kipoi/kipoi: Kipoi with metadata and containers
Bibliographic record
Abstract
In this release we have addressed the following One can output metadata (such as gene_id, transcript_id, exon regions etc.) along with the predictions from kipoi now. The relevant CLI flags are -m or --keep_metadata. By default it is true. Docker containers for all the models are released. These containers create the model specific conda environments, activate them and return a bash shell with the activated environment. Each model group page now has a tab named docker which gives information about which docker container is compatible with which model and how to use the containers with user defined datasets. For example, look here. We are hosting 13 containers for existing 29 model groups here. The repository responsible for building the containers and testing them is here. You will also find information about how to build singularity containers from these docker containers in the README. Continuous integration tests are fixed across this repository, kipoi models and kipoi website.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.003 | 0.011 |
| Meta-epidemiology (narrow) | 0.003 | 0.003 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.006 | 0.009 |
| Open science | 0.004 | 0.007 |
| Research integrity | 0.002 | 0.004 |
| Insufficient payload (model declined to judge) | 0.188 | 0.284 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".