| --- |
| datasets: |
| - multimolecule/deltasplice |
| library_name: multimolecule |
| license: agpl-3.0 |
| pipeline: splice-site |
| pipeline_tag: other |
| tags: |
| - Biology |
| - 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 |
| --- |
| |
| # DeltaSplice |
|
|
| Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. |
|
|
| ## Disclaimer |
|
|
| This is an UNOFFICIAL implementation of [Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences](https://doi.org/10.1101/gr.279044.124) by Chencheng Xu, Suying Bao, et al. |
|
|
| The OFFICIAL repository of DeltaSplice is at [chaolinzhanglab/DeltaSplice](https://github.com/chaolinzhanglab/DeltaSplice). |
|
|
| > [!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 DeltaSplice did not write this model card for this model so this model card has been written by the MultiMolecule team.** |
|
|
| ## Model Details |
|
|
| DeltaSplice predicts splice-site usage (SSU) and splicing-altering mutation effects from sequence. The model uses a valid-convolution dilated residual encoder and three prediction modules: splice-site usage, reference-informed delta-SSU, and an auxiliary splice-site head. The official package uses the average prediction of five checkpoints for SSU and delta-SSU prediction; MultiMolecule stores the five seed checkpoints of each released data variant as internal ensemble members and returns their average prediction. |
|
|
| ### Variants |
|
|
| - **[multimolecule/deltasplice](https://huggingface.co/multimolecule/deltasplice)**: DeltaSplice trained on the multi-species training set used by the upstream default checkpoints. |
| - **[multimolecule/deltasplice-human](https://huggingface.co/multimolecule/deltasplice-human)**: DeltaSplice human-only comparison checkpoint set released by the upstream project. |
|
|
| ### Model Specification |
|
|
| | Variant | Num Layers | Hidden Size | Context | Ensemble Members | Num Parameters (M) | FLOPs (M) | MACs (M) | |
| | ----------------- | ---------- | ----------- | ------- | ---------------- | ------------------ | ---------- | --------- | |
| | DeltaSplice | 24 | 64 | 30000 | 5 | 40.376 | 1642965.72 | 820284.36 | |
| | DeltaSplice-Human | 24 | 64 | 30000 | 5 | 40.376 | 1642965.72 | 820284.36 | |
|
|
| (FLOPs and MACs measured on one requested output nucleotide with the default 30 kb padded context.) |
|
|
| ### Links |
|
|
| - **Code**: [multimolecule.deltasplice](https://github.com/DLS5-Omics/multimolecule/tree/master/multimolecule/models/deltasplice) |
| - **Paper**: [Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences](https://doi.org/10.1101/gr.279044.124) |
| - **Developed by**: Chencheng Xu, Suying Bao, Ye Wang, Wenxing Li, Hao Chen, Yufeng Shen, Tao Jiang, Chaolin Zhang |
| - **Model type**: Dilated residual 1D CNN ensemble for splice-site usage and delta-SSU prediction |
| - **Original Repository**: [chaolinzhanglab/DeltaSplice](https://github.com/chaolinzhanglab/DeltaSplice) |
|
|
| ## 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 |
|
|
| #### Splice-Site Usage |
|
|
| ```python |
| >>> from multimolecule import RnaTokenizer |
| >>> from multimolecule.models.deltasplice import DeltaSpliceModel |
| |
| >>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/deltasplice") |
| >>> model = DeltaSpliceModel.from_pretrained("multimolecule/deltasplice") |
| >>> inputs = tokenizer("AGCAGUCAUUAUGGCGAAUCUGGCAAGUA", return_tensors="pt") |
| >>> output = model(**inputs) |
| >>> output["probabilities"].shape |
| torch.Size([1, 30, 3]) |
| ``` |
|
|
| #### Variant Effect |
|
|
| ```python |
| >>> from multimolecule import RnaTokenizer |
| >>> from multimolecule.models.deltasplice import DeltaSpliceModel |
| |
| >>> tokenizer = RnaTokenizer.from_pretrained("multimolecule/deltasplice") |
| >>> model = DeltaSpliceModel.from_pretrained("multimolecule/deltasplice") |
| >>> reference = tokenizer("AGCAGUCAUUAUGGCGAAUCUGGCAAGUA", return_tensors="pt") |
| >>> alternative = tokenizer("AGCAGUCAUUAUGGCUAAUCUGGCAAGUA", return_tensors="pt") |
| >>> output = model(reference["input_ids"], alternative_input_ids=alternative["input_ids"], use_reference=True) |
| >>> output["delta"].shape |
| torch.Size([1, 30, 3]) |
| ``` |
|
|
| ### Interface |
|
|
| - **Input**: RNA sequence tokenized with `RnaTokenizer`; `N` is encoded as zero nucleotide channels |
| - **Output channels**: `no_splice`, `acceptor`, `donor` |
| - **Reference-only call**: returns per-position splice-site usage probabilities in `probabilities` |
| - **Reference + alternative call**: pass the reference sequence as `input_ids` and the alternate sequence as `alternative_input_ids` |
| - **Reference usage**: pass `reference_usage` with shape `(batch_size, sequence_length, 3)` or omit it to use the model's own reference usage as the reference signal |
|
|
| ## Training Details |
|
|
| DeltaSplice was trained to predict splice-site usage from gene sequence and to improve mutation-effect prediction by incorporating reference splice-site usage. |
|
|
| ### Training Data |
|
|
| The upstream repository describes training from `gene_dataset.tsu.txt`, which contains splice-site usage in adult brains of eight mammalian species. |
|
|
| ### Training Procedure |
|
|
| The official release provides five seed checkpoints with the same architecture and data split. MultiMolecule represents these seed checkpoints as internal ensemble members rather than public model variants. |
|
|
| ## Citation |
|
|
| ```bibtex |
| @article{xu2024deltasplice, |
| title = {Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences}, |
| author = {Xu, Chencheng and Bao, Suying and Wang, Ye and Li, Wenxing and Chen, Hao and Shen, Yufeng and Jiang, Tao and Zhang, Chaolin}, |
| journal = {Genome Research}, |
| volume = {34}, |
| number = {7}, |
| pages = {1052--1065}, |
| year = {2024}, |
| doi = {10.1101/gr.279044.124} |
| } |
| ``` |
|
|
| > [!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 [DeltaSplice paper](https://doi.org/10.1101/gr.279044.124) 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 |
| ``` |
