13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps,โฆ
Trains and evaluates single-agent reinforcement learning with Stable Baselines3 (PPO, SAC, DQN, TD3, DDPG, A2C), Gymnasium custom environments, vectorized rollouts, callbacks, and checkpoint normalization. Applies to reproducible RL experiments, continuous control, discrete
Claude Code
$ npx -y skills add K-Dense-AI/scientific-agent-skills --skill stable-baselines3 --agent claude-code
Codex
$ npx skills add K-Dense-AI/scientific-agent-skills --skill stable-baselines3 -a codex -y
Cursor
$ npx skills add K-Dense-AI/scientific-agent-skills --skill stable-baselines3 -a cursor -y
Gemini CLI
$ npx skills add K-Dense-AI/scientific-agent-skills --skill stable-baselines3 -a gemini-cli -y
GitHub Copilot
$ npx skills add K-Dense-AI/scientific-agent-skills --skill stable-baselines3 -a github-copilot -y
OpenCode
$ npx skills add K-Dense-AI/scientific-agent-skills --skill stable-baselines3 -a opencode -y
Windsurf
$ npx skills add K-Dense-AI/scientific-agent-skills --skill stable-baselines3 -a windsurf -y
name: stable-baselines3 description: Trains and evaluates single-agent reinforcement learning with Stable Baselines3 (PPO, SAC, DQN, TD3, DDPG, A2C), Gymnasium custom environments, vectorized rollouts, callbacks, and checkpoint normalization. Applies to reproducible RL experiments, continuous control, discrete actions, and SB3-Contrib recurrent or masked policies. license: MIT license allowed-tools: Read Write Edit Bash compatibility: Requires Python 3.10+, PyTorch >= 2.8, and stable-baselines3 2.9.0. Gymnasium environments; optional extras for TensorBoard and Atari (ale-py). metadata: version: "2.0" last-reviewed: "2026-10-01" upstream-version: "2.9.0" skill-author: K-Dense Inc.
Stable Baselines3 (SB3) is a PyTorch-based library providing reliable implementations of reinforcement learning algorithms. This skill provides comprehensive guidance for training RL agents, creating custom environments, implementing callbacks, and optimizing training workflows using SB3's unified API.
**Current upstream:** SB3 **2.9.0** (June 15, 2026). Docs: [stable-baselines3.readthedocs.io](https://stable-baselines3.readthedocs.io/en/v2.9.0/).
Tested against **stable-baselines3 2.9.0**. Requires **Python 3.10+** (3.9 dropped in 2.8.0) and **PyTorch >= 2.8**.
# Basic installation uv pip install "stable-baselines3==2.9.0" # With extra dependencies (TensorBoard, ale-py for Atari, etc.) uv pip install "stable-baselines3[extra]==2.9.0"
The 2.9.0 release supports Gymnasium >=0.29.1,<2.0; this review exercised Gymnasium 1.3.0, PyTorch 2.14.1 and Python 3.13 on CPU. pandas/matplotlib are now optional extras. Installation requires network unless packages are cached; local RL training needs no credentials or service endpoints.
On zsh, quote brackets: `uv pip install 'stable-baselines3[extra]==2.9.0'`.
For MuJoCo continuous-control benchmarks:
uv pip install "gymnasium[mujoco]"
Check your version:
import stable_baselines3 print(stable_baselines3.__version__)
**Basic Training Pattern:**
import gymnasium as gym
from stable_baselines3 import PPO
# Create environment
env = gym.make("CartPole-v1")
# Initialize agent (device="cpu" is often faster for MlpPolicy on small envs)
model = PPO("MlpPolicy", env, verbose=1, device="cpu", seed=0)
# Train the agent
model.learn(total_timesteps=10000)
# Save the model
model.save("ppo_cartpole")
# Load the model (without prior instantiation)
model = PPO.load("ppo_cartpole", env=env, device="cpu")
env.close()**Important Notes:**
**Algorithm Selection:** Use `references/algorithms.md` for detailed algorithm characteristics and selection guidance. Quick reference:
See `scripts/train_rl_agent.py` for a complete training template with best practices.
**Requirements:** Custom environments must inherit from `gymnasium.Env` and implement:
**Key Constraints:**
**Validation:**
from stable_baselines3.common.env_checker import check_env check_env(env, warn=True)
See [the template](scripts/custom_env_template.py) and [environment guide](references/custom_environments.md). The template now observes both agent and random goal coordinates, shape `(4,)`; old shape `(2,)` checkpoints require retraining. `gym.make("CustomEnv-v0")` adds the 100-step time limit; direct `CustomEnv()` does not. `check_env` checks API consistency, not Markov sufficiency, reward correctness or learnability.
**Purpose:** Vectorized environments run multiple environment instances in parallel, accelerating training and enabling certain wrappers (frame-stacking, normalization).
**Types:**
**Quick Setup:**
from stable_baselines3 import PPO
from stable_baselines3.common.env_util import make_vec_env
# DummyVecEnv batches 4 lightweight environments sequentially.
env = make_vec_env("CartPole-v1", n_envs=4, seed=0)
try:
model = PPO("MlpPolicy", env, verbose=1, device="cpu")
model.learn(total_timesteps=25000)
finally:
env.close()**Off-Policy Optimization:** With step-based `tr
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