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CELL-FM

Commit History

27 days ago

  1. Virtual OpenCell: show the 2D/3D switch again (3D set regenerated) Running

    BoHuangLab
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    664846d

28 days ago

  1. Virtual OpenCell: hide the 3D view while the 3D set is regenerated

    BoHuangLab
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    188d57a

  2. Virtual OpenCell: switch between 2D and 3D virtual staining; 3D shown one confocal slice at a time

    BoHuangLab
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    2d03a2d

  3. Centre the full virtual staining map

    BoHuangLab
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    e57ebbb

  4. Center the full virtual staining map heading

    BoHuangLab
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    7ddfa77

29 days ago

  1. ZeroGPU duration 75 s: ~2x a measured run, two anonymous runs a day

    BoHuangLab
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    10b2d78

  2. Condensate Titration: input-only panel, row/column comparison in the scan, ZeroGPU duration 120 s

    BoHuangLab
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    f2dfd29

  3. Condensate Titration: Virtual OpenCell layout and style; GPU only generates and classifies

    BoHuangLab
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    e8ad02e

  4. Condensate Titration: the paper's ΔAUC and ΔAAC substitution matrices, click a cell for its distribution

    BoHuangLab
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    3c4fb84

  1. Condensate Titration: let the generated-images gallery scroll

    BoHuangLab
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    bebb3a0

  2. Condensate Titration: caption each generated image with its expression level only

    BoHuangLab
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    0211f62

  3. Condensate Titration: show all 512 generated images in a gallery, captioned with level and call

    BoHuangLab
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    815c5e5

  4. Condensate Titration: report only AUC, AAC and sequence length

    BoHuangLab
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    8ea4a96

  5. Add the citation: paper link under the title, BibTeX in the app and the README

    BoHuangLab
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    69a3abb

  6. Virtual OpenCell: show the full map by default, below the viewer

    BoHuangLab
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    19e0b4f

  7. Virtual OpenCell: click the map to open the full map, every image and every protein named

    BoHuangLab
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    59ab251

  1. Virtual OpenCell: let the sample strip scroll instead of clipping past two rows

    BoHuangLab
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    cef16d5

  1. Virtual OpenCell: say plainly what the map draws (12 images per protein, all of the selected one)

    BoHuangLab
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    a40e7e4

  2. Virtual OpenCell: add the interactive virtual staining map (UMAP), with the selected protein outlined

    BoHuangLab
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    f8138ed

  3. Use the notebook's condensate titration flow diagram (notebooks/images/cellfm_flow_diagram.png)

    BoHuangLab
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    14249e1

  4. Add the Virtual OpenCell tab: browse CELL-FM's virtual staining of 1,276 OpenCell proteins

    BoHuangLab
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    a657a30

  1. Drop the top-level copies; they live in cell_fm/apps/condenseq now

    BoHuangLab
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    b52b2a8

  2. Import the CondenSeq app modules from cell_fm.apps.condenseq; add vit_cls

    BoHuangLab
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    a46a831

  1. Lead the noise section with pairing; a paired single-residue change is resolvable

    BoHuangLab
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    0f4badf

  2. Correct the reference values (they were unseeded) and state the seed noise; document the numpy<2 constraint

    BoHuangLab
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    9992a87

  3. Use the supplied flow diagram artwork; drop the generated figure

    BoHuangLab
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    2a0a28d

  4. Diagram: ViT label, larger in-box type, AUC/AAC anchored in their regions

    BoHuangLab
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    2b3e69d

  5. Trim the section text to one line; let the flow diagram carry the explanation

    BoHuangLab
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    0167225

  6. Replace the explainer with a pipeline flow diagram

    BoHuangLab
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    48261ce

  7. Add a schematic explaining the pipeline and what AUC and AAC measure

    BoHuangLab
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    3642b56

  8. Label the input 'IDP sequence'

    BoHuangLab
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    e3b797d

  9. Drop the preset dropdown; label the box IDP sequence (66 aa)

    BoHuangLab
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    9494da9

  10. Sequence is the only input, fixed at 66 aa; sampling settings pinned

    BoHuangLab
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    09d5e2c

  11. Say Intrinsically Disordered Peptide (IDP) rather than region/IDR

    BoHuangLab
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    d6e8796

  12. Reword the model description

    BoHuangLab
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    7bc588d

  13. Rename to CELL-FM; make Condensate Titration the first of several app sections

    BoHuangLab
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    6ef271b

  14. Add MIT license

    BoHuangLab
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    75c241d

  15. Fix 500 on /gradio_api/info: handle bool additionalProperties schemas

    BoHuangLab
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    485fb8a

  16. Let Spaces install gradio from sdk_version (5.9.1); fixes 500 on /

    BoHuangLab
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    060ee97

  17. Do not pass share= on Spaces; it aborts launch when localhost is unreachable

    BoHuangLab
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    5e7868c

  18. Pin gradio/gradio_client together to fix the startup schema crash

    BoHuangLab
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    5827da8

  19. Add loguru/tqdm/torchdiffeq; make wandb optional

    BoHuangLab
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    6e7dc7d

  20. Pin torch 2.8.0 for ZeroGPU; build models on CPU at startup

    BoHuangLab
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    7fb4074

  21. CELL-FM CondenSeq demo: sequence -> titration curve, AUC and AAC

    BoHuangLab
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    e794567

  22. initial commit

    BoHuangLab
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    1b8a37e