| --- |
| 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 |
| ``` |
