Improve model card: Add pipeline tag, library name, and clean up metadata (#1)
Browse files- Improve model card: Add pipeline tag, library name, and clean up metadata (53ee029065b91afdae00b6c4b737cf6e796f5017)
Co-authored-by: Niels Rogge <nielsr@users.noreply.huggingface.co>
README.md
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license: apache-2.0
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version: v1.0
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model_summary: ConfRover base model trained for conformation interpolation
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model_description: '
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ConfRover is a deep generative model for protein 3D conformation and motion dynamics.
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It leverages diffusion probability model to learn the distribution of protein 3D
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conformations and captures the their temporal dependencies between frames through
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temporal causal transformers.
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Models are trained using molecular dynamics (MD) trajectories data and can generate
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protein conformation ensembles and motion trajectories conditioned on the input
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protein amino acid sequence.
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This variant was continued trained from the base model with additional conformation
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interpolation task.'
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recommend: For interpolation tasks
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model_id: ConfRover-interp-20M-v1.0
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name: ConfRover
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repo: https://github.com/ByteDance-Seed/ConfRover
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paper: https://arxiv.org/abs/2505.17478
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demo: https://ByteDance-Seed.github.io/ConfRover
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get_started_code: "\n```python\nfrom confrover import ConfRover\n\nmodel = ConfRover.from_pretrained(<model_name>)\n\
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\nmodel.to(\"cuda\")\n\nmodel.generate(\n case_id=<case_name>,\n seqres=<amino_acid_sequence>,\n\
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\ output_dir=</path/to/save/output>,\n task_mode=<\"forward\"|\"iid\"|\"interp\"\
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>,\n n_replicates=<int>, # number of replicated trajectories (forward and interp)\
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\ or total number of conformation samples (iid)\n n_frames=<int>, # number of\
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\ frames in the trajectory, including the conditioning frames.\n stride_in_10ps=256,\
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\ # time interval between frames in the unit of 10 ps.\n conditions=..., # information\
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\ for conditioning frames for forward simulation and interp. See `ConfRover.generate`\
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\ for more details.\n)\n```\n"
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model_specs: '
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ConfRover contains encoder, temporal module, and diffusion decoder.
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- The encoder maps the input amino acid sequence (through a folding model) and coordinates
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of context frames to a latent representation.
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- The temporal module models the temporal dependencies between frames using an interleaving
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of causal transformers (across the temporal dimension) and pairformers (to update
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structures).
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- The diffusion model learns the probability distribution of protein conformations
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and generates samples conditioned on the input sequence and conditioning representation.
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'
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bias_risks_limitations: '
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ConfRover is trained on limited MD trajectories data and may not generalize well
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to out-of-distribution data.
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The quality of generated conformations is also limited by the quality of the input
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data and the computational resources.
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Currently, ConfRover only supports protein conformation generation and models the
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coordinates of heavy atoms.
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'
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citation_bibtex: "\n```text\n@article{confrover2025,\n title={Simultaneous Modeling\
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\ of Protein Conformation and Dynamics via Autoregression},\n author={Shen, Yuning\
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\ and Wang, Lihao and Yuan, Huizhuo and Wang, Yan and Yang, Bangji and Gu, Quanquan},\n\
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\ journal={arXiv preprint arXiv:2505.17478},\n year={2025}\n}\n```\n"
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---
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# Model Card for `ConfRover-interp-20M-v1.0`
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It leverages diffusion probability model to learn the distribution of protein 3D conformations and captures the their temporal dependencies between frames through temporal causal transformers.
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Models are trained using molecular dynamics (MD) trajectories data and can generate protein conformation ensembles and motion trajectories conditioned on the input protein amino acid sequence.
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This variant was continued trained from the base model with additional conformation interpolation task.
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**Basic info**
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<!-- This section is meant to convey both technical and sociotechnical limitations. -->
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ConfRover is trained on limited MD trajectories data and may not generalize well
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journal={arXiv preprint arXiv:2505.17478},
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year={2025}
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}
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```
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---
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license: apache-2.0
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pipeline_tag: other
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library_name: confrover
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---
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# Model Card for `ConfRover-interp-20M-v1.0`
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It leverages diffusion probability model to learn the distribution of protein 3D conformations and captures the their temporal dependencies between frames through temporal causal transformers.
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Models are trained using molecular dynamics (MD) trajectories data and can generate protein conformation ensembles and motion trajectories conditioned on the input protein amino acid sequence.
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+
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This variant was continued trained from the base model with additional conformation interpolation task.
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**Basic info**
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<!-- This section is meant to convey both technical and sociotechnical limitations. -->
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ConfRover is trained on limited MD trajectories data and may not generalize well
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to out-of-distribution data.
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The quality of generated conformations is also limited by the quality of the input
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data and the computational resources.
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Currently, ConfRover only supports protein conformation generation and models the
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coordinates of heavy atoms.
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journal={arXiv preprint arXiv:2505.17478},
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year={2025}
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}
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```
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