multimolecule/hal

1---2library_name: multimolecule3license: agpl-3.04pipeline: splice-variant-effect5pipeline_tag: other6tags:7- Biology8- RNA9- Splicing10- rna11widget:12- example_title: microRNA 2113  pipeline_tag: splice-variant-effect14  sequence_type: ncRNA15  task: splice-variant-effect16  text: UAGCUUAUCAGACUGAUGUUGA17- example_title: microRNA 146a18  pipeline_tag: splice-variant-effect19  sequence_type: ncRNA20  task: splice-variant-effect21  text: UGAGAACUGAAUUCCAUGGGUU22- example_title: microRNA 15523  pipeline_tag: splice-variant-effect24  sequence_type: ncRNA25  task: splice-variant-effect26  text: UUAAUGCUAAUCGUGAUAGGGGUU27- example_title: RNA component of mitochondrial RNA processing endoribonuclease28  pipeline_tag: splice-variant-effect29  sequence_type: ncRNA30  task: splice-variant-effect31  text: GGUUCGUGCUGAAGGCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCUCAUUCUCAGCGCGGCUGUAAAAAAAAA32- example_title: 7SK small nuclear RNA33  pipeline_tag: splice-variant-effect34  sequence_type: ncRNA35  task: splice-variant-effect36  text: GGAUGUGAGGGCGAUCUGGCUGCGACAUCUGUCACCCCAUUGAUCGCCAGGGUUGAUUCGGCUGAUCUGGCUGGCUAGGCGGGUGUCCCCUUCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGCGCUCGGUCGAAGAGGACGACCAUCCCCGAUAGAGGAGGACCGGUCUUCGGUCAAGGGUAUACGAGUAGCUGCGCUCCCCUGCUAGAACCUCCAAACAAGCUCUCAAGGUCCAUUUGUAGGAGAACGUAGGGUAGUCAAGCUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGCAUGUGGCAGUCUGCCUUUCUUUU37- example_title: telomerase RNA component38  pipeline_tag: splice-variant-effect39  sequence_type: ncRNA40  task: splice-variant-effect41  text: GGGUUGCGGAGGGUGGGCCUGGGAGGGGUGGUGGCCAUUUUUUGUCUAACCCUAACUGAGAAGGGCGUAGGCGCCGUGCUUUUGCUCCCCGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGAAAAGCCUCGGCCUGCCGCCUUCCACCGUUCAUUCUAGAGCAAACAAAAAAUGUCAGCUGCUGGCCCGUUCGCCCCUCCCGGGGACCUGCGGCGGGUCGCCUGCCCAGCCCCCGAACCCCGCCUGGAGGCCGCGGUCGGCCCGGGGCUUCUCCGGAGGCACCCACUGCCACCGCGAAGAGUUGGGCUCUGUCAGCCGCGGGUCUCUCGGGGGCGAGGGCGAGGUUCAGGCCUUUCAGGCCGCAGGAAGAGGAACGGAGCGAGUCCCCGCGCGCGGCGCGAUUCCCUGAGCUGUGGGACGUGCACCCAGGACUCGGCUCACACAUGC42- example_title: vault RNA 2-143  pipeline_tag: splice-variant-effect44  sequence_type: ncRNA45  task: splice-variant-effect46  text: CGGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUUAUGCAA47- example_title: brain cytoplasmic RNA 148  pipeline_tag: splice-variant-effect49  sequence_type: ncRNA50  task: splice-variant-effect51  text: GGCCGGGCGCGGUGGCUCACGCCUGUAAUCCCAGCUCUCAGGGAGGCUAAGAGGCGGGAGGAUAGCUUGAGCCCAGGAGUUCGAGACCUGCCUGGGCAAUAUAGCGAGACCCCGUUCUCCAGAAAAAGGAAAAAAAAAAACAAAAGACAAAAAAAAAAUAAGCGUAACUUCCCUCAAAGCAACAACCCCCCCCCCCCUUU52- example_title: HIV-1 TAR-WT53  pipeline_tag: splice-variant-effect54  sequence_type: ncRNA55  task: splice-variant-effect56  text: GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACC57- example_title: prion protein (Kanno blood group)58  pipeline_tag: splice-variant-effect59  sequence_type: mRNA60  task: splice-variant-effect61  text: AUGGCGAACCUUGGCUGCUGGAUGCUGGUUCUCUUUGUGGCCACAUGGAGUGACCUGGGCCUCUGC62- example_title: interleukin 1063  pipeline_tag: splice-variant-effect64  sequence_type: mRNA65  task: splice-variant-effect66  text: AUGCACAGCUCAGCACUGCUCUGUUGCCUGGUCCUCCUGACUGGGGUGAGGGCC67- example_title: Zaire ebolavirus68  pipeline_tag: splice-variant-effect69  sequence_type: mRNA70  task: splice-variant-effect71  text: AAUGUUCAAACACUUUGUGAAGCUCUGUUAGCUGAUGGUCUUGCUAAAGCAUUUCCUAGCAAUAUGAUGGUAGUCACAGAGCGUGAGCAAAAAGAAAGCUUAUUGCAUCAAGCAUCAUGGCACCACACAAGUGAUGAUUUUGGUGAGCAUGCCACAGUUAGAGGGAGUAGCUUUGUAACUGAUUUAGAGAAAUACAAUCUUGCAUUUAGAUAUGAGUUUACAGCACCUUUUAUAGAAUAUUGUAACCGUUGCUAUGGUGUUAAGAAUGUUUUUAAUUGGAUGCAUUAUACAAUCCCACAGUGUUAU72- example_title: SARS coronavirus73  pipeline_tag: splice-variant-effect74  sequence_type: mRNA75  task: splice-variant-effect76  text: AUGUUUAUUUUCUUAUUAUUUCUUACUCUCACUAGUGGUAGUGACCUUGACCGGUGCACCACUUUUGAUGAUGUUCAAGCUCCUAAUUACACUCAACAUACUUCAUCUAUGAGGGGGGUUUACUAUCCUGAUGAAAUUUUUAGAUCAGACACUCUUUAUUUAACUCAGGAUUUAUUUCUUCCAUUUUAUUCUAAUGUUACAGGGUUUCAUACUAUUAAUCAUACGUUUGACAACCCUGUCAUACCUUUUAAGGAUGGUAUUUAUUUUGCUGCCACAGAGAAAUCAAAUGUUGUCCGUGGUUGGGUUUUUGGUUCUACCAUGAACAACAAGUCACAGUCGGUGAUUAUUAUUAACAAUUCUACUAAUGUUGUUAUACGAGCAUGUAACUUUGAAUUGUGUGACAACCCUUUCUUUGCUGUUUCUAAACCCAUGGGUACACAGACACAUACUAUGAUAUUCGAUAAUGCAUUUAAAUGCACUUUCGAGUACAUAUCU77- example_title: insulin78  pipeline_tag: splice-variant-effect79  sequence_type: mRNA80  task: splice-variant-effect81  text: AUGGCCCUGUGGAUGCGCCUCCUGCCCCUGCUGGCGCUGCUGGCCCUCUGGGGACCUGACCCAGCCGCAGCCUUUGUGAACCAACACCUGUGCGGCUCACACCUGGUGGAAGCUCUCUACCUAGUGUGCGGGGAACGAGGCUUCUUCUACACACCCAAGACCCGCCGGGAGGCAGAGGACCUGCAGGUGGGGCAGGUGGAGCUGGGCGGGGGCCCUGGUGCAGGCAGCCUGCAGCCCUUGGCCCUGGAGGGGUCCCUGCAGAAGCGUGGCAUUGUGGAACAAUGCUGUACCAGCAUCUGCUCCCUCUACCAGCUGGAGAACUACUGCAACUAG82- example_title: cyclin dependent kinase inhibitor 2A83  pipeline_tag: splice-variant-effect84  sequence_type: mRNA85  task: splice-variant-effect86  text: AUGGAGCCGGCGGCGGGGAGCAGCAUGGAGCCUUCGGCUGACUGGCUGGCCACGGCCGCGGCCCGGGGUCGGGUAGAGGAGGUGCGGGCGCUGCUGGAGGCGGGGGCGCUGCCCAACGCACCGAAUAGUUACGGUCGGAGGCCGAUCCAGGUCAUGAUGAUGGGCAGCGCCCGAGUGGCGGAGCUGCUGCUGCUCCACGGCGCGGAGCCCAACUGCGCCGACCCCGCCACUCUCACCCGACCCGUGCACGACGCUGCCCGGGAGGGCUUCCUGGACACGCUGGUGGUGCUGCACCGGGCCGGGGCGCGGCUGGACGUGCGCGAUGCCUGGGGCCGUCUGCCCGUGGACCUGGCUGAGGAGCUGGGCCAUCGCGAUGUCGCACGGUACCUGCGCGCGGCUGCGGGGGGCACCAGAGGCAGUAACCAUGCCCGCAUAGAUGCCGCGGAAGGUCCCUCAGACAUCCCCGAUUGA87- example_title: human papillomavirus type 16 E688  pipeline_tag: splice-variant-effect89  sequence_type: mRNA90  task: splice-variant-effect91  text: AUGCACCAAAAGAGAACUGCAAUGUUUCAGGACCCACAGGAGCGACCCAGAAAGUUACCACAGUUAUGCACAGAGCUGCAAACAACUAUACAUGAUAUAAUAUUAGAAUGUGUGUACUGCAAGCAACAGUUACUGCGACGUGAGGUAUAUGACUUUGCUUUUCGGGAUUUAUGCAUAGUAUAUAGAGAUGGGAAUCCAUAUGCUGUAUGUGAUAAAUGUUUAAAGUUUUAUUCUAAAAUUAGUGAGUAUAGACAUUAUUGUUAUAGUUUGUAUGGAACAACAUUAGAACAGCAAUACAACAAACCGUUGUGUGAUUUGUUAAUUAGGUGUAUUAACUGUCAAAAGCCACUGUGUCCUGAAGAAAAGCAAAGACAUCUGGACAAAAAGCAAAGAUUCCAUAAUAUAAGGGGUCGGUGGACCGGUCGAUGUAUGUCUUGUUGCAGAUCAUCAAGAACACGUAGAGAAACCCAGCUGUAA92- example_title: NRAS proto-oncogene93  pipeline_tag: splice-variant-effect94  sequence_type: 5' UTR95  task: splice-variant-effect96  text: GGGGCCGGAAGUGCCGCUCCUUGGUGGGGGCUGUUCAUGGCGGUUCCGGGGUCUCCAACAUUUUUCCCGGCUGUGGUCCUAAAUCUGUCCAAAGCAGAGGCAGUGGAGCUUGAGGUUCUUGCUGGUGUGAA97- example_title: amyloid beta precursor protein98  pipeline_tag: splice-variant-effect99  sequence_type: 5' UTR100  task: splice-variant-effect101  text: GUCAGUUUCCUCGGCAGCGGUAGGCGAGAGCACGCGGAGGAGCGUGCGCGGGGGCCCCGGGAGACGGCGGCGGUGGCGGCGCGGGCAGAGCAAGGACGCGGCGGAUCCCACUCGCACAGCAGCGCACUCGGUGCCCCGCGCAGGGUCGCG102- example_title: RUNX family transcription factor 1103  pipeline_tag: splice-variant-effect104  sequence_type: 5' UTR105  task: splice-variant-effect106  text: ACUUCUUUGGGCCUCAUAAACAACCACAGAACCACAAGUUGGGUAGCCUGGCAGUGUCAGAAGUCUGAACCCAGCAUAGUGGUCAGCAGGCAGGACGAAUCACACUGAAUGCAAACCACAGGGUUUCGCAGCGUGGUAAAAGAAAUCAUUGAGUCCCCCGCCUUCAGAAGAGGGUGCAUUUUCAGGAGGAAGCG107- example_title: fragile X messenger ribonucleoprotein 1108  pipeline_tag: splice-variant-effect109  sequence_type: 5' UTR110  task: splice-variant-effect111  text: CUCAGUCAGGCGCUCAGCUCCGUUUCGGUUUCACUUCCGGUGGAGGGCCGCCUCUGAGCGGGCGGCGGGCCGACGGCGAGCGCGGGCGGCGGCGGUGACGGAGGCGCCGCUGCCAGGGGGCGUGCGGCAGCGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCUGGGCCUCGAGCGCCCGCAGCCCACCUCUCGGGGGCGGGCUCCCGGCGCUAGCAGGGCUGAAGAGAAG112- example_title: MYC proto-oncogene113  pipeline_tag: splice-variant-effect114  sequence_type: 5' UTR115  task: splice-variant-effect116  text: AACUCGCUGUAGUAAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGCCGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCUGAUCCCCCAGCCAGCGGUCCGCAACCCUUGCCGCAUCCACGAAACUUUGCCCAUAGCAGCGGGCGGGCACUUUGCACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCUAUUCUGCCCAUUUGGGGACACUUCCCCGCCGCUGCCAGGACCCGCUUCUCUGAAAGGCUCUCCUUGCAGCUGCUUAGACG117- example_title: activating transcription factor 4118  pipeline_tag: splice-variant-effect119  sequence_type: 5' UTR120  task: splice-variant-effect121  text: CAUUUCUACUUUGCCCGCCCACAGAUGUAGUUUUCUCUGCGCGUGUGCGUUUUCCCUCCUCCCCGCCCUCAGGGUCCACGGCCACCAUGGCGUAUUAGGGGCAGCAGUGCCUGCGGCAGCAUUGGCCUUUGCAGCGGCGGCAGCAGCACCAGGCUCUGCAGCGGCAACCCCCAGCGGCUUAAGCCAUGGCGCUUCUCACGGCAUUCAGCAGCAGCGUUGCUGUAACCGACAAAGACACCUUCGAAUUAAGCACAUUCCUCGAUUCCAGCAAAGCACCGCAAC122- example_title: Human GPI protein p137123  pipeline_tag: splice-variant-effect124  sequence_type: 3' UTR125  task: splice-variant-effect126  text: UUUUUAAAAGGAAAAGAUACCAAAUGCCUGCUGCUACCACCCUUUUCAAUUGCUAUGUUUUGAAAGGCACCAGUAUGUGUUUUAGAUUGAUUUAAAUGUUUCAUUUAAAUCACGGACAGUAGUUUCAGUUCUGAUGGUAUAAGCAAAACAAAUAAAACGUUUAUAAAAGUUGUAUCUUGAAACACUGGUGUUCAACAGCUAGCAGCUUAUGUGAUUCACCCCAUGCCACGUUAGUGUCACAAAUUUUAUGGUUUAUCUCCAGCAACAUUUCUCUAGUACUUGCACUUAUUAUCUGAAUUC127- example_title: nucleophosmin 1128  pipeline_tag: splice-variant-effect129  sequence_type: 3' UTR130  task: splice-variant-effect131  text: GAAAAUAGUUUAAACAAUUUGUUAAAAAAUUUUCCGUCUUAUUUCAUUUCUGUAACAGUUGAUAUCUGGCUGUCCUUUUUAUAAUGCAGAGUGAGAACUUUCCCUACCGUGUUUGAUAAAUGUUGUCCAGGUUCUAUUGCCAAGAAUGUGUUGUCCAAAAUGCCUGUUUAGUUUUUAAAGAUGGAACUCCACCCUUUGCUUGGUUUUAAGUAUGUAUGGAAUGUUAUGAUAGGACAUAGUAGUAGCGGUGGUCAGACAUGGAAAUGGUGGGGAGACAAAAAUAUACAUGUGAAAUAAAACUCAGUAUUUUAAUAAAGUAGCACGGUUUCUAUUGA132- example_title: superoxide dismutase 1133  pipeline_tag: splice-variant-effect134  sequence_type: 3' UTR135  task: splice-variant-effect136  text: ACAUUCCCUUGGAUGUAGUCUGAGGCCCCUUAACUCAUCUGUUAUCCUGCUAGCUGUAGAAAUGUAUCCUGAUAAACAUUAAACACUGUAAUCUUAAAAGUGUAAUUGUGUGACUUUUUCAGAGUUGCUUUAAAGUACCUGUAGUGAGAAACUGAUUUAUGAUCACUUGGAAGAUUUGUAUAGUUUUAUAAAACUCAGUUAAAAUGUCUGUUUCAAUGACCUGUAUUUUGCCAGACUUAAAUCACAGAUGGGUAUUAAACUUGUCAGAAUUUCUUUGUCAUUCAAGCCUGUGAAUAAAAACCCUGUAUGGCACUUAUUAUGAGGCUAUUAAAAGAAUCCAAAUUCAAACUAAA137- example_title: hemoglobin subunit alpha 2138  pipeline_tag: splice-variant-effect139  sequence_type: 3' UTR140  task: splice-variant-effect141  text: CUGGAGCCUCGGUAGCCGUUCCUCCUGCCCGCUGGGCCUCCCAACGGGCCCUCCUCCCCUCCUUGCACCGGCCCUUCCUGGUCUUUGAAUAAAGUCUGAGUGGGCAGCA142- example_title: BRAF proto-oncogene143  pipeline_tag: splice-variant-effect144  sequence_type: 3' UTR145  task: splice-variant-effect146  text: AACAAAUGAGUGAGAGAGUUCAGGAGAGUAGCAACAAAAGGAAAAUAAAUGAACAUAUGUUUGCUUAUAUGUUAAAUUGAAUAAAAUACUCUCUUUUUUUUUAAGGUGAACCAAAGAACACUUGUGUGGUUAAAGACUAGAUAUAAUUUUUCCCCAAACUAAAAUUUAUACUUAACAUUGGAUUUUUAACAUCCAAGGGUUAAAAUACAUAGACAUUGCUAAAAAUUGGCAGAGCCUCUUCUAGAGGCUUUACUUUCUGUUCCGGGUUUGUAUCAUUCACUUGGUUAUUUUAAGUAGUAAACUUCAGUUUCUCAUGCAACUUUUGUUGCCAGCUAUCACAUGUCCACUAGGGACUCCAGAAGAAGACCCUACCUAUGCCUGUGUUUGCAGGUGAGAAGUUGGCAGUCGGUUAGCCUGGG147- example_title: H3 clustered histone 1148  pipeline_tag: splice-variant-effect149  sequence_type: 3' UTR150  task: splice-variant-effect151  text: UUACUGUGGUCUCUCUGACGGUCCAAGCAAAGGCUCUUUUCAGAGCCACCACCUUUUC152---153 154# HAL155 156Hexamer Additive Linear model for predicting alternative splicing from sequence.157 158## Disclaimer159 160This is an UNOFFICIAL implementation of [Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences](https://doi.org/10.1016/j.cell.2015.09.054) by Alexander B. Rosenberg, et al.161 162The OFFICIAL repository of HAL is at [Alex-Rosenberg/cell-2015](https://github.com/Alex-Rosenberg/cell-2015).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 HAL did not write this model card for this model so this model card has been written by the MultiMolecule team.**168 169## Model Details170 171HAL is a linear (additive) model that scores alternative 5' splice-site usage from normalized hexamer (6-mer) frequencies across a 160-nucleotide donor-region window. It was learned from massively parallel reporter assays measuring splicing of millions of random synthetic sequences. The published coefficient table contains a `(4096, 8)` matrix of hexamer effects; the model averages the eight coefficient columns into one effect per hexamer and applies those effects to normalized hexamer frequencies.172 173### Model Specification174 175| Window | Published Coefficient Columns | Hexamer Features | Num Parameters (M) | FLOPs | MACs  |176| ------ | ----------------------------- | ---------------- | ------------------ | ----- | ----- |177| 160 nt | 8 averaged                    | 4,096            | 0.004              | 8,192 | 4,096 |178 179### Links180 181- **Code**: [multimolecule.hal](https://github.com/DLS5-Omics/multimolecule/tree/master/multimolecule/models/hal)182- **Data**: Rosenberg lab random-library 5' splice-site MPRA183- **Paper**: [Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences](https://doi.org/10.1016/j.cell.2015.09.054)184- **Developed by**: Alexander B. Rosenberg, Rupali P. Patwardhan, Jay Shendure, Georg Seelig185- **Model type**: Linear regression over normalized hexamer-frequency features with learned per-hexamer effect coefficients186- **Original Repository**: [Alex-Rosenberg/cell-2015](https://github.com/Alex-Rosenberg/cell-2015)187 188## Usage189 190The model file depends on the [`multimolecule`](https://multimolecule.danling.org) library. You can install it using pip:191 192```bash193pip install multimolecule194```195 196### Direct Use197 198#### Alternative Splicing Prediction199 200You can use this model directly to predict a splicing score for a 160-nucleotide RNA sequence window:201 202```python203>>> import torch204>>> from multimolecule import RnaTokenizer, HalForSequencePrediction205 206>>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/hal")207>>> model = HalForSequencePrediction.from_pretrained("multimolecule/hal")208>>> sequence = "ACGU" * 40209>>> input = tokenizer(sequence, add_special_tokens=False, return_tensors="pt")210>>> output = model(**input)211 212>>> output.logits.shape213torch.Size([1, 1])214```215 216### Interface217 218- **Input length**: 160 nt fixed donor-region window219- **Alphabet**: `ACGU` only; any hexamer spanning an unknown / `N` token is ignored220- **Special tokens**: do not add (`add_special_tokens=False`)221- **Output**: single scalar splicing score per window222- **Variant effect**: subtract two window scores and apply sigmoid externally for paired donor comparisons223 224## Training Details225 226HAL was learned from massively parallel splicing reporter assays in which millions of random synthetic sequences were inserted into an alternatively spliced reporter minigene. Splicing outcomes were measured by high-throughput sequencing of the resulting mRNA isoforms.227 228### Training Data229 230The model was trained on the splicing measurements of millions of degenerate (random) sequences from the reporter library described in the HAL paper. Hexamer coefficients were estimated by regressing the measured splicing index against the hexamer composition of each sequence.231 232### Training Procedure233 234#### Pre-training235 236HAL is a linear regression model. The published hexamer coefficient table is fit to the measured splicing index, and the model prediction is the linear combination of normalized hexamer frequencies with the averaged hexamer effects.237 238The HAL model uses the published `HAL_mer_scores.npz` hexamer coefficient table from Rosenberg et al. The table stores 4,096 hexamer rows and eight coefficient columns; the eight columns are averaged into the single per-hexamer effect used by the HAL formula.239 240## Citation241 242```bibtex243@article{rosenberg2015learning,244  author    = {Rosenberg, Alexander B. and Patwardhan, Rupali P. and Shendure, Jay and Seelig, Georg},245  journal   = {Cell},246  number    = 3,247  pages     = {698--711},248  publisher = {Elsevier BV},249  title     = {Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences},250  volume    = 163,251  year      = 2015,252  doi       = {10.1016/j.cell.2015.09.054}253}254```255 256> [!NOTE]257> The artifacts distributed in this repository are part of the MultiMolecule project.258> If MultiMolecule supports your research, please cite the MultiMolecule project as follows:259 260```bibtex261@software{chen_2024_12638419,262  author    = {Chen, Zhiyuan and Zhu, Sophia Y.},263  title     = {MultiMolecule},264  doi       = {10.5281/zenodo.12638419},265  publisher = {Zenodo},266  url       = {https://doi.org/10.5281/zenodo.12638419},267  year      = 2024,268  month     = may,269  day       = 4270}271```272 273## Contact274 275Please use GitHub issues of [MultiMolecule](https://github.com/DLS5-Omics/multimolecule/issues) for any questions or comments on the model card.276 277Please contact the authors of the [HAL paper](https://doi.org/10.1016/j.cell.2015.09.054) for questions or comments on the paper/model.278 279## License280 281This model implementation is licensed under the [GNU Affero General Public License](license.md).282 283For additional terms and clarifications, please refer to our [License FAQ](license-faq.md).284 285```spdx286SPDX-License-Identifier: AGPL-3.0-or-later287```