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Single-sequence model #354
Commits on Oct 11, 2022
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Added embedder for handling single-sequence embeddings.
- Added a `PreembeddingEmbedder` for embedding single-sequence (NUM_RESIDUE, ...) shaped embeddings as input.
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Commits on Oct 14, 2022
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Added sequence-embedding mode config.
- Added configuration options in `config.py` for toggling seq-emb mode - Added list for specifying features to be used in seq-emb mode.
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Added dummy MSA generation for seq-emb mode.
- New method for generating dummy MSA features.
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Added switch in inference flow for using sequence embedding instead o…
…f MSAs. - Added a `seq_emb` bool flag to `data_pipeline > process_fasta()` - In `seqemb_mode` use dummy MSA features instead of full ones.
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Added loading of sequence embeddings in inference flow when in seq_em…
…b mode. - Added a method to load and process sequence embedding `*.pt` files. - In `seqemb_mode`, now add seqemb features to the feature dictionary.
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Added single seq mode in inference script and forwarded to the FASTA …
…processors. - Added `use_single_seq_mode` flag in inference script arguments. - Passed on the flag to the FASTA file `data_processor`.
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Commits on Oct 18, 2022
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Added switch for using the single sequence embedder when using the mo…
…del in `seqemb` mode. - `seqemb_mode_enabled` added as a configuration option. - `model.py` switches to using the `PreembeddingEmbedder` when the flag is `True`.
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Added configuration options for the new PreembeddingEmbedder.
- Added `preembedding_embedder` config dictionary in `config` - Added `preemb_dim_size` property in `config` for specifying single seq embedding size.
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Added switching off of column attention in evoformer when using seque…
…nce embeddings. - Added flag `no_column_attention` in evoformer config. - Added check in `evoformer.py` to switch off `MSAColumnAttention` when the config flag `no_column_attention` is `True`.
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Added switch in the MMCIF processing pipeline for using sequence embe…
…ddings when in `seqemb` mode. - Use sequence embedding files when in `seqemb` mode. - Make dummy MSA features for MMCIF when using `seqemb` mode.
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Added passing of sequence embedding mode flag from
data_modules
to ……`data_pipeline` for training and inference pipelines. - Passing the config.data.seqemb_mode.enabled flag to the FASTA, PDB, and MMCIF data pipelines.
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Added training preset for sequence embedding initial training.
- Turn on `seqemb` mode in `data`, `model`, and `globals` config when using `seqemb` training preset.
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Added training preset for sequence embedding finetuning training.
- Turn on `seqemb` mode in `data`, `model`, and `globals` config when using `seqemb` training preset. - Set configuration options specific for finetuning in general.
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Commits on Oct 19, 2022
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Optimized type-changing of features from numpy to torch
- Bugfix: `torch` throws warnings when copying a tensor via initialization - Added lambda to `.clone()` those tensors instead
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Commits on Oct 21, 2022
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Changed the seq embedding tensor passed to the data pipeline to be a …
…seqemb feature dictionary. - `_process_seqemb_features` now returns a dictionary instead of a tensor.
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Commits on Oct 28, 2022
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Added the seq_emb features to the list of features to be processed by…
… feature pipeline , if using seq_emb mode - In `seq_emb` mode, add list of `seq_emb` features to `feature_names`
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Added a separate AlignmentRunner for handling seq_emb mode.
- In `seq_emb` mode, the AlignmentRunner works only on generating templates.
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Commits on Oct 29, 2022
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Added switch for sequence embedding mode to the PDB file pipeline.
- In `seqemb_mode`, `process_pdb` loads sequence embedding for the PDB's protein, and a dummy MSA
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Commits on Nov 1, 2022
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Fix for a bug in data_transforms which wouldn't allow creation of MSA…
… mask if there is only input sequence in MSA. - Set `max_msa_clusters=1` in model presets for allowing the input sequence to be a MSA cluster centre.
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Commits on Sep 12, 2023
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Commits on Sep 13, 2023
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Commits on Sep 15, 2023
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Commits on Sep 18, 2023
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Commits on Sep 19, 2023
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Commits on Sep 28, 2023
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Commits on Sep 29, 2023
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Commits on Oct 5, 2023
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