| --- |
| datasets: |
| - multimolecule/gencode |
| library_name: multimolecule |
| license: agpl-3.0 |
| pipeline: splice-site |
| pipeline_tag: other |
| tags: |
| - Biology |
| - Genomics |
| - RNA |
| - Splicing |
| - rna |
| widget: |
| - example_title: microRNA 21 |
| pipeline_tag: splice-site |
| sequence_type: ncRNA |
| task: splice-site |
| text: UAGCUUAUCAGACUGAUGUUGA |
| - example_title: microRNA 146a |
| pipeline_tag: splice-site |
| sequence_type: ncRNA |
| task: splice-site |
| text: UGAGAACUGAAUUCCAUGGGUU |
| - example_title: microRNA 155 |
| pipeline_tag: splice-site |
| sequence_type: ncRNA |
| task: splice-site |
| text: UUAAUGCUAAUCGUGAUAGGGGUU |
| - example_title: RNA component of mitochondrial RNA processing endoribonuclease |
| pipeline_tag: splice-site |
| sequence_type: ncRNA |
| task: splice-site |
| text: GGUUCGUGCUGAAGGCCUGUAUCCUAGGCUACACACUGAGGACUCUGUUCCUCCCCUUUCCGCCUAGGGGAAAGUCCCCGGACCUCGGGCAGAGAGUGCCACGUGCAUACGCACGUAGACAUUCCCCGCUUCCCACUCCAAAGUCCGCCAAGAAGCGUAUCCCGCUGAGCGGCGUGGCGCGGGGGCGUCAUCCGUCAGCUCCCUCUAGUUACGCAGGCAGUGCGUGUCCGCGCACCAACCACACGGGGCUCAUUCUCAGCGCGGCUGUAAAAAAAAA |
| - example_title: 7SK small nuclear RNA |
| pipeline_tag: splice-site |
| sequence_type: ncRNA |
| task: splice-site |
| text: GGAUGUGAGGGCGAUCUGGCUGCGACAUCUGUCACCCCAUUGAUCGCCAGGGUUGAUUCGGCUGAUCUGGCUGGCUAGGCGGGUGUCCCCUUCCUCCCUCACCGCUCCAUGUGCGUCCCUCCCGAAGCUGCGCGCUCGGUCGAAGAGGACGACCAUCCCCGAUAGAGGAGGACCGGUCUUCGGUCAAGGGUAUACGAGUAGCUGCGCUCCCCUGCUAGAACCUCCAAACAAGCUCUCAAGGUCCAUUUGUAGGAGAACGUAGGGUAGUCAAGCUUCCAAGACUCCAGACACAUCCAAAUGAGGCGCUGCAUGUGGCAGUCUGCCUUUCUUUU |
| - example_title: telomerase RNA component |
| pipeline_tag: splice-site |
| sequence_type: ncRNA |
| task: splice-site |
| text: GGGUUGCGGAGGGUGGGCCUGGGAGGGGUGGUGGCCAUUUUUUGUCUAACCCUAACUGAGAAGGGCGUAGGCGCCGUGCUUUUGCUCCCCGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGAAAAGCCUCGGCCUGCCGCCUUCCACCGUUCAUUCUAGAGCAAACAAAAAAUGUCAGCUGCUGGCCCGUUCGCCCCUCCCGGGGACCUGCGGCGGGUCGCCUGCCCAGCCCCCGAACCCCGCCUGGAGGCCGCGGUCGGCCCGGGGCUUCUCCGGAGGCACCCACUGCCACCGCGAAGAGUUGGGCUCUGUCAGCCGCGGGUCUCUCGGGGGCGAGGGCGAGGUUCAGGCCUUUCAGGCCGCAGGAAGAGGAACGGAGCGAGUCCCCGCGCGCGGCGCGAUUCCCUGAGCUGUGGGACGUGCACCCAGGACUCGGCUCACACAUGC |
| - example_title: vault RNA 2-1 |
| pipeline_tag: splice-site |
| sequence_type: ncRNA |
| task: splice-site |
| text: CGGGUCGGAGUUAGCUCAAGCGGUUACCUCCUCAUGCCGGACUUUCUAUCUGUCCAUCUCUGUGCUGGGGUUCGAGACCCGCGGGUGCUUACUGACCCUUUUAUGCAA |
| - example_title: brain cytoplasmic RNA 1 |
| pipeline_tag: splice-site |
| sequence_type: ncRNA |
| task: splice-site |
| text: GGCCGGGCGCGGUGGCUCACGCCUGUAAUCCCAGCUCUCAGGGAGGCUAAGAGGCGGGAGGAUAGCUUGAGCCCAGGAGUUCGAGACCUGCCUGGGCAAUAUAGCGAGACCCCGUUCUCCAGAAAAAGGAAAAAAAAAAACAAAAGACAAAAAAAAAAUAAGCGUAACUUCCCUCAAAGCAACAACCCCCCCCCCCCUUU |
| - example_title: HIV-1 TAR-WT |
| pipeline_tag: splice-site |
| sequence_type: ncRNA |
| task: splice-site |
| text: GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACC |
| - example_title: prion protein (Kanno blood group) |
| pipeline_tag: splice-site |
| sequence_type: mRNA |
| task: splice-site |
| text: AUGGCGAACCUUGGCUGCUGGAUGCUGGUUCUCUUUGUGGCCACAUGGAGUGACCUGGGCCUCUGC |
| - example_title: interleukin 10 |
| pipeline_tag: splice-site |
| sequence_type: mRNA |
| task: splice-site |
| text: AUGCACAGCUCAGCACUGCUCUGUUGCCUGGUCCUCCUGACUGGGGUGAGGGCC |
| - example_title: Zaire ebolavirus |
| pipeline_tag: splice-site |
| sequence_type: mRNA |
| task: splice-site |
| text: AAUGUUCAAACACUUUGUGAAGCUCUGUUAGCUGAUGGUCUUGCUAAAGCAUUUCCUAGCAAUAUGAUGGUAGUCACAGAGCGUGAGCAAAAAGAAAGCUUAUUGCAUCAAGCAUCAUGGCACCACACAAGUGAUGAUUUUGGUGAGCAUGCCACAGUUAGAGGGAGUAGCUUUGUAACUGAUUUAGAGAAAUACAAUCUUGCAUUUAGAUAUGAGUUUACAGCACCUUUUAUAGAAUAUUGUAACCGUUGCUAUGGUGUUAAGAAUGUUUUUAAUUGGAUGCAUUAUACAAUCCCACAGUGUUAU |
| - example_title: SARS coronavirus |
| pipeline_tag: splice-site |
| sequence_type: mRNA |
| task: splice-site |
| text: AUGUUUAUUUUCUUAUUAUUUCUUACUCUCACUAGUGGUAGUGACCUUGACCGGUGCACCACUUUUGAUGAUGUUCAAGCUCCUAAUUACACUCAACAUACUUCAUCUAUGAGGGGGGUUUACUAUCCUGAUGAAAUUUUUAGAUCAGACACUCUUUAUUUAACUCAGGAUUUAUUUCUUCCAUUUUAUUCUAAUGUUACAGGGUUUCAUACUAUUAAUCAUACGUUUGACAACCCUGUCAUACCUUUUAAGGAUGGUAUUUAUUUUGCUGCCACAGAGAAAUCAAAUGUUGUCCGUGGUUGGGUUUUUGGUUCUACCAUGAACAACAAGUCACAGUCGGUGAUUAUUAUUAACAAUUCUACUAAUGUUGUUAUACGAGCAUGUAACUUUGAAUUGUGUGACAACCCUUUCUUUGCUGUUUCUAAACCCAUGGGUACACAGACACAUACUAUGAUAUUCGAUAAUGCAUUUAAAUGCACUUUCGAGUACAUAUCU |
| - example_title: insulin |
| pipeline_tag: splice-site |
| sequence_type: mRNA |
| task: splice-site |
| text: AUGGCCCUGUGGAUGCGCCUCCUGCCCCUGCUGGCGCUGCUGGCCCUCUGGGGACCUGACCCAGCCGCAGCCUUUGUGAACCAACACCUGUGCGGCUCACACCUGGUGGAAGCUCUCUACCUAGUGUGCGGGGAACGAGGCUUCUUCUACACACCCAAGACCCGCCGGGAGGCAGAGGACCUGCAGGUGGGGCAGGUGGAGCUGGGCGGGGGCCCUGGUGCAGGCAGCCUGCAGCCCUUGGCCCUGGAGGGGUCCCUGCAGAAGCGUGGCAUUGUGGAACAAUGCUGUACCAGCAUCUGCUCCCUCUACCAGCUGGAGAACUACUGCAACUAG |
| - example_title: cyclin dependent kinase inhibitor 2A |
| pipeline_tag: splice-site |
| sequence_type: mRNA |
| task: splice-site |
| text: AUGGAGCCGGCGGCGGGGAGCAGCAUGGAGCCUUCGGCUGACUGGCUGGCCACGGCCGCGGCCCGGGGUCGGGUAGAGGAGGUGCGGGCGCUGCUGGAGGCGGGGGCGCUGCCCAACGCACCGAAUAGUUACGGUCGGAGGCCGAUCCAGGUCAUGAUGAUGGGCAGCGCCCGAGUGGCGGAGCUGCUGCUGCUCCACGGCGCGGAGCCCAACUGCGCCGACCCCGCCACUCUCACCCGACCCGUGCACGACGCUGCCCGGGAGGGCUUCCUGGACACGCUGGUGGUGCUGCACCGGGCCGGGGCGCGGCUGGACGUGCGCGAUGCCUGGGGCCGUCUGCCCGUGGACCUGGCUGAGGAGCUGGGCCAUCGCGAUGUCGCACGGUACCUGCGCGCGGCUGCGGGGGGCACCAGAGGCAGUAACCAUGCCCGCAUAGAUGCCGCGGAAGGUCCCUCAGACAUCCCCGAUUGA |
| - example_title: human papillomavirus type 16 E6 |
| pipeline_tag: splice-site |
| sequence_type: mRNA |
| task: splice-site |
| text: AUGCACCAAAAGAGAACUGCAAUGUUUCAGGACCCACAGGAGCGACCCAGAAAGUUACCACAGUUAUGCACAGAGCUGCAAACAACUAUACAUGAUAUAAUAUUAGAAUGUGUGUACUGCAAGCAACAGUUACUGCGACGUGAGGUAUAUGACUUUGCUUUUCGGGAUUUAUGCAUAGUAUAUAGAGAUGGGAAUCCAUAUGCUGUAUGUGAUAAAUGUUUAAAGUUUUAUUCUAAAAUUAGUGAGUAUAGACAUUAUUGUUAUAGUUUGUAUGGAACAACAUUAGAACAGCAAUACAACAAACCGUUGUGUGAUUUGUUAAUUAGGUGUAUUAACUGUCAAAAGCCACUGUGUCCUGAAGAAAAGCAAAGACAUCUGGACAAAAAGCAAAGAUUCCAUAAUAUAAGGGGUCGGUGGACCGGUCGAUGUAUGUCUUGUUGCAGAUCAUCAAGAACACGUAGAGAAACCCAGCUGUAA |
| - example_title: NRAS proto-oncogene |
| pipeline_tag: splice-site |
| sequence_type: 5' UTR |
| task: splice-site |
| text: GGGGCCGGAAGUGCCGCUCCUUGGUGGGGGCUGUUCAUGGCGGUUCCGGGGUCUCCAACAUUUUUCCCGGCUGUGGUCCUAAAUCUGUCCAAAGCAGAGGCAGUGGAGCUUGAGGUUCUUGCUGGUGUGAA |
| - example_title: amyloid beta precursor protein |
| pipeline_tag: splice-site |
| sequence_type: 5' UTR |
| task: splice-site |
| text: GUCAGUUUCCUCGGCAGCGGUAGGCGAGAGCACGCGGAGGAGCGUGCGCGGGGGCCCCGGGAGACGGCGGCGGUGGCGGCGCGGGCAGAGCAAGGACGCGGCGGAUCCCACUCGCACAGCAGCGCACUCGGUGCCCCGCGCAGGGUCGCG |
| - example_title: RUNX family transcription factor 1 |
| pipeline_tag: splice-site |
| sequence_type: 5' UTR |
| task: splice-site |
| text: ACUUCUUUGGGCCUCAUAAACAACCACAGAACCACAAGUUGGGUAGCCUGGCAGUGUCAGAAGUCUGAACCCAGCAUAGUGGUCAGCAGGCAGGACGAAUCACACUGAAUGCAAACCACAGGGUUUCGCAGCGUGGUAAAAGAAAUCAUUGAGUCCCCCGCCUUCAGAAGAGGGUGCAUUUUCAGGAGGAAGCG |
| - example_title: fragile X messenger ribonucleoprotein 1 |
| pipeline_tag: splice-site |
| sequence_type: 5' UTR |
| task: splice-site |
| text: CUCAGUCAGGCGCUCAGCUCCGUUUCGGUUUCACUUCCGGUGGAGGGCCGCCUCUGAGCGGGCGGCGGGCCGACGGCGAGCGCGGGCGGCGGCGGUGACGGAGGCGCCGCUGCCAGGGGGCGUGCGGCAGCGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCUGGGCCUCGAGCGCCCGCAGCCCACCUCUCGGGGGCGGGCUCCCGGCGCUAGCAGGGCUGAAGAGAAG |
| - example_title: MYC proto-oncogene |
| pipeline_tag: splice-site |
| sequence_type: 5' UTR |
| task: splice-site |
| text: AACUCGCUGUAGUAAUUCCAGCGAGAGGCAGAGGGAGCGAGCGGGCGGCCGGCUAGGGUGGAAGAGCCGGGCGAGCAGAGCUGCGCUGCGGGCGUCCUGGGAAGGGAGAUCCGGAGCGAAUAGGGGGCUUCGCCUCUGGCCCAGCCCUCCCGCUGAUCCCCCAGCCAGCGGUCCGCAACCCUUGCCGCAUCCACGAAACUUUGCCCAUAGCAGCGGGCGGGCACUUUGCACUGGAACUUACAACACCCGAGCAAGGACGCGACUCUCCCGACGCGGGGAGGCUAUUCUGCCCAUUUGGGGACACUUCCCCGCCGCUGCCAGGACCCGCUUCUCUGAAAGGCUCUCCUUGCAGCUGCUUAGACG |
| - example_title: activating transcription factor 4 |
| pipeline_tag: splice-site |
| sequence_type: 5' UTR |
| task: splice-site |
| text: CAUUUCUACUUUGCCCGCCCACAGAUGUAGUUUUCUCUGCGCGUGUGCGUUUUCCCUCCUCCCCGCCCUCAGGGUCCACGGCCACCAUGGCGUAUUAGGGGCAGCAGUGCCUGCGGCAGCAUUGGCCUUUGCAGCGGCGGCAGCAGCACCAGGCUCUGCAGCGGCAACCCCCAGCGGCUUAAGCCAUGGCGCUUCUCACGGCAUUCAGCAGCAGCGUUGCUGUAACCGACAAAGACACCUUCGAAUUAAGCACAUUCCUCGAUUCCAGCAAAGCACCGCAAC |
| - example_title: Human GPI protein p137 |
| pipeline_tag: splice-site |
| sequence_type: 3' UTR |
| task: splice-site |
| text: UUUUUAAAAGGAAAAGAUACCAAAUGCCUGCUGCUACCACCCUUUUCAAUUGCUAUGUUUUGAAAGGCACCAGUAUGUGUUUUAGAUUGAUUUAAAUGUUUCAUUUAAAUCACGGACAGUAGUUUCAGUUCUGAUGGUAUAAGCAAAACAAAUAAAACGUUUAUAAAAGUUGUAUCUUGAAACACUGGUGUUCAACAGCUAGCAGCUUAUGUGAUUCACCCCAUGCCACGUUAGUGUCACAAAUUUUAUGGUUUAUCUCCAGCAACAUUUCUCUAGUACUUGCACUUAUUAUCUGAAUUC |
| - example_title: nucleophosmin 1 |
| pipeline_tag: splice-site |
| sequence_type: 3' UTR |
| task: splice-site |
| text: GAAAAUAGUUUAAACAAUUUGUUAAAAAAUUUUCCGUCUUAUUUCAUUUCUGUAACAGUUGAUAUCUGGCUGUCCUUUUUAUAAUGCAGAGUGAGAACUUUCCCUACCGUGUUUGAUAAAUGUUGUCCAGGUUCUAUUGCCAAGAAUGUGUUGUCCAAAAUGCCUGUUUAGUUUUUAAAGAUGGAACUCCACCCUUUGCUUGGUUUUAAGUAUGUAUGGAAUGUUAUGAUAGGACAUAGUAGUAGCGGUGGUCAGACAUGGAAAUGGUGGGGAGACAAAAAUAUACAUGUGAAAUAAAACUCAGUAUUUUAAUAAAGUAGCACGGUUUCUAUUGA |
| - example_title: superoxide dismutase 1 |
| pipeline_tag: splice-site |
| sequence_type: 3' UTR |
| task: splice-site |
| text: ACAUUCCCUUGGAUGUAGUCUGAGGCCCCUUAACUCAUCUGUUAUCCUGCUAGCUGUAGAAAUGUAUCCUGAUAAACAUUAAACACUGUAAUCUUAAAAGUGUAAUUGUGUGACUUUUUCAGAGUUGCUUUAAAGUACCUGUAGUGAGAAACUGAUUUAUGAUCACUUGGAAGAUUUGUAUAGUUUUAUAAAACUCAGUUAAAAUGUCUGUUUCAAUGACCUGUAUUUUGCCAGACUUAAAUCACAGAUGGGUAUUAAACUUGUCAGAAUUUCUUUGUCAUUCAAGCCUGUGAAUAAAAACCCUGUAUGGCACUUAUUAUGAGGCUAUUAAAAGAAUCCAAAUUCAAACUAAA |
| - example_title: hemoglobin subunit alpha 2 |
| pipeline_tag: splice-site |
| sequence_type: 3' UTR |
| task: splice-site |
| text: CUGGAGCCUCGGUAGCCGUUCCUCCUGCCCGCUGGGCCUCCCAACGGGCCCUCCUCCCCUCCUUGCACCGGCCCUUCCUGGUCUUUGAAUAAAGUCUGAGUGGGCAGCA |
| - example_title: BRAF proto-oncogene |
| pipeline_tag: splice-site |
| sequence_type: 3' UTR |
| task: splice-site |
| text: AACAAAUGAGUGAGAGAGUUCAGGAGAGUAGCAACAAAAGGAAAAUAAAUGAACAUAUGUUUGCUUAUAUGUUAAAUUGAAUAAAAUACUCUCUUUUUUUUUAAGGUGAACCAAAGAACACUUGUGUGGUUAAAGACUAGAUAUAAUUUUUCCCCAAACUAAAAUUUAUACUUAACAUUGGAUUUUUAACAUCCAAGGGUUAAAAUACAUAGACAUUGCUAAAAAUUGGCAGAGCCUCUUCUAGAGGCUUUACUUUCUGUUCCGGGUUUGUAUCAUUCACUUGGUUAUUUUAAGUAGUAAACUUCAGUUUCUCAUGCAACUUUUGUUGCCAGCUAUCACAUGUCCACUAGGGACUCCAGAAGAAGACCCUACCUAUGCCUGUGUUUGCAGGUGAGAAGUUGGCAGUCGGUUAGCCUGGG |
| - example_title: H3 clustered histone 1 |
| pipeline_tag: splice-site |
| sequence_type: 3' UTR |
| task: splice-site |
| text: UUACUGUGGUCUCUCUGACGGUCCAAGCAAAGGCUCUUUUCAGAGCCACCACCUUUUC |
| --- |
| |
| # OpenSpliceAI |
|
|
| Modular native-PyTorch reimplementation of SpliceAI for predicting pre-mRNA splice sites from nucleotide sequence. |
|
|
| ## Disclaimer |
|
|
| This is an UNOFFICIAL implementation of [OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species](https://doi.org/10.7554/eLife.107454.3) by Kuan-Hao Chao, Alan Mao, et al. |
|
|
| The OFFICIAL repository of OpenSpliceAI is at [Kuanhao-Chao/OpenSpliceAI](https://github.com/Kuanhao-Chao/OpenSpliceAI). |
|
|
| > [!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 OpenSpliceAI did not write this model card for this model so this model card has been written by the MultiMolecule team.** |
|
|
| ## Model Details |
|
|
| OpenSpliceAI is a deep dilated residual convolutional neural network that reimplements the SpliceAI architecture in native PyTorch. It predicts, for each nucleotide of a pre-mRNA transcript, whether the position is a splice acceptor, a splice donor, or neither. The model stacks dilated residual units with increasing kernel size and atrous rate so that a wide genomic context window contributes to each per-nucleotide prediction, while skip connections aggregate multi-scale features. OpenSpliceAI reproduces the predictive behavior of SpliceAI while providing an efficient, modular training pipeline that can be retrained on non-human species. |
|
|
| ### Variants |
|
|
| OpenSpliceAI ships trained model families for human MANE and four non-human species. Each family provides four |
| flanking-context sizes. |
|
|
| | Family | 80 nt | 400 nt | 2,000 nt | 10,000 nt | |
| | ------------- | ------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------- | |
| | MANE / human | [`openspliceai-mane.80`](https://huggingface.co/multimolecule/openspliceai-mane.80) | [`openspliceai-mane.400`](https://huggingface.co/multimolecule/openspliceai-mane.400) | [`openspliceai-mane.2000`](https://huggingface.co/multimolecule/openspliceai-mane.2000) | [`openspliceai-mane.10000`](https://huggingface.co/multimolecule/openspliceai-mane.10000) | |
| | Mouse | [`openspliceai-mouse.80`](https://huggingface.co/multimolecule/openspliceai-mouse.80) | [`openspliceai-mouse.400`](https://huggingface.co/multimolecule/openspliceai-mouse.400) | [`openspliceai-mouse.2000`](https://huggingface.co/multimolecule/openspliceai-mouse.2000) | [`openspliceai-mouse.10000`](https://huggingface.co/multimolecule/openspliceai-mouse.10000) | |
| | Zebrafish | [`openspliceai-zebrafish.80`](https://huggingface.co/multimolecule/openspliceai-zebrafish.80) | [`openspliceai-zebrafish.400`](https://huggingface.co/multimolecule/openspliceai-zebrafish.400) | [`openspliceai-zebrafish.2000`](https://huggingface.co/multimolecule/openspliceai-zebrafish.2000) | [`openspliceai-zebrafish.10000`](https://huggingface.co/multimolecule/openspliceai-zebrafish.10000) | |
| | Honeybee | [`openspliceai-honeybee.80`](https://huggingface.co/multimolecule/openspliceai-honeybee.80) | [`openspliceai-honeybee.400`](https://huggingface.co/multimolecule/openspliceai-honeybee.400) | [`openspliceai-honeybee.2000`](https://huggingface.co/multimolecule/openspliceai-honeybee.2000) | [`openspliceai-honeybee.10000`](https://huggingface.co/multimolecule/openspliceai-honeybee.10000) | |
| | _Arabidopsis_ | [`openspliceai-arabidopsis.80`](https://huggingface.co/multimolecule/openspliceai-arabidopsis.80) | [`openspliceai-arabidopsis.400`](https://huggingface.co/multimolecule/openspliceai-arabidopsis.400) | [`openspliceai-arabidopsis.2000`](https://huggingface.co/multimolecule/openspliceai-arabidopsis.2000) | [`openspliceai-arabidopsis.10000`](https://huggingface.co/multimolecule/openspliceai-arabidopsis.10000) | |
|
|
| ### Model Specification |
|
|
| <table> |
| <thead> |
| <tr> |
| <th>Flanking Context</th> |
| <th>Residual Blocks</th> |
| <th>Hidden Size</th> |
| <th>Num Parameters (M)</th> |
| <th>FLOPs (G)</th> |
| <th>MACs (G)</th> |
| </tr> |
| </thead> |
| <tbody> |
| <tr> |
| <td>80 nt</td> |
| <td>4</td> |
| <td rowspan="4">32</td> |
| <td>0.09</td> |
| <td>0.95</td> |
| <td>0.47</td> |
| </tr> |
| <tr> |
| <td>400 nt</td> |
| <td>8</td> |
| <td>0.19</td> |
| <td>2.00</td> |
| <td>0.99</td> |
| </tr> |
| <tr> |
| <td>2,000 nt</td> |
| <td>12</td> |
| <td>0.36</td> |
| <td>5.03</td> |
| <td>2.50</td> |
| </tr> |
| <tr> |
| <td>10,000 nt</td> |
| <td>16</td> |
| <td>0.70</td> |
| <td>20.90</td> |
| <td>10.40</td> |
| </tr> |
| </tbody> |
| </table> |
| |
| Model size is determined by flanking context and is shared across species for the same context. FLOPs and MACs are |
| reported for a single 5,000-nucleotide output sequence. |
|
|
| ### Links |
|
|
| - **Code**: [multimolecule.openspliceai](https://github.com/DLS5-Omics/multimolecule/tree/master/multimolecule/models/openspliceai) |
| - **Data**: Human MANE/GENCODE for the MANE variants; species annotations follow the original OpenSpliceAI release. |
| - **Paper**: [OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species](https://doi.org/10.7554/eLife.107454.3) |
| - **Developed by**: Kuan-Hao Chao, Alan Mao, Anqi Liu, Steven L. Salzberg, Mihaela Pertea |
| - **Model type**: Dilated residual 1D CNN over pre-mRNA sequence for per-nucleotide three-class splice-site classification |
| - **Original Repository**: [Kuanhao-Chao/OpenSpliceAI](https://github.com/Kuanhao-Chao/OpenSpliceAI) |
|
|
| ## 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 |
|
|
| #### RNA Splicing Site Prediction |
|
|
| You can use this model directly to predict the splice sites of a pre-mRNA sequence: |
|
|
| ```python |
| >>> from multimolecule import RnaTokenizer, OpenSpliceAiForTokenPrediction |
| |
| >>> model_id = "multimolecule/openspliceai-mouse.2000" |
| >>> tokenizer = RnaTokenizer.from_pretrained(model_id) |
| >>> model = OpenSpliceAiForTokenPrediction.from_pretrained(model_id) |
| >>> output = model(tokenizer("AGCAGUCAUUAUGGCGAA", return_tensors="pt")["input_ids"]) |
| |
| >>> output.keys() |
| odict_keys(['logits']) |
| ``` |
|
|
| Each output position carries three logits corresponding to _neither_, _acceptor_, and _donor_. |
|
|
| ### Interface |
|
|
| - **Input length**: variable pre-mRNA sequence |
| - **Flanking context**: 80 / 400 / 2,000 / 10,000 nt per variant family, split evenly on both sides of every predicted position |
| - **Padding**: sequence ends padded with `N` |
| - **Output**: per-position 3-class logits (`neither`, `acceptor`, `donor`) |
|
|
| ## Training Details |
|
|
| OpenSpliceAI was trained to predict the location of splice donor and acceptor sites from nucleotide sequence, following the SpliceAI training methodology. |
|
|
| ### Training Data |
|
|
| The MANE variants were trained on transcripts from the [GENCODE](https://multimolecule.danling.org/datasets/gencode)/MANE human reference annotation. The non-human variants use the species annotations released by OpenSpliceAI for mouse, zebrafish, honeybee, and _Arabidopsis_. For each predicted nucleotide, the model receives a flanking context of 80, 400, 2,000, or 10,000 nucleotides, split evenly across the two sides of the output sequence, with sequence ends padded with `N`. Annotated splice donor and acceptor sites serve as positive labels; all other positions are negative. |
|
|
| ### Training Procedure |
|
|
| #### Pre-training |
|
|
| The model was trained to minimize a cross-entropy loss between predicted splice-site probabilities and the reference annotation. |
|
|
| - Optimizer: Adam |
| - Loss: cross-entropy |
|
|
| Please refer to the [OpenSpliceAI paper](https://doi.org/10.7554/eLife.107454.3) for the full training protocol and hardware details. |
|
|
| ## Citation |
|
|
| ```bibtex |
| @article{chao2025openspliceai, |
| author = {Chao, Kuan-Hao and Mao, Alan and Liu, Anqi and Salzberg, Steven L and Pertea, Mihaela}, |
| title = {OpenSpliceAI: An efficient, modular implementation of SpliceAI enabling easy retraining on non-human species}, |
| journal = {eLife}, |
| volume = 14, |
| pages = {RP107454}, |
| year = 2025, |
| doi = {10.7554/eLife.107454.3}, |
| publisher = {eLife Sciences Publications, Ltd} |
| } |
| ``` |
|
|
| > [!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 [OpenSpliceAI paper](https://doi.org/10.7554/eLife.107454.3) 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 |
| ``` |
