| --- |
| 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 |
| --- |
| |
| # APARENT |
|
|
| Convolutional neural network for predicting human 3'UTR Alternative Polyadenylation (APA) from sequence. |
|
|
| ## Disclaimer |
|
|
| This 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. |
|
|
| The OFFICIAL repository of APARENT is at [johli/aparent](https://github.com/johli/aparent). |
|
|
| > [!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 APARENT did not write this model card for this model so this model card has been written by the MultiMolecule team.** |
|
|
| ## Model Details |
|
|
| APARENT (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. |
|
|
| The base, non-normalised APARENT model is recommended by the original authors for isoform and variant-effect prediction. |
|
|
| ### Model Specification |
|
|
| | Num Layers | Hidden Size | Num Parameters (M) | FLOPs (G) | MACs (G) | Max Num Tokens | |
| | ---------- | ----------- | ------------------ | --------- | -------- | -------------- | |
| | 4 | 256 | 6.43 | 0.03 | 0.01 | 205 | |
|
|
| ### Links |
|
|
| - **Code**: [multimolecule.aparent](https://github.com/DLS5-Omics/multimolecule/tree/master/multimolecule/models/aparent) |
| - **Data**: Massively-parallel polyadenylation MPRA, GEO [GSE113849](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE113849) |
| - **Paper**: [A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation](https://doi.org/10.1016/j.cell.2019.04.046) |
| - **Developed by**: Nicholas Bogard, Johannes Linder, Alexander B. Rosenberg, Georg Seelig |
| - **Model type**: 1D CNN for alternative polyadenylation isoform and cleavage prediction from 3'UTR sequence |
| - **Original Repository**: [johli/aparent](https://github.com/johli/aparent) |
|
|
| ## 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 |
|
|
| #### APA Isoform Prediction |
|
|
| You can use this model directly to predict the APA isoform proportion of a 3'UTR/polyA sequence: |
|
|
| ```python |
| >>> from multimolecule import RnaTokenizer, AparentForSequencePrediction |
| |
| >>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/aparent") |
| >>> model = AparentForSequencePrediction.from_pretrained("multimolecule/aparent") |
| >>> output = model(**tokenizer("ACGUACGUACGU", return_tensors="pt")) |
| |
| >>> output.keys() |
| odict_keys(['logits']) |
| ``` |
|
|
| The full APARENT isoform and cleavage outputs are available on the backbone: |
|
|
| ```python |
| >>> from multimolecule import RnaTokenizer, AparentModel |
| |
| >>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/aparent") |
| >>> model = AparentModel.from_pretrained("multimolecule/aparent") |
| >>> output = model(**tokenizer("ACGUACGUACGU", return_tensors="pt")) |
| |
| >>> output.keys() |
| odict_keys(['pooler_output', 'isoform_logits', 'cleavage_logits']) |
| ``` |
|
|
| ### Interface |
|
|
| - **Input length**: fixed 205 nt 3'UTR / polyA sequence |
| - **Output (`AparentModel`)**: `isoform_logits` (scalar APA proportion) + `cleavage_logits` (206-dim positional cleavage distribution) |
| - **Output (`AparentForSequencePrediction`)**: APA isoform scalar only (`logits`) |
|
|
| ## Training Details |
|
|
| APARENT was trained to jointly predict the APA isoform proportion and the positional cleavage distribution of randomized 3'UTR poly-A signals. |
|
|
| ### Training Data |
|
|
| APARENT 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. |
|
|
| This 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. |
|
|
| ### Training Procedure |
|
|
| #### Pre-training |
|
|
| The 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. |
|
|
| ## Citation |
|
|
| ```bibtex |
| @article{bogard2019adeep, |
| author = {Bogard, Nicholas and Linder, Johannes and Rosenberg, Alexander B. and Seelig, Georg}, |
| title = {A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation}, |
| journal = {Cell}, |
| volume = {178}, |
| number = {1}, |
| pages = {91--106.e23}, |
| year = {2019}, |
| publisher = {Elsevier BV}, |
| doi = {10.1016/j.cell.2019.04.046} |
| } |
| ``` |
|
|
| > [!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 [APARENT paper](https://doi.org/10.1016/j.cell.2019.04.046) 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 |
| ``` |
