sacdallago/bio_embeddings issues and pull requests

#247 - Installation error in installing bio embedding package via pip

Issue - State: open - Opened by amalislam675 3 months ago

#246 - Can't install well to run bio_embed

Issue - State: open - Opened by Lsz-20 3 months ago - 1 comment

#245 - Not able to run and pip install bioembeddings

Issue - State: open - Opened by rmagesh148 3 months ago - 4 comments

#244 - Protocol prottrans_t5_bfd: HTTPError: HTTP Error 406: Not Acceptable

Issue - State: open - Opened by jiaming28 5 months ago

#243 - Can Word2Vec be used for 4, 5 and 6 kmer? If possible, which file I need to changed and which parameter. I am seeking Guidance on Adapting Word2Vec Code for 4kmer Sequences

Issue - State: open - Opened by faruk17035 7 months ago

#242 - Protocol prottrans_bert_bfd: OSError: Unable to load weights from pytorch checkpoint file for .catch/bio_embeddings/prottrans_bert_bfd/model_directory/pytorch_model.bin' at '.catch/bio_embeddings/prottrans_bert_bfd/model_directory/pytorch_model.bin'. If you tried to load a PyTorch model from a TF 2.0 checkpoint, please set from_tf=True.

Issue - State: open - Opened by Meng-AnunaAI 8 months ago

#241 - Cannot Import Any Embedder "load()" has been removed, use yaml = YAML(typ='rt') yaml.load(...)

Issue - State: open - Opened by wijuliano 8 months ago

#240 - Protocol esm1b: AttributeError: 'dict' object has no attribute 'startswith'

Issue - State: open - Opened by dvonkan 10 months ago

#239 - from where comes the models in "bio_embeddings/utilities /defaults.yml", where is docs, parameters, dataset ?

Issue - State: open - Opened by laraque 12 months ago

#238 - Protocol prottrans_t5_xl_u50: PermissionError: [Errno 13] Permission denied: 'C:\\Users\\user\\AppData\\Local\\Temp\\tmpk7e1m0jg'

Issue - State: open - Opened by jbattjes about 1 year ago - 1 comment

#237 - Tensor size issue

Issue - State: closed - Opened by J-JEMINA about 1 year ago

#236 - Cant install bio_embeddings in colab

Issue - State: open - Opened by IliasGewr about 1 year ago - 3 comments

#235 - AttributeError: 'dict' object has no attribute '__NUMPY_SETUP__'

Issue - State: open - Opened by VarianZhou about 1 year ago

#234 - 3D Protein Embeddings

Issue - State: open - Opened by ChatterjeeAyan about 1 year ago

#233 - Error during first step - greenlet size changed, may indicate binary incompatibility.

Issue - State: open - Opened by igwill over 1 year ago - 1 comment

#232 - Hard times trying to run the bindEmbed21 example.

Issue - State: open - Opened by Ravy-LFL over 1 year ago

#231 - Can not install bioembedings on ubuntu? Please help

Issue - State: open - Opened by faruk17035 over 1 year ago - 1 comment

#230 - Can not install bio-embedding in wsl

Issue - State: open - Opened by faruk17035 over 1 year ago - 2 comments

#229 - Bump werkzeug from 2.0.3 to 2.2.3

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#228 - Docker containers shutting down within a few seconds of starting

Issue - State: open - Opened by kthurimella over 1 year ago

#227 - Bump ipython from 8.4.0 to 8.10.0

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#226 - Bump oauthlib from 3.2.0 to 3.2.2

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#225 - Custom embeddings

Issue - State: open - Opened by rhysnewell over 1 year ago

#224 - OSError: Unable to open file (truncated file: eof = 63504384, sblock->base_addr = 0, stored_eof = 374434776)

Issue - State: open - Opened by gerdos over 1 year ago - 1 comment

#223 - Protocol prottrans_t5_xl_u50: URLError: <urlopen error [Errno 113] No route to host>

Issue - State: open - Opened by Azai-yx over 1 year ago - 1 comment

#222 - Allow torch up to next major version

Pull Request - State: open - Opened by ecederstrand almost 2 years ago - 1 comment

#221 - Bump certifi from 2022.6.15 to 2022.12.7

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#220 - Bump pillow from 9.1.1 to 9.3.0

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#219 - Update jax-unirep dependency version

Issue - State: open - Opened by fedorn almost 2 years ago

#218 - Add support for ESM-2 and ESMFold

Issue - State: open - Opened by fedorn almost 2 years ago - 3 comments

#217 - CUDA out of memory.

Issue - State: open - Opened by wenyuhaokikika almost 2 years ago - 2 comments

#216 - I want to know the configuration of the people who run successfully

Issue - State: open - Opened by sudo349 almost 2 years ago - 2 comments

#215 - AssertionError: Failed in nopython mode pipeline (step: native lowering) Storing i64 to ptr of i32 ('dim'). FE type int32

Issue - State: open - Opened by sudo349 almost 2 years ago

#212 - It may be better to let the user define whether the same redundant is allowed or not

Issue - State: closed - Opened by wenyuhaokikika almost 2 years ago - 1 comment

#211 - segmentation fault

Issue - State: open - Opened by yangyangdotcom almost 2 years ago - 1 comment

#210 - Feature Request: Add Worker version to status API

Issue - State: open - Opened by t03i almost 2 years ago
Labels: enhancement

#209 - Bump joblib from 1.1.0 to 1.2.0

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#208 - Bump protobuf from 3.19.4 to 3.19.5

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#207 - Bump oauthlib from 3.2.0 to 3.2.1

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#206 - Bump mako from 1.2.1 to 1.2.2

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#205 - Package dependency error.

Issue - State: open - Opened by DimitrisAlivas about 2 years ago - 3 comments

#204 - Protocol esm: UnpicklingError: invalid load key, '<'.

Issue - State: closed - Opened by wenyuhaokikika about 2 years ago - 1 comment

#203 - Protocol deepblast: AttributeError: can't set attribute

Issue - State: closed - Opened by XiaofangJ about 2 years ago

#202 - Text on embed.predictprotein.org

Issue - State: closed - Opened by C-Marquet about 2 years ago - 1 comment

#201 - render_3D_scatter_plotly Error

Issue - State: open - Opened by drorhunvural about 2 years ago

#200 - ImportError when importing ProtTransT5XLU50Embedder

Issue - State: open - Opened by AugustEhl about 2 years ago - 1 comment

#199 - detokenize/reverse embedded array

Issue - State: open - Opened by drorhunvural over 2 years ago - 1 comment

#198 - Bump notebook from 6.4.3 to 6.4.12

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#197 - webserver worker failing on no flask?

Issue - State: closed - Opened by sacdallago over 2 years ago - 1 comment

#196 - How to solve this error?

Issue - State: closed - Opened by faruk17035 over 2 years ago - 2 comments

#195 - pytorch compatibility with NVIDIA A100

Issue - State: closed - Opened by abdush over 2 years ago - 2 comments

#194 - docker: Error response from daemon: could not select device driver "" with capabilities: [[gpu]].

Issue - State: closed - Opened by avilella over 2 years ago - 4 comments
Labels: question, wontfix

#193 - Solubility / Aggregability / Stability

Issue - State: closed - Opened by avilella over 2 years ago - 5 comments
Labels: question

#192 - Bump notebook from 6.4.3 to 6.4.10

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#191 - Feature importances with protein embedders

Issue - State: closed - Opened by evabalini over 2 years ago - 2 comments

#190 - Import error

Issue - State: closed - Opened by kvetab over 2 years ago - 7 comments

#189 - Protocol prottrans_bert_bfd: BadZipFile: File is not a zip file

Issue - State: closed - Opened by pskvins over 2 years ago - 2 comments

#188 - Bump jupyter-server from 1.10.2 to 1.15.4

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#187 - Add merck/sapiens

Issue - State: open - Opened by sacdallago over 2 years ago - 1 comment
Labels: Language model

#186 - Add nferruz/ProtGPT2

Issue - State: open - Opened by sacdallago over 2 years ago
Labels: Language model, prio:low

#185 - Bump pillow from 8.3.2 to 9.0.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#184 - ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

Issue - State: open - Opened by FYY99117 over 2 years ago - 5 comments
Labels: bug, prio:medium

#162 - Protocol unirep: ImportError: cannot import name 'cusolver' from 'jaxlib' (/mnt/lsf-nas-1/os-shared/anaconda3/envs/hannes_bio_embeddings/lib/python3.7/site-packages/jaxlib/init.py)

Issue - State: open - Opened by HannesStark about 3 years ago - 4 comments

#152 - the bio_embeddings Give me error of Invalid fasta sequence? But I think I could give the correct sequence as input in fasta file. How could I solve this error?(I use '>' before my fasta file.Please give me some guideline dear Dallago Sir)

Issue - State: open - Opened by faruk17035 about 3 years ago - 1 comment

#151 - How to solve this error, I put a DNA sequence here in fasta format...But it gives me error(When convet to numerical form using wor2vec). Please give me some guideline.

Issue - State: closed - Opened by faruk17035 about 3 years ago - 2 comments

#150 - Can A DNA sequence be converted to numbers using word2vec,Glove and Fasttext protocol? Please give me some guideline

Issue - State: closed - Opened by faruk17035 about 3 years ago - 1 comment

#149 - Which is my output embedding file from these files(converted to numerical form) and how I work with it ? Please help dear Dallago Sir

Issue - State: closed - Opened by faruk17035 about 3 years ago - 3 comments

GitHub / sacdallago/bio_embeddings issues and pull requests