13c-metabolic-flux
Estimates intracellular metabolic fluxes from steady-state carbon-13 isotope-tracing measurements using validated atom maps,โฆ
Performs zero-shot time-series forecasting with Google's TimesFM, including regular-grid CSV preparation, quantile forecasts, XReg covariates, and held-out evaluation. Uses the Apache-licensed TimesFM 2.5 checkpoint by default and documents the distinct TimesFM 3.0 multivariate
Claude Code
$ npx -y skills add K-Dense-AI/scientific-agent-skills --skill timesfm-forecasting --agent claude-code
Codex
$ npx skills add K-Dense-AI/scientific-agent-skills --skill timesfm-forecasting -a codex -y
Cursor
$ npx skills add K-Dense-AI/scientific-agent-skills --skill timesfm-forecasting -a cursor -y
Gemini CLI
$ npx skills add K-Dense-AI/scientific-agent-skills --skill timesfm-forecasting -a gemini-cli -y
GitHub Copilot
$ npx skills add K-Dense-AI/scientific-agent-skills --skill timesfm-forecasting -a github-copilot -y
OpenCode
$ npx skills add K-Dense-AI/scientific-agent-skills --skill timesfm-forecasting -a opencode -y
Windsurf
$ npx skills add K-Dense-AI/scientific-agent-skills --skill timesfm-forecasting -a windsurf -y
name: timesfm-forecasting description: Performs zero-shot time-series forecasting with Google's TimesFM, including regular-grid CSV preparation, quantile forecasts, XReg covariates, and held-out evaluation. Uses the Apache-licensed TimesFM 2.5 checkpoint by default and documents the distinct TimesFM 3.0 multivariate API and weight-license requirements. allowed-tools: Read Write Edit Bash license: Apache-2.0 license compatibility: Requires Python 3.10+ and timesfm 3.0.2 with PyTorch; CSV tooling also needs NumPy and pandas. Network access and cache space are needed for initial Hugging Face checkpoint download. Optional XReg needs JAX and scikit-learn; current JAX requires Python 3.12+. metadata: version: "3.0" skill-author: Clayton Young / Superior Byte Works, LLC (@borealBytes) last-reviewed: "2026-10-01" tested-package: "timesfm 3.0.2"
The **Python package version is 3.0.2**; checkpoint versions are separate.
| Checkpoint | Interface | Quantile output | Usage terms | | --- | --- | --- | --- | | 2.5, 200M | `timesfm.TimesFM_2p5_200M_torch`, `compile`, `forecast` | mean + 9 deciles, median index 5 | Apache-2.0 weights; bundled CLI default | | 3.0, about 330M | `timesfm3.TimesFM3Forecaster`, `predict` / `predict_batch` | 9 deciles, median index 4 | Downloaded weights restricted to non-commercial, non-production use |
Upstream identifies 3.0 as the latest model. This skill retains 2.5 as its default local workflow because its Apache-licensed weights have different usage terms. For 3.0 multivariate targets, past-only covariates or Apple MLX, read [references/timesfm3.md](references/timesfm3.md) before adapting code. Authorized Google Cloud services have separate terms; a Cloud entitlement does not change the license of downloaded weights. See the [upstream license notice](https://github.com/google-research/timesfm#license-notice-for-pretrained-weights).
Use TimesFM for forecasting an ordered temporal target without task-specific model training. It is not a causal effect estimator, clinical detector, or physics-based climate model. Zero-shot describes fitting; it does not establish absence of benchmark overlap in pretraining or good accuracy in a new domain.
1. Establish cadence, units, forecast origin, horizon, known-at-origin covariates, evaluation cutoffs and a naive/seasonal-naive baseline. 2. Validate a sorted, unique, regular time grid. Do not `dropna()` internal gaps: that changes temporal spacing. Reject nonfinite inputs, or explicitly impute inside each training history. Never fill using held-out future targets. 3. Run `python scripts/check_system.py` before downloading/loading weights. Its available-RAM and cache-volume thresholds are heuristics, not a guarantee against OOM. Start with batch size 1; measure actual peak usage. 4. Load the chosen checkpoint with a recorded immutable revision. For 2.5, compile explicit positive context/horizon settings; zero does **not** mean โuse the maximum.โ Keep patch-rounded context + horizon <=16,384 and horizon <=1,024 when using the continuous quantile head. 5. Forecast, validate shapes/finite values/quantile ordering and export the forecast origin, frequency, configuration and checkpoint revision. 6. Evaluate across rolling origins with preprocessing fitted independently per origin. Report accuracy, interval coverage and interval width by horizon; label quantile intervals **nominal** until calibrated on relevant data.
Run in a separate environment. The commands below target the reviewed release. Shell extras and version constraints must be quoted, particularly in zsh.
uv venv .venv-timesfm uv pip install --python .venv-timesfm/bin/python "timesfm[torch]==3.0.2" numpy pandas .venv-timesfm/bin/python scripts/check_system.py
Use the current [PyTorch installation selector](https://pytorch.org/get-started/locally/) for a CUDA wheel matching the host. The 2.5 loader in this release chooses `cuda:0` if CUDA exists, otherwise CPU; detecting MPS does **not** enable MPS inference. Do not use `model.to(...)` on the wrapper as if it were an `nn.Module`. For CPU-only XReg, install `jax` and `scikit-learn` alongside the PyTorch profile; the upstream `[xreg]` extra requests `jax[cuda]`, which is not appropriate for macOS. Flax is a separate optional backend; it is not required by the bundled scripts.
from importlib.metadata import version
import timesfm
print(version("timesfm")) # package has no guaranteed timesfm.__version__
assert hasattr(timesfm, "TimesFM_2p5_200M_torch")The checkpoint-load examples are illustrative: validation of this refresh used native package code with tiny random models and controlled decode fixtures, without downloading pretrained weights. That verifies mechanics, not accuracy.
import numpy as np
import timesfm
model = timesfm.TimesFM_2p5_200M_torch.from_pretrained(
"google/timesfm-2.5-200m-pytorch",
revision="1d952420fba87f3c6dee4f240de0f1a0fbc790e3",
torch_compile=False, # avoid compilation startup during an initial smoke run
)
model.compile(timesfm.ForecastConfig(
max_context=512, max_horizon=128, per_core_batch_size=1,
normalize_inputs=True, use_continuous_quantile_head=True,
force_flip_invariance=True, infer_is_positive=False,
fix_quantile_crossing=True,
))
histories = [np.sin(np.linspace(0, 20, 200)).astype(np.float32)]
# 2.5 may append dummy series to its input list during batching; pass a fresh list.
point, q = model.forecast(horizon=24, inputs=list(histories))
assert point.shape == (1, 24) and q.shape == (1, 24, 10)
assert np.isfinite(q).all() and np.all(np.diff(q[..., 1:], axis=-1) >= 0)
assert np.allclose(point, q[..., 5])
lower_80, upper_80 = q[..., 1], q[..., 9] # q10-q90: nominal 80% PI
lower_60, upper_60 = q[..., 2], q[..., 8] # q20-q80: nominal 60% PISet `infer_is_positive=
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