task: polyadenylation136  text: ACAUUCCCUUGGAUGUAGUCUGAGGCCCCUUAACUCAUCUGUUAUCCUGCUAGCUGUAGAAAUGUAUCCUGAUAAACAUUAAACACUGUAAUCUUAAAAGUGUAAUUGUGUGACUUUUUCAGAGUUGCUUUAAAGUACCUGUAGUGAGAAACUGAUUUAUGAUCACUUGGAAGAUUUGUAUAGUUUUAUAAAACUCAGUUAAAAUGUCUGUUUCAAUGACCUGUAUUUUGCCAGACUUAAAUCACAGAUGGGUAUUAAACUUGUCAGAAUUUCUUUGUCAUUCAAGCCUGUGAAUAAAAACCCUGUAUGGCACUUAUUAUGAGGCUAUUAAAAGAAUCCAAAUUCAAACUAAA137- example_title: hemoglobin subunit alpha 2138  pipeline_tag: polyadenylation139  sequence_type: 3' UTR140  task: polyadenylation141  text: CUGGAGCCUCGGUAGCCGUUCCUCCUGCCCGCUGGGCCUCCCAACGGGCCCUCCUCCCCUCCUUGCACCGGCCCUUCCUGGUCUUUGAAUAAAGUCUGAGUGGGCAGCA142- example_title: BRAF proto-oncogene143  pipeline_tag: polyadenylation144  sequence_type: 3' UTR145  task: polyadenylation146  text: AACAAAUGAGUGAGAGAGUUCAGGAGAGUAGCAACAAAAGGAAAAUAAAUGAACAUAUGUUUGCUUAUAUGUUAAAUUGAAUAAAAUACUCUCUUUUUUUUUAAGGUGAACCAAAGAACACUUGUGUGGUUAAAGACUAGAUAUAAUUUUUCCCCAAACUAAAAUUUAUACUUAACAUUGGAUUUUUAACAUCCAAGGGUUAAAAUACAUAGACAUUGCUAAAAAUUGGCAGAGCCUCUUCUAGAGGCUUUACUUUCUGUUCCGGGUUUGUAUCAUUCACUUGGUUAUUUUAAGUAGUAAACUUCAGUUUCUCAUGCAACUUUUGUUGCCAGCUAUCACAUGUCCACUAGGGACUCCAGAAGAAGACCCUACCUAUGCCUGUGUUUGCAGGUGAGAAGUUGGCAGUCGGUUAGCCUGGG147- example_title: H3 clustered histone 1148  pipeline_tag: polyadenylation149  sequence_type: 3' UTR150  task: polyadenylation151  text: UUACUGUGGUCUCUCUGACGGUCCAAGCAAAGGCUCUUUUCAGAGCCACCACCUUUUC152---153 154# APARENT155 156Convolutional neural network for predicting human 3'UTR Alternative Polyadenylation (APA) from sequence.157 158## Disclaimer159 160This is an UNOFFICIAL implementation of [A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation](https://doi.org/10.1016/j.cell.2019.04.046) by Nicholas Bogard, Johannes Linder, et al.161 162The OFFICIAL repository of APARENT is at [johli/aparent](https://github.com/johli/aparent).163 164> [!TIP]165> The MultiMolecule team has confirmed that the provided model and checkpoints are producing the same intermediate representations as the original implementation.166 167**The team releasing APARENT did not write this model card for this model so this model card has been written by the MultiMolecule team.**168 169## Model Details170 171APARENT (APA REgression NeT) is a convolutional neural network trained on more than 3.5 million randomized 3'UTR poly-A signals expressed on mini-gene reporters in HEK293. Given a fixed-length 205 nt 3'UTR/polyA sequence, APARENT predicts the alternative-polyadenylation isoform proportion (a scalar) and a positional cleavage distribution. The model is primarily used to score the impact of genetic variants on APA regulation and to engineer new polyadenylation signals. Please refer to the [Training Details](#training-details) section for more information on the training process.172 173The base, non-normalised APARENT model is recommended by the original authors for isoform and variant-effect prediction.174 175### Model Specification176 177| Num Layers | Hidden Size | Num Parameters (M) | FLOPs (G) | MACs (G) | Max Num Tokens |178| ---------- | ----------- | ------------------ | --------- | -------- | -------------- |179| 4          | 256         | 6.43               | 0.03      | 0.01     | 205            |180 181### Links182 183- **Code**: [multimolecule.aparent](https://github.com/DLS5-Omics/multimolecule/tree/master/multimolecule/models/aparent)184- **Data**: Massively-parallel polyadenylation MPRA, GEO [GSE113849](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE113849)185- **Paper**: [A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation](https://doi.org/10.1016/j.cell.2019.04.046)186- **Developed by**: Nicholas Bogard, Johannes Linder, Alexander B. Rosenberg, Georg Seelig187- **Model type**: 1D CNN for alternative polyadenylation isoform and cleavage prediction from 3'UTR sequence188- **Original Repository**: [johli/aparent](https://github.com/johli/aparent)189 190## Usage191 192The model file depends on the [`multimolecule`](https://multimolecule.danling.org) library. You can install it using pip:193 194```bash195pip install multimolecule196```197 198### Direct Use199 200#### APA Isoform Prediction201 202You can use this model directly to predict the APA isoform proportion of a 3'UTR/polyA sequence:203 204```python205>>> from multimolecule import RnaTokenizer, AparentForSequencePrediction206 207>>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/aparent")208>>> model = AparentForSequencePrediction.from_pretrained("multimolecule/aparent")209>>> output = model(**tokenizer("ACGUACGUACGU", return_tensors="pt"))210 211>>> output.keys()212odict_keys(['logits'])213```214 215The full APARENT isoform and cleavage outputs are available on the backbone:216 217```python218>>> from multimolecule import RnaTokenizer, AparentModel219 220>>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/aparent")221>>> model = AparentModel.from_pretrained("multimolecule/aparent")222>>> output = model(**tokenizer("ACGUACGUACGU", return_tensors="pt"))223 224>>> output.keys()225odict_keys(['pooler_output', 'isoform_logits', 'cleavage_logits'])226```227 228### Interface229 230- **Input length**: fixed 205 nt 3'UTR / polyA sequence231- **Output (`AparentModel`)**: `isoform_logits` (scalar APA proportion) + `cleavage_logits` (206-dim positional cleavage distribution)232- **Output (`AparentForSequencePrediction`)**: APA isoform scalar only (`logits`)233 234## Training Details235 236APARENT was trained to jointly predict the APA isoform proportion and the positional cleavage distribution of randomized 3'UTR poly-A signals.237 238### Training Data239 240APARENT was trained on more than 3.5 million randomized 3'UTR poly-A signal sequences expressed on mini-gene reporters in HEK293 cells (a massively parallel reporter assay, MPRA). The raw sequencing data for the 3'UTR MPRA libraries are available at GEO accession GSE113849.241 242This APARENT model was trained on all MPRA libraries (no libraries held out) to produce the best general-purpose APA predictor; it differs from the per-library held-out model evaluated in the paper.243 244### Training Procedure245 246#### Pre-training247 248The model was trained to minimize a combined objective: a sigmoid KL-divergence on the isoform proportion and a KL-divergence on the positional cleavage distribution, weighted equally.249 250## Citation251 252```bibtex253@article{bogard2019adeep,254  author    = {Bogard, Nicholas and Linder, Johannes and Rosenberg, Alexander B. and Seelig, Georg},255  title     = {A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation},256  journal   = {Cell},257  volume    = {178},258  number    = {1},259  pages     = {91--106.e23},260  year      = {2019},261  publisher = {Elsevier BV},262  doi       = {10.1016/j.cell.2019.04.046}263}264```265 266> [!NOTE]267> The artifacts distributed in this repository are part of the MultiMolecule project.268> If MultiMolecule supports your research, please cite the MultiMolecule project as follows:269 270```bibtex271@software{chen_2024_12638419,272  author    = {Chen, Zhiyuan and Zhu, Sophia Y.},273  title     = {MultiMolecule},274  doi       = {10.5281/zenodo.12638419},275  publisher = {Zenodo},276  url       = {https://doi.org/10.5281/zenodo.12638419},277  year      = 2024,278  month     = may,279  day       = 4280}281```282 283## Contact284 285Please use GitHub issues of [MultiMolecule](https://github.com/DLS5-Omics/multimolecule/issues) for any questions or comments on the model card.286 287Please contact the authors of the [APARENT paper](https://doi.org/10.1016/j.cell.2019.04.046) for questions or comments on the paper/model.288 289## License290 291This model implementation is licensed under the [GNU Affero General Public License](license.md).292 293For additional terms and clarifications, please refer to our [License FAQ](license-faq.md).294 295```spdx296SPDX-License-Identifier: AGPL-3.0-or-later297```