After encountering the same problems discussed in issue #1, I managed to install all the necessary dependencies under Python 3.9, however only tensorflow>=2.5 is currently available for Python 3.9. This causes the very same error described here when running GeneNER_SpeAss_run.py - irrespective of using Bioformer or PubMedBert.
Using Python 3.8 and setting protobuf>=3.19.0,<=3.20.x in requirements.txt allows to install tensorflow==2.3.0 and fixes the problem.
Please fix the bug raised when using Python 3.9 or change the README file with accurate installation instructions.
(reproduced on linux 5.4.0-167-generic #184-Ubuntu SMP)