--- library_name: multimolecule license: agpl-3.0 pipeline: polyadenylation pipeline_tag: other tags: - Biology - RNA - 3' UTR - rna widget: - example_title: microRNA 21 pipeline_tag: polyadenylation sequence_type: ncRNA task: polyadenylation text: UAGCUUAUCAGACUGAUGUUGA - example_title: microRNA 146a pipeline_tag: polyadenylation sequence_type: ncRNA task: polyadenylation text: UGAGAACUGAAUUCCAUGGGUU - example_title: microRNA 155 pipeline_tag: polyadenylation sequence_type: ncRNA task: polyadenylation text: UUAAUGCUAAUCGUGAUAGGGGUU - example_title: RNA component of mitochondrial RNA processing endoribonuclease pipeline_tag: polyadenylation sequence_type: ncRNA task: polyadenylation text: GGUUCGUGCUGAAGGCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCUCAUUCUCAGCGCGGCUGUAAAAAAAAA - example_title: 7SK small nuclear RNA pipeline_tag: polyadenylation sequence_type: ncRNA task: polyadenylation text: GGAUGUGAGGGCGAUCUGGCUGCGACAUCUGUCACCCCAUUGAUCGCCAGGGUUGAUUCGGCUGAUCUGGCUGGCUAGGCGGGUGUCCCCUUCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGCGCUCGGUCGAAGAGGACGACCAUCCCCGAUAGAGGAGGACCGGUCUUCGGUCAAGGGUAUACGAGUAGCUGCGCUCCCCUGCUAGAACCUCCAAACAAGCUCUCAAGGUCCAUUUGUAGGAGAACGUAGGGUAGUCAAGCUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGCAUGUGGCAGUCUGCCUUUCUUUU - example_title: telomerase RNA component pipeline_tag: polyadenylation sequence_type: ncRNA task: polyadenylation text: GGGUUGCGGAGGGUGGGCCUGGGAGGGGUGGUGGCCAUUUUUUGUCUAACCCUAACUGAGAAGGGCGUAGGCGCCGUGCUUUUGCUCCCCGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGAAAAGCCUCGGCCUGCCGCCUUCCACCGUUCAUUCUAGAGCAAACAAAAAAUGUCAGCUGCUGGCCCGUUCGCCCCUCCCGGGGACCUGCGGCGGGUCGCCUGCCCAGCCCCCGAACCCCGCCUGGAGGCCGCGGUCGGCCCGGGGCUUCUCCGGAGGCACCCACUGCCACCGCGAAGAGUUGGGCUCUGUCAGCCGCGGGUCUCUCGGGGGCGAGGGCGAGGUUCAGGCCUUUCAGGCCGCAGGAAGAGGAACGGAGCGAGUCCCCGCGCGCGGCGCGAUUCCCUGAGCUGUGGGACGUGCACCCAGGACUCGGCUCACACAUGC - example_title: vault RNA 2-1 pipeline_tag: polyadenylation sequence_type: ncRNA task: polyadenylation text: CGGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUUAUGCAA - example_title: brain cytoplasmic RNA 1 pipeline_tag: polyadenylation sequence_type: ncRNA task: polyadenylation text: GGCCGGGCGCGGUGGCUCACGCCUGUAAUCCCAGCUCUCAGGGAGGCUAAGAGGCGGGAGGAUAGCUUGAGCCCAGGAGUUCGAGACCUGCCUGGGCAAUAUAGCGAGACCCCGUUCUCCAGAAAAAGGAAAAAAAAAAACAAAAGACAAAAAAAAAAUAAGCGUAACUUCCCUCAAAGCAACAACCCCCCCCCCCCUUU - example_title: HIV-1 TAR-WT pipeline_tag: polyadenylation sequence_type: ncRNA task: polyadenylation text: GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACC - example_title: prion protein (Kanno blood group) pipeline_tag: polyadenylation sequence_type: mRNA task: polyadenylation text: AUGGCGAACCUUGGCUGCUGGAUGCUGGUUCUCUUUGUGGCCACAUGGAGUGACCUGGGCCUCUGC - example_title: interleukin 10 pipeline_tag: polyadenylation sequence_type: mRNA task: polyadenylation text: AUGCACAGCUCAGCACUGCUCUGUUGCCUGGUCCUCCUGACUGGGGUGAGGGCC - example_title: Zaire ebolavirus pipeline_tag: polyadenylation sequence_type: mRNA task: polyadenylation text: AAUGUUCAAACACUUUGUGAAGCUCUGUUAGCUGAUGGUCUUGCUAAAGCAUUUCCUAGCAAUAUGAUGGUAGUCACAGAGCGUGAGCAAAAAGAAAGCUUAUUGCAUCAAGCAUCAUGGCACCACACAAGUGAUGAUUUUGGUGAGCAUGCCACAGUUAGAGGGAGUAGCUUUGUAACUGAUUUAGAGAAAUACAAUCUUGCAUUUAGAUAUGAGUUUACAGCACCUUUUAUAGAAUAUUGUAACCGUUGCUAUGGUGUUAAGAAUGUUUUUAAUUGGAUGCAUUAUACAAUCCCACAGUGUUAU - example_title: SARS coronavirus pipeline_tag: polyadenylation sequence_type: mRNA task: polyadenylation text: AUGUUUAUUUUCUUAUUAUUUCUUACUCUCACUAGUGGUAGUGACCUUGACCGGUGCACCACUUUUGAUGAUGUUCAAGCUCCUAAUUACACUCAACAUACUUCAUCUAUGAGGGGGGUUUACUAUCCUGAUGAAAUUUUUAGAUCAGACACUCUUUAUUUAACUCAGGAUUUAUUUCUUCCAUUUUAUUCUAAUGUUACAGGGUUUCAUACUAUUAAUCAUACGUUUGACAACCCUGUCAUACCUUUUAAGGAUGGUAUUUAUUUUGCUGCCACAGAGAAAUCAAAUGUUGUCCGUGGUUGGGUUUUUGGUUCUACCAUGAACAACAAGUCACAGUCGGUGAUUAUUAUUAACAAUUCUACUAAUGUUGUUAUACGAGCAUGUAACUUUGAAUUGUGUGACAACCCUUUCUUUGCUGUUUCUAAACCCAUGGGUACACAGACACAUACUAUGAUAUUCGAUAAUGCAUUUAAAUGCACUUUCGAGUACAUAUCU - example_title: insulin pipeline_tag: polyadenylation sequence_type: mRNA task: polyadenylation text: AUGGCCCUGUGGAUGCGCCUCCUGCCCCUGCUGGCGCUGCUGGCCCUCUGGGGACCUGACCCAGCCGCAGCCUUUGUGAACCAACACCUGUGCGGCUCACACCUGGUGGAAGCUCUCUACCUAGUGUGCGGGGAACGAGGCUUCUUCUACACACCCAAGACCCGCCGGGAGGCAGAGGACCUGCAGGUGGGGCAGGUGGAGCUGGGCGGGGGCCCUGGUGCAGGCAGCCUGCAGCCCUUGGCCCUGGAGGGGUCCCUGCAGAAGCGUGGCAUUGUGGAACAAUGCUGUACCAGCAUCUGCUCCCUCUACCAGCUGGAGAACUACUGCAACUAG - example_title: cyclin dependent kinase inhibitor 2A pipeline_tag: polyadenylation sequence_type: mRNA task: polyadenylation text: AUGGAGCCGGCGGCGGGGAGCAGCAUGGAGCCUUCGGCUGACUGGCUGGCCACGGCCGCGGCCCGGGGUCGGGUAGAGGAGGUGCGGGCGCUGCUGGAGGCGGGGGCGCUGCCCAACGCACCGAAUAGUUACGGUCGGAGGCCGAUCCAGGUCAUGAUGAUGGGCAGCGCCCGAGUGGCGGAGCUGCUGCUGCUCCACGGCGCGGAGCCCAACUGCGCCGACCCCGCCACUCUCACCCGACCCGUGCACGACGCUGCCCGGGAGGGCUUCCUGGACACGCUGGUGGUGCUGCACCGGGCCGGGGCGCGGCUGGACGUGCGCGAUGCCUGGGGCCGUCUGCCCGUGGACCUGGCUGAGGAGCUGGGCCAUCGCGAUGUCGCACGGUACCUGCGCGCGGCUGCGGGGGGCACCAGAGGCAGUAACCAUGCCCGCAUAGAUGCCGCGGAAGGUCCCUCAGACAUCCCCGAUUGA - example_title: human papillomavirus type 16 E6 pipeline_tag: polyadenylation sequence_type: mRNA task: polyadenylation text: AUGCACCAAAAGAGAACUGCAAUGUUUCAGGACCCACAGGAGCGACCCAGAAAGUUACCACAGUUAUGCACAGAGCUGCAAACAACUAUACAUGAUAUAAUAUUAGAAUGUGUGUACUGCAAGCAACAGUUACUGCGACGUGAGGUAUAUGACUUUGCUUUUCGGGAUUUAUGCAUAGUAUAUAGAGAUGGGAAUCCAUAUGCUGUAUGUGAUAAAUGUUUAAAGUUUUAUUCUAAAAUUAGUGAGUAUAGACAUUAUUGUUAUAGUUUGUAUGGAACAACAUUAGAACAGCAAUACAACAAACCGUUGUGUGAUUUGUUAAUUAGGUGUAUUAACUGUCAAAAGCCACUGUGUCCUGAAGAAAAGCAAAGACAUCUGGACAAAAAGCAAAGAUUCCAUAAUAUAAGGGGUCGGUGGACCGGUCGAUGUAUGUCUUGUUGCAGAUCAUCAAGAACACGUAGAGAAACCCAGCUGUAA - example_title: NRAS proto-oncogene pipeline_tag: polyadenylation sequence_type: 5' UTR task: polyadenylation text: GGGGCCGGAAGUGCCGCUCCUUGGUGGGGGCUGUUCAUGGCGGUUCCGGGGUCUCCAACAUUUUUCCCGGCUGUGGUCCUAAAUCUGUCCAAAGCAGAGGCAGUGGAGCUUGAGGUUCUUGCUGGUGUGAA - example_title: amyloid beta precursor protein pipeline_tag: polyadenylation sequence_type: 5' UTR task: polyadenylation text: GUCAGUUUCCUCGGCAGCGGUAGGCGAGAGCACGCGGAGGAGCGUGCGCGGGGGCCCCGGGAGACGGCGGCGGUGGCGGCGCGGGCAGAGCAAGGACGCGGCGGAUCCCACUCGCACAGCAGCGCACUCGGUGCCCCGCGCAGGGUCGCG - example_title: RUNX family transcription factor 1 pipeline_tag: polyadenylation sequence_type: 5' UTR task: polyadenylation text: ACUUCUUUGGGCCUCAUAAACAACCACAGAACCACAAGUUGGGUAGCCUGGCAGUGUCAGAAGUCUGAACCCAGCAUAGUGGUCAGCAGGCAGGACGAAUCACACUGAAUGCAAACCACAGGGUUUCGCAGCGUGGUAAAAGAAAUCAUUGAGUCCCCCGCCUUCAGAAGAGGGUGCAUUUUCAGGAGGAAGCG - example_title: fragile X messenger ribonucleoprotein 1 pipeline_tag: polyadenylation sequence_type: 5' UTR task: polyadenylation text: CUCAGUCAGGCGCUCAGCUCCGUUUCGGUUUCACUUCCGGUGGAGGGCCGCCUCUGAGCGGGCGGCGGGCCGACGGCGAGCGCGGGCGGCGGCGGUGACGGAGGCGCCGCUGCCAGGGGGCGUGCGGCAGCGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCUGGGCCUCGAGCGCCCGCAGCCCACCUCUCGGGGGCGGGCUCCCGGCGCUAGCAGGGCUGAAGAGAAG - example_title: MYC proto-oncogene pipeline_tag: polyadenylation sequence_type: 5' UTR task: polyadenylation text: AACUCGCUGUAGUAAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGCCGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCUGAUCCCCCAGCCAGCGGUCCGCAACCCUUGCCGCAUCCACGAAACUUUGCCCAUAGCAGCGGGCGGGCACUUUGCACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCUAUUCUGCCCAUUUGGGGACACUUCCCCGCCGCUGCCAGGACCCGCUUCUCUGAAAGGCUCUCCUUGCAGCUGCUUAGACG - example_title: activating transcription factor 4 pipeline_tag: polyadenylation sequence_type: 5' UTR task: polyadenylation text: CAUUUCUACUUUGCCCGCCCACAGAUGUAGUUUUCUCUGCGCGUGUGCGUUUUCCCUCCUCCCCGCCCUCAGGGUCCACGGCCACCAUGGCGUAUUAGGGGCAGCAGUGCCUGCGGCAGCAUUGGCCUUUGCAGCGGCGGCAGCAGCACCAGGCUCUGCAGCGGCAACCCCCAGCGGCUUAAGCCAUGGCGCUUCUCACGGCAUUCAGCAGCAGCGUUGCUGUAACCGACAAAGACACCUUCGAAUUAAGCACAUUCCUCGAUUCCAGCAAAGCACCGCAAC - example_title: Human GPI protein p137 pipeline_tag: polyadenylation sequence_type: 3' UTR task: polyadenylation text: UUUUUAAAAGGAAAAGAUACCAAAUGCCUGCUGCUACCACCCUUUUCAAUUGCUAUGUUUUGAAAGGCACCAGUAUGUGUUUUAGAUUGAUUUAAAUGUUUCAUUUAAAUCACGGACAGUAGUUUCAGUUCUGAUGGUAUAAGCAAAACAAAUAAAACGUUUAUAAAAGUUGUAUCUUGAAACACUGGUGUUCAACAGCUAGCAGCUUAUGUGAUUCACCCCAUGCCACGUUAGUGUCACAAAUUUUAUGGUUUAUCUCCAGCAACAUUUCUCUAGUACUUGCACUUAUUAUCUGAAUUC - example_title: nucleophosmin 1 pipeline_tag: polyadenylation sequence_type: 3' UTR task: polyadenylation text: GAAAAUAGUUUAAACAAUUUGUUAAAAAAUUUUCCGUCUUAUUUCAUUUCUGUAACAGUUGAUAUCUGGCUGUCCUUUUUAUAAUGCAGAGUGAGAACUUUCCCUACCGUGUUUGAUAAAUGUUGUCCAGGUUCUAUUGCCAAGAAUGUGUUGUCCAAAAUGCCUGUUUAGUUUUUAAAGAUGGAACUCCACCCUUUGCUUGGUUUUAAGUAUGUAUGGAAUGUUAUGAUAGGACAUAGUAGUAGCGGUGGUCAGACAUGGAAAUGGUGGGGAGACAAAAAUAUACAUGUGAAAUAAAACUCAGUAUUUUAAUAAAGUAGCACGGUUUCUAUUGA - example_title: superoxide dismutase 1 pipeline_tag: polyadenylation sequence_type: 3' UTR task: polyadenylation text: ACAUUCCCUUGGAUGUAGUCUGAGGCCCCUUAACUCAUCUGUUAUCCUGCUAGCUGUAGAAAUGUAUCCUGAUAAACAUUAAACACUGUAAUCUUAAAAGUGUAAUUGUGUGACUUUUUCAGAGUUGCUUUAAAGUACCUGUAGUGAGAAACUGAUUUAUGAUCACUUGGAAGAUUUGUAUAGUUUUAUAAAACUCAGUUAAAAUGUCUGUUUCAAUGACCUGUAUUUUGCCAGACUUAAAUCACAGAUGGGUAUUAAACUUGUCAGAAUUUCUUUGUCAUUCAAGCCUGUGAAUAAAAACCCUGUAUGGCACUUAUUAUGAGGCUAUUAAAAGAAUCCAAAUUCAAACUAAA - example_title: hemoglobin subunit alpha 2 pipeline_tag: polyadenylation sequence_type: 3' UTR task: polyadenylation text: CUGGAGCCUCGGUAGCCGUUCCUCCUGCCCGCUGGGCCUCCCAACGGGCCCUCCUCCCCUCCUUGCACCGGCCCUUCCUGGUCUUUGAAUAAAGUCUGAGUGGGCAGCA - example_title: BRAF proto-oncogene pipeline_tag: polyadenylation sequence_type: 3' UTR task: polyadenylation text: AACAAAUGAGUGAGAGAGUUCAGGAGAGUAGCAACAAAAGGAAAAUAAAUGAACAUAUGUUUGCUUAUAUGUUAAAUUGAAUAAAAUACUCUCUUUUUUUUUAAGGUGAACCAAAGAACACUUGUGUGGUUAAAGACUAGAUAUAAUUUUUCCCCAAACUAAAAUUUAUACUUAACAUUGGAUUUUUAACAUCCAAGGGUUAAAAUACAUAGACAUUGCUAAAAAUUGGCAGAGCCUCUUCUAGAGGCUUUACUUUCUGUUCCGGGUUUGUAUCAUUCACUUGGUUAUUUUAAGUAGUAAACUUCAGUUUCUCAUGCAACUUUUGUUGCCAGCUAUCACAUGUCCACUAGGGACUCCAGAAGAAGACCCUACCUAUGCCUGUGUUUGCAGGUGAGAAGUUGGCAGUCGGUUAGCCUGGG - example_title: H3 clustered histone 1 pipeline_tag: polyadenylation sequence_type: 3' UTR task: polyadenylation text: UUACUGUGGUCUCUCUGACGGUCCAAGCAAAGGCUCUUUUCAGAGCCACCACCUUUUC --- # APARENT2 Deep residual neural network for predicting human 3' UTR Alternative Polyadenylation (APA) and cleavage magnitude at nucleotide resolution, and for deciphering the impact of genetic variants on polyadenylation. ## Disclaimer This is an UNOFFICIAL implementation of [Deciphering the impact of genetic variation on human polyadenylation using APARENT2](https://doi.org/10.1186/s13059-022-02799-4) by Johannes Linder, Samantha E. Koplik, et al. The OFFICIAL repository of APARENT2 is at [johli/aparent-resnet](https://github.com/johli/aparent-resnet). > [!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 APARENT2 did not write this model card for this model so this model card has been written by the MultiMolecule team.** ## Model Details APARENT2 is a residual convolutional neural network (a ResNet successor to the original [APARENT](https://github.com/johli/aparent)) trained on a 3' UTR massively parallel reporter assay (MPRA). Given a fixed 205 nt polyadenylation signal (PAS) sequence, it predicts a nucleotide-resolution cleavage probability distribution as well as the overall isoform abundance. It is primarily used to score the effect of genetic variants on polyadenylation by comparing the predictions for a reference and an alternate sequence. ### Model Specification | Num Layers | Hidden Size | Num Parameters (M) | FLOPs (G) | MACs (G) | Max Num Tokens | | ---------- | ----------- | ------------------ | --------- | -------- | -------------- | | 28 | 32 | 0.19 | 0.08 | 0.04 | 205 | ### Links - **Code**: [multimolecule.aparent2](https://github.com/DLS5-Omics/multimolecule/tree/master/multimolecule/models/aparent2) - **Data**: Massively-parallel polyadenylation MPRA with variant-effect evaluation data - **Paper**: [Deciphering the impact of genetic variation on human polyadenylation using APARENT2](https://doi.org/10.1186/s13059-022-02799-4) - **Developed by**: Johannes Linder, Samantha E. Koplik, Anshul Kundaje, Georg Seelig - **Model type**: 1D residual CNN successor to APARENT for polyadenylation isoform, cleavage, and variant-effect prediction - **Original Repository**: [johli/aparent-resnet](https://github.com/johli/aparent-resnet) ## 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 #### Polyadenylation Cleavage Prediction You can use this model directly to predict the cleavage distribution of a 205 nt polyadenylation signal sequence (core hexamer starting at position 70): ```python >>> import torch >>> from multimolecule import RnaTokenizer, Aparent2Model >>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/aparent2") >>> model = Aparent2Model.from_pretrained("multimolecule/aparent2") >>> sequence = "A" * 70 + "AAUAAA" + "A" * 129 >>> output = model(**tokenizer(sequence, return_tensors="pt")) >>> output.logits.shape torch.Size([1, 206]) ``` #### Variant Effect Scoring Score a reference and an alternate sequence separately, then compare: ```python >>> import torch >>> ref = "A" * 70 + "AAUAAA" + "A" * 129 >>> alt = "A" * 70 + "AAUACA" + "A" * 129 >>> ref_prob = torch.softmax(model(**tokenizer(ref, return_tensors="pt")).logits, dim=-1) >>> alt_prob = torch.softmax(model(**tokenizer(alt, return_tensors="pt")).logits, dim=-1) >>> ref_iso = ref_prob[:, 77:127].sum(dim=-1) >>> alt_iso = alt_prob[:, 77:127].sum(dim=-1) >>> delta_logodds = torch.log(alt_iso / (1 - alt_iso)) - torch.log(ref_iso / (1 - ref_iso)) ``` ### Interface - **Input length**: fixed 205 nt window - **Hexamer position**: core hexamer (e.g., `AAUAAA`) at position 70 (0-indexed) of the 205 nt window - **Output**: 206-dim cleavage distribution (one score per input position + trailing "no cleavage in window" bucket) ### Variant Effect - Score reference and alternate sequences separately and compare their cleavage / isoform predictions - There is no separate ref/alt output dataclass ## Training Details APARENT2 was trained to predict nucleotide-resolution cleavage and isoform abundance from 3' UTR MPRA measurements. ### Training Data The model was trained on the 3' UTR MPRA library used by the original APARENT, re-processed with additional improvements (exact cleavage positions for the Alien1 Random sublibrary and a 20 nt random barcode upstream of the USE in the Alien1 sublibrary). The measured variant data and processed data repository are available at the original [APARENT GitHub](https://github.com/johli/aparent). ### Training Procedure #### Pre-training The model minimizes a combination of a sigmoid KL-divergence isoform loss and a KL-divergence cleavage loss, weighted equally. The released inference model corresponds to the residual-network model trained for 5 epochs on all sublibraries (excluding ClinVar wild-type sequences), with dropout disabled for inference. ## Citation ```bibtex @article{linder2022deciphering, author = {Linder, Johannes and Koplik, Samantha E. and Kundaje, Anshul and Seelig, Georg}, title = {Deciphering the impact of genetic variation on human polyadenylation using APARENT2}, journal = {Genome Biology}, volume = {23}, number = {1}, pages = {232}, year = {2022}, doi = {10.1186/s13059-022-02799-4}, publisher = {Springer Science and Business Media LLC} } ``` > [!NOTE] > The artifacts distributed in this repository are part of the MultiMolecule project. > If MultiMolecule supports your research, please 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 [APARENT2 paper](https://doi.org/10.1186/s13059-022-02799-4) for questions or comments on the paper/model. ## License This model implementation 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 ```