| --- |
| license: mit |
| task_categories: |
| - text-generation |
| tags: |
| - protein-sequence-generation |
| - bioinformatics |
| - pfam |
| - ancestral-sequence-reconstruction |
| - protein-family |
| --- |
| |
| # LineageFlow Pfam Assets |
|
|
| This dataset contains the preprocessed Pfam assets used by the released LineageFlow inference pipeline, as presented in the paper [LineageFlow: Flow Matching for High-Fidelity Family-Aware Protein Sequence Generation](https://huggingface.co/papers/2605.22252). |
|
|
| **Resources:** |
| - **Paper:** [https://huggingface.co/papers/2605.22252](https://huggingface.co/papers/2605.22252) |
| - **GitHub:** [https://github.com/Jinx-byebye/LineageFlow](https://github.com/Jinx-byebye/LineageFlow) |
|
|
| ## Contents |
|
|
| - `pfam_priors_asr_mad/`: family-specific ASR Dirichlet priors. |
| - `pfam_gap_rates/`: family-specific alignment gap statistics. |
| - `pfam_fastas_clean/`: cleaned Pfam family alignments. |
| - `pfam_pi_smooth_tau0.5_gap060_gt80_020.csv`: family sampling distribution. |
| - `pfam_priors_keep_ids_gap060_gt80_020.txt`: family keep list used by the default sampler. |
|
|
| ## Usage |
|
|
| You can download the preprocessed Pfam assets using the Hugging Face CLI: |
|
|
| ```bash |
| hf download jinxbye/LineageFlow-assets \ |
| --repo-type dataset \ |
| --local-dir dataset |
| ``` |
|
|
| The inference scripts in the GitHub repository expect these assets under `dataset/` by default. All paths can be overridden from the command line. |
|
|
| ## Citation |
|
|
| ```bibtex |
| @inproceedings{liang2026lineageflow, |
| title = {LineageFlow: Flow Matching for High-Fidelity Family-Aware Protein Sequence Generation}, |
| author = {Liang, Langzhang and Yang, Ming and Feng, Yi and Li, Junfan and Pan, Shirui and Xu, Yinghui and Ying, Tianlei and Zheng, Yizhen and Xu, Zenglin}, |
| booktitle = {Proceedings of the 43rd International Conference on Machine Learning}, |
| year = {2026} |
| } |
| ``` |
|
|
| ## Notes |
|
|
| These files are preprocessed from Pfam family alignments. Please follow the license and usage terms of the original Pfam resource when using the data. |
