diff --git a/requirements.txt b/requirements.txt
index c52639a..65d6c73 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,10 +1,10 @@
 antlr4-python3-runtime==4.9.3
-biopython==1.81
-black==22.3.0
+biopython==1.87
+black==26.3.1
 blessed==1.20.0
 click==8.1.3
 contextlib2==21.6.0
-deepspeed==0.8.0
+deepspeed==0.15.1
 docker-pycreds==0.4.0
 fair-esm==2.0.0
 gitdb==4.0.10
@@ -27,21 +27,21 @@ omegaconf==2.3.0
 omegaconf==2.3.0
 pathtools==0.1.2
 pre-commit==2.19.0
-protobuf==4.21.12
+protobuf==5.29.6
 py-cpuinfo==9.0.0
-pydantic==1.10.4
-pytest==7.3.1
-pytest==7.3.1
+pydantic==1.10.13
+pytest==9.0.3
+pytest==9.0.3
 pytest-cov==4.0.0
 pytest-mock==3.11.1
 pytest-xdist==3.2.1
 ruff==0.0.231
 s3fs==2023.1.0
-scikit-learn==1.2.1
-sentry-sdk==1.15.0
+scikit-learn==1.5.0
+sentry-sdk==1.45.1
 setproctitle==1.3.2
 smmap==5.0.0
 threadpoolctl==3.1.0
 tmtools==0.0.2
-tqdm==4.64.1
+tqdm==4.66.3
 types-tqdm==4.65.0.1