sacdallago/biotrainer issues and pull requests

#90 - v0.8.3

Pull Request - State: closed - Opened by SebieF 7 months ago
Labels: enhancement, maintenance

#89 - Version 0-8-2

Pull Request - State: closed - Opened by SebieF 9 months ago
Labels: enhancement

#88 - Version 0.8.1

Pull Request - State: closed - Opened by SebieF 11 months ago
Labels: documentation, enhancement, maintenance

#87 - Version 0.8.0

Pull Request - State: closed - Opened by SebieF 11 months ago
Labels: documentation, refactoring

#86 - Version 0.7.0

Pull Request - State: closed - Opened by SebieF about 1 year ago
Labels: testing, refactoring

#85 - :woman_scientist: Add LoRA layers to fine-tune protein language models for embeddings calculation

Issue - State: open - Opened by SebieF about 1 year ago
Labels: enhancement, refactoring

#84 - Renaming wrong test class name to InferencerTests

Pull Request - State: closed - Opened by SebieF over 1 year ago
Labels: bug

#83 - Do a sanity check of the inferencer module

Issue - State: open - Opened by SebieF over 1 year ago
Labels: good first issue, testing

#82 - Version 0.6.0

Pull Request - State: closed - Opened by SebieF over 1 year ago
Labels: bug, documentation, enhancement, testing

#81 - Version 0.5.1

Pull Request - State: closed - Opened by SebieF over 1 year ago
Labels: bug

#80 - Version 0.5.0

Pull Request - State: closed - Opened by SebieF over 1 year ago
Labels: bug

#79 - Value Error when Early stopping was engaged

Issue - State: closed - Opened by HenrikOtterstedt over 1 year ago - 2 comments
Labels: bug, enhancement

#78 - Version 0.4.0

Pull Request - State: closed - Opened by SebieF over 1 year ago
Labels: bug, documentation, enhancement, refactoring

#77 - Update dependencies

Issue - State: closed - Opened by SebieF over 1 year ago
Labels: refactoring

#76 - Create tutorial how-to use a custom embedder

Issue - State: open - Opened by SebieF over 1 year ago
Labels: documentation

#75 - Create CI and docker image

Issue - State: closed - Opened by SebieF over 1 year ago - 1 comment
Labels: enhancement

#74 - Version 0.3.1

Pull Request - State: closed - Opened by SebieF over 1 year ago
Labels: bug, breaking

#73 - Inferencer does not set correct device

Issue - State: closed - Opened by SebieF over 1 year ago
Labels: bug

#72 - [ppi] Interaction mode not compatible with all protocols yet

Issue - State: open - Opened by SebieF over 1 year ago
Labels: enhancement

#71 - Interaction and cross validation modes (version 0.3.0)

Pull Request - State: closed - Opened by SebieF over 1 year ago
Labels: documentation, enhancement, testing, refactoring

#70 - Adding BERT model and protocol = transformer encoder model + masked language modeling (MLM)

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

#69 - [ppi] Concat does not work for 0-dimensional (scalar) tensors

Issue - State: open - Opened by SebieF almost 2 years ago
Labels: bug

#68 - Support multiple hyperparameters for hold_out cross validation

Issue - State: open - Opened by SebieF almost 2 years ago
Labels: enhancement, good first issue

#67 - Class weights need to be sent to the device when use_class_weights=True

Issue - State: closed - Opened by joaquimgomez almost 2 years ago
Labels: bug

#66 - Include output_dir as a config option

Pull Request - State: closed - Opened by joaquimgomez almost 2 years ago
Labels: enhancement

#65 - Updating dependencies

Pull Request - State: closed - Opened by SebieF almost 2 years ago
Labels: refactoring

#64 - Development November 2022

Pull Request - State: closed - Opened by SebieF almost 2 years ago
Labels: bug, enhancement, refactoring

#63 - Fixing metrics calculation in ClassificationSolver

Pull Request - State: closed - Opened by SebieF about 2 years ago
Labels: bug

#62 - Fixing loss device handling

Pull Request - State: closed - Opened by SebieF about 2 years ago
Labels: bug

#61 - Config - Embeddings - Targets pipeline is inefficient

Issue - State: open - Opened by SebieF about 2 years ago
Labels: refactoring

#60 - Add random comparison baseline

Issue - State: open - Opened by SebieF about 2 years ago
Labels: enhancement, good first issue

#59 - Split annotations are more complicated than necessary

Issue - State: closed - Opened by SebieF about 2 years ago - 1 comment
Labels: refactoring, breaking

#58 - Implement embeddings calculation "on the fly"

Issue - State: open - Opened by SebieF about 2 years ago
Labels: enhancement

#57 - Ignore fix

Pull Request - State: closed - Opened by sacdallago about 2 years ago - 1 comment
Labels: bug

#56 - Torchmetrics

Pull Request - State: closed - Opened by sacdallago about 2 years ago - 1 comment
Labels: bug, refactoring

#55 - Inconsistency error

Issue - State: closed - Opened by sacdallago about 2 years ago - 1 comment
Labels: bug

#54 - torchmetrics missing form requirements

Issue - State: closed - Opened by sacdallago about 2 years ago
Labels: bug

#53 - Using time.perf_counter() instead of time.time()

Pull Request - State: closed - Opened by SebieF about 2 years ago
Labels: refactoring

#52 - Refactoring inference

Pull Request - State: closed - Opened by SebieF about 2 years ago
Labels: bug, refactoring

#51 - Fixing missing embedder name for pre-defined embeddings

Pull Request - State: closed - Opened by SebieF about 2 years ago
Labels: bug

#50 - Embeddings do not get re-computed automatically

Issue - State: open - Opened by SebieF about 2 years ago
Labels: bug, wontfix

#49 - BatchNorm1D does not work with batches of size 1

Issue - State: open - Opened by SebieF about 2 years ago - 1 comment
Labels: bug, wontfix

#48 - Improving documentation

Pull Request - State: closed - Opened by SebieF about 2 years ago
Labels: documentation

#47 - Fixing class weights calculation for sequence level tasks

Pull Request - State: closed - Opened by SebieF about 2 years ago
Labels: bug

#46 - Adding ignore_redundant_sequences flag

Pull Request - State: closed - Opened by SebieF about 2 years ago - 4 comments
Labels: enhancement

#45 - Removing unused ConvNeXt model

Pull Request - State: closed - Opened by SebieF about 2 years ago
Labels: refactoring

#44 - Improving handling of embeddings

Pull Request - State: closed - Opened by SebieF about 2 years ago
Labels: bug, enhancement

#43 - Enable URLs for embedding files

Issue - State: closed - Opened by SebieF about 2 years ago
Labels: enhancement

#42 - Support more visualization platforms

Issue - State: open - Opened by SebieF about 2 years ago - 1 comment
Labels: enhancement, good first issue

#41 - Adding auto resume mode

Pull Request - State: closed - Opened by SebieF about 2 years ago
Labels: enhancement

#40 - Adding continue training of pretrained model

Pull Request - State: closed - Opened by SebieF about 2 years ago - 2 comments
Labels: enhancement

#39 - Improve user documentation

Issue - State: closed - Opened by SebieF about 2 years ago - 1 comment
Labels: documentation

#38 - Update dependencies before release

Issue - State: closed - Opened by SebieF about 2 years ago
Labels: refactoring

#37 - Adding additional metrics

Pull Request - State: closed - Opened by joaquimgomez about 2 years ago - 7 comments
Labels: enhancement

#36 - Adding additional logger statements for evaluation

Pull Request - State: closed - Opened by SebieF over 2 years ago
Labels: enhancement

#35 - Adding example notebooks for h5file enhancement

Pull Request - State: closed - Opened by SebieF over 2 years ago
Labels: enhancement

#34 - Adding residues_to_class protocol

Pull Request - State: closed - Opened by SebieF over 2 years ago - 1 comment
Labels: enhancement

#33 - Improving handling of erroneous input files for residue_to_class

Pull Request - State: closed - Opened by SebieF over 2 years ago
Labels: bug

#32 - Improve error messages for non-matching sequence and labels files

Issue - State: closed - Opened by SebieF over 2 years ago
Labels: bug

#31 - Add additional metrics

Issue - State: closed - Opened by SebieF over 2 years ago - 1 comment
Labels: enhancement

#30 - Adding setuptools version 59.5.0 to poetry dependencies

Pull Request - State: closed - Opened by SebieF over 2 years ago
Labels: bug

#29 - Capitalizing validation value

Pull Request - State: closed - Opened by SebieF over 2 years ago
Labels: bug

#28 - Multi-class prediction

Issue - State: open - Opened by joaquimgomez over 2 years ago - 1 comment
Labels: enhancement, question

#27 - Add residue_to_value protocol

Issue - State: open - Opened by SebieF over 2 years ago
Labels: enhancement

#26 - Issue with setuptools version

Issue - State: closed - Opened by HenrikOtterstedt over 2 years ago - 2 comments
Labels: bug

#25 - Using sorted class labels

Pull Request - State: closed - Opened by SebieF over 2 years ago - 2 comments

#24 - TargetManager does not check if residues and targets have same length (for residue_to_class)

Issue - State: closed - Opened by SebieF over 2 years ago
Labels: bug

#23 - Add the possibility to add extra features to the h5 file

Issue - State: closed - Opened by SebieF over 2 years ago
Labels: enhancement

#22 - Add residues_to_class protocol

Issue - State: closed - Opened by SebieF over 2 years ago
Labels: enhancement

#21 - MSE Loss is not capable of handling ignored targets

Issue - State: open - Opened by SebieF over 2 years ago

#20 - Add input mask to residue_to_class protocol

Pull Request - State: closed - Opened by SebieF over 2 years ago - 2 comments
Labels: enhancement

#19 - Create better logging output of evaluation

Issue - State: closed - Opened by SebieF over 2 years ago
Labels: enhancement

#18 - Code refactoring

Pull Request - State: closed - Opened by SebieF over 2 years ago - 1 comment
Labels: refactoring

#17 - Adding sequence to value protocol

Pull Request - State: closed - Opened by SebieF over 2 years ago - 1 comment
Labels: enhancement

#16 - Add mask to input

Issue - State: closed - Opened by mheinzinger over 2 years ago
Labels: enhancement

#15 - [DRAFT] Adding sequence_to_value protocol

Pull Request - State: closed - Opened by SebieF over 2 years ago - 2 comments
Labels: enhancement

#14 - Adding poetry and docker for reproducibility (Closes #9)

Pull Request - State: closed - Opened by SebieF over 2 years ago - 2 comments
Labels: enhancement

#13 - Check dataset creation from list

Issue - State: closed - Opened by SebieF over 2 years ago - 3 comments

#12 - Creating temporary config file instead of re-using the existing one

Pull Request - State: closed - Opened by SebieF over 2 years ago
Labels: bug, testing

#11 - Metrics Calculation device handling is problematic

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

#10 - Fixing rebase issues

Pull Request - State: closed - Opened by SebieF over 2 years ago
Labels: bug

#9 - issue with dependencies

Issue - State: closed - Opened by jahnl over 2 years ago - 9 comments

#8 - residue_to_class -> Remove predictions for padding

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

#7 - Add facilities to make inference on trainer run

Pull Request - State: closed - Opened by sacdallago over 2 years ago - 5 comments

#6 - Small fixes and adding "before getting started" section to data standardization doc

Pull Request - State: closed - Opened by SebieF over 2 years ago
Labels: documentation, enhancement

#5 - Check Residue2Class accuracy calculation

Issue - State: closed - Opened by SebieF over 2 years ago

#4 - Add basic automated configuration testing

Pull Request - State: closed - Opened by SebieF over 2 years ago - 1 comment
Labels: enhancement, testing

#3 - Adding data standardization document

Pull Request - State: closed - Opened by SebieF over 2 years ago - 2 comments
Labels: documentation

#2 - Adding sequence to class prediction

Pull Request - State: closed - Opened by SebieF over 2 years ago - 3 comments
Labels: enhancement

#1 - Fixing relative paths in executor and making cli more accessbile

Pull Request - State: closed - Opened by SebieF over 2 years ago
Labels: enhancement

GitHub / sacdallago/biotrainer issues and pull requests