Bio Embeddings¶
Resources to learn about bio_embeddings:
Quickly predict protein structure and function from sequence via embeddings: embed.protein.properties.
Read the current documentation: docs.bioembeddings.com.
Chat with us: chat.bioembeddings.com.
We presented the bio_embeddings pipeline as a talk at ISMB 2020 & LMRL 2020. You can find the talk on YouTube, the poster on F1000, and our Current Protocol Manuscript.
Check out the
examples
of pipeline configurations a andnotebooks
.
Project aims:
Facilitate the use of language model based biological sequence representations for transfer-learning by providing a single, consistent interface and close-to-zero-friction
Reproducible workflows
Depth of representation (different models from different labs trained on different dataset for different purposes)
Extensive examples, handle complexity for users (e.g. CUDA OOM abstraction) and well documented warnings and error messages.
The project includes:
General purpose python embedders based on open models trained on biological sequence representations (SeqVec, ProtTrans, UniRep,…)
A pipeline which:
embeds sequences into matrix-representations (per-amino-acid) or vector-representations (per-sequence) that can be used to train learning models or for analytical purposes
projects per-sequence embedidngs into lower dimensional representations using UMAP or t-SNE (for lightwieght data handling and visualizations)
visualizes low dimensional sets of per-sequence embeddings onto 2D and 3D interactive plots (with and without annotations)
extracts annotations from per-sequence and per-amino-acid embeddings using supervised (when available) and unsupervised approaches (e.g. by network analysis)
A webserver that wraps the pipeline into a distributed API for scalable and consistent workfolws
Installation¶
You can install bio_embeddings
via pip or use it via docker. Mind the additional dependencies for align
.
Pip¶
Install the pipeline like so:
pip install bio-embeddings[all]
To install the unstable version, please install the pipeline like so:
pip install -U "bio-embeddings[all] @ git+https://github.com/sacdallago/bio_embeddings.git"
Docker¶
We provide a docker image at ghcr.io/bioembeddings/bio_embeddings
. Simple usage example:
docker run --rm --gpus all \
-v "$(pwd)/examples/docker":/mnt \
-v bio_embeddings_weights_cache:/root/.cache/bio_embeddings \
-u $(id -u ${USER}):$(id -g ${USER}) \
ghcr.io/bioembeddings/bio_embeddings:v0.1.6 /mnt/config.yml
See the docker
example in the examples
folder for instructions. You can also use ghcr.io/bioembeddings/bio_embeddings:latest
which is built from the latest commit.
Dependencies¶
To use the mmseqs_search
protocol, or the mmsesq2
functions in align
, you additionally need to have mmseqs2 in your path.
Installation notes¶
bio_embeddings
was developed for unix machines with GPU capabilities and CUDA installed. If your setup diverges from this, you may encounter some inconsistencies (e.g. speed is significantly affected by the absence of a GPU and CUDA). For Windows users, we strongly recommend the use of Windows Subsystem for Linux.
What model is right for you?¶
Each models has its strengths and weaknesses (speed, specificity, memory footprint…). There isn’t a “one-fits-all” and we encourage you to at least try two different models when attempting a new exploratory project.
The models prottrans_t5_xl_u50
, esm1b
, esm
, prottrans_bert_bfd
, prottrans_albert_bfd
, seqvec
and prottrans_xlnet_uniref100
were all trained with the goal of systematic predictions. From this pool, we believe the optimal model to be prottrans_t5_xl_u50
, followed by esm1b
.
Usage and examples¶
We highly recommend you to check out the examples
folder for pipeline examples, and the notebooks
folder for post-processing pipeline runs and general purpose use of the embedders.
After having installed the package, you can:
Use the pipeline like:
bio_embeddings config.yml
A blueprint of the configuration file, and an example setup can be found in the
examples
directory of this repository.Use the general purpose embedder objects via python, e.g.:
from bio_embeddings.embed import SeqVecEmbedder embedder = SeqVecEmbedder() embedding = embedder.embed("SEQVENCE")
More examples can be found in the
notebooks
folder of this repository.
Cite¶
If you use bio_embeddings
for your research, we would appreciate it if you could cite the following paper:
Dallago, C., Schütze, K., Heinzinger, M., Olenyi, T., Littmann, M., Lu, A. X., Yang, K. K., Min, S., Yoon, S., Morton, J. T., & Rost, B. (2021). Learned embeddings from deep learning to visualize and predict protein sets. Current Protocols, 1, e113. doi: 10.1002/cpz1.113
The corresponding bibtex:
@article{https://doi.org/10.1002/cpz1.113,
author = {Dallago, Christian and Schütze, Konstantin and Heinzinger, Michael and Olenyi, Tobias and Littmann, Maria and Lu, Amy X. and Yang, Kevin K. and Min, Seonwoo and Yoon, Sungroh and Morton, James T. and Rost, Burkhard},
title = {Learned Embeddings from Deep Learning to Visualize and Predict Protein Sets},
journal = {Current Protocols},
volume = {1},
number = {5},
pages = {e113},
keywords = {deep learning embeddings, machine learning, protein annotation pipeline, protein representations, protein visualization},
doi = {https://doi.org/10.1002/cpz1.113},
url = {https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpz1.113},
eprint = {https://currentprotocols.onlinelibrary.wiley.com/doi/pdf/10.1002/cpz1.113},
year = {2021}
}
Additionally, we invite you to cite the work from others that was collected in `bio_embeddings` (see section _"Tools by category"_ below). We are working on an enhanced user guide which will include proper references to all citable work collected in `bio_embeddings`.
Contributors¶
Christian Dallago (lead)
Konstantin Schütze
Tobias Olenyi
Michael Heinzinger
Want to add your own model? See contributing for instructions.
Non-exhaustive list of tools available (see following section for more details):¶
Fastext
Glove
Word2Vec
SeqVec (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3220-8)
SeqVecSec and SeqVecLoc for secondary structure and subcellularlocalization prediction
ProtTrans (ProtBert, ProtAlbert, ProtT5) (https://doi.org/10.1101/2020.07.12.199554)
ProtBertSec and ProtBertLoc for secondary structure and subcellular localization prediction
UniRep (https://www.nature.com/articles/s41592-019-0598-1)
ESM/ESM1b (https://www.biorxiv.org/content/10.1101/622803v3)
PLUS (https://github.com/mswzeus/PLUS/)
CPCProt (https://www.biorxiv.org/content/10.1101/2020.09.04.283929v1.full.pdf)
PB-Tucker (https://www.biorxiv.org/content/10.1101/2021.01.21.427551v1)
GoPredSim (https://www.nature.com/articles/s41598-020-80786-0)
DeepBlast (https://www.biorxiv.org/content/10.1101/2020.11.03.365932v1)
Datasets¶
Tools by category¶
Pipeline
align:
DeepBlast (https://www.biorxiv.org/content/10.1101/2020.11.03.365932v1)
embed:
ProtTrans BERT trained on BFD (https://doi.org/10.1101/2020.07.12.199554)
SeqVec (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3220-8)
ProtTrans ALBERT trained on BFD (https://doi.org/10.1101/2020.07.12.199554)
ProtTrans XLNet trained on UniRef100 (https://doi.org/10.1101/2020.07.12.199554)
ProtTrans T5 trained on BFD (https://doi.org/10.1101/2020.07.12.199554)
ProtTrans T5 trained on BFD and fine-tuned on UniRef50 (in-house)
UniRep (https://www.nature.com/articles/s41592-019-0598-1)
ESM/ESM1b (https://www.biorxiv.org/content/10.1101/622803v3)
PLUS (https://github.com/mswzeus/PLUS/)
CPCProt (https://www.biorxiv.org/content/10.1101/2020.09.04.283929v1.full.pdf)
project:
t-SNE
UMAP
PB-Tucker (https://www.biorxiv.org/content/10.1101/2021.01.21.427551v1)
visualize:
2D/3D sequence embedding space
extract:
supervised:
SeqVec: DSSP3, DSSP8, disorder, subcellular location and membrane boundness as in https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3220-8
ProtBertSec and ProtBertLoc as reported in https://doi.org/10.1101/2020.07.12.199554
unsupervised:
via sequence-level (reduced_embeddings), pairwise distance (euclidean like goPredSim, more options available, e.g. cosine)
General purpose embedders
ProtTrans BERT trained on BFD (https://doi.org/10.1101/2020.07.12.199554)
SeqVec (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3220-8)
ProtTrans ALBERT trained on BFD (https://doi.org/10.1101/2020.07.12.199554)
ProtTrans XLNet trained on UniRef100 (https://doi.org/10.1101/2020.07.12.199554)
ProtTrans T5 trained on BFD (https://doi.org/10.1101/2020.07.12.199554)
ProtTrans T5 trained on BFD + fine-tuned on UniRef50 (https://doi.org/10.1101/2020.07.12.199554)
Fastext
Glove
Word2Vec
UniRep (https://www.nature.com/articles/s41592-019-0598-1)
ESM/ESM1b (https://www.biorxiv.org/content/10.1101/622803v3)
PLUS (https://github.com/mswzeus/PLUS/)
CPCProt (https://www.biorxiv.org/content/10.1101/2020.09.04.283929v1.full.pdf)