Ml Training Recipes Agent Skill

ML Training Recipes

Battle-tested patterns for PyTorch training across domains. Drawn from production codebases

(Karpathy's autoresearch/nanochat, torchvision, HuggingFace) and modern training practice.

Reference files (read when needed)

• references/architecture.md — Transformer/LLM architecture code patterns, weight init
• references/optimizers.md — Muon, AdamW hybrid, per-group LR, compiled optimizer steps
• references/domain-specific.md — Vision, diffusion, contrastive, distributed, checkpointing, data loading
• references/scaling-and-selection.md — Scaling laws, compute budget tables, decision trees, DGX Spark
• references/biomedical.md — Drug discovery, protein models, medical imaging, genomics, clinical NLP
• references/experiment-loop.md — Autonomous experiment loop (autoresearch keep/discard/revert)

Architecture Selection

Pick the right model by data type and data scale:

| Data Type | < 10K samples | 10K-100K | > 100K |

|-----------|--------------|----------|--------|

| Images | Pretrained CNN + fine-tune | Fine-tune ViT or CNN | ViT from scratch |

| Text (gen) | Few-shot prompting | Fine-tune GPT/LLaMA (LoRA) | Pretrain from scratch |

| Tabular | XGBoost/LightGBM | Still XGBoost | Neural viable |

| Audio | Pretrained Whisper | Fine-tune AST | Train from scratch |

| Molecules | Pretrained GNN | Fine-tune molecular LM | Train GNN from scratch |

| Proteins | ESM-2 embeddings + head | Fine-tune ESM-2 | Train protein LM |

| Medical img | Pretrained CNN | nnU-Net (auto-config) | Swin-UNETR / MedSAM |

Key principle: architecture matters less than training recipe at equal compute. A well-tuned

ResNet beats a poorly-tuned ViT (ref: "ResNet Strikes Back", Wightman 2021).

For biomedical domains, see references/biomedical.md.

For sequence model selection and compute planning, see references/scaling-and-selection.md.

Scaling Laws

Chinchilla rule (Hoffmann et al., 2022)

Compute-optimal training: ~20 tokens per parameter.

| Model Size | Compute-Optimal | Inference-Optimal (100×) |

|-----------|----------------|--------------------------|

| 125M | 2.5B tokens | 12.5B tokens |

| 1B | 20B tokens | 100B tokens |

| 7B | 140B tokens | 700B tokens |

FLOPs ≈ 6 × N × D (N=params, D=tokens). Data repetition limit: ~4 epochs before diminishing returns.

Training Loop

import gc, time, torch

torch.manual_seed(42)
torch.set_float32_matmul_precision("high")  # TF32 on Ampere+
autocast_ctx = torch.amp.autocast(device_type="cuda", dtype=torch.bfloat16)

grad_accum_steps = total_batch_size // (batch_size * seq_len)
step = 0

while not done:
    t0 = time.time()
    for micro_step in range(grad_accum_steps):
        with autocast_ctx:
            loss = model(x, y)
        (loss / grad_accum_steps).backward()
        x, y = next(train_loader)

    update_lr(optimizer, progress)
    optimizer.step()
    model.zero_grad(set_to_none=True)  # frees memory vs zeroing

    if loss.item() > 100:  # fast-fail on divergence
        print("FAIL: loss exploded"); exit(1)

    torch.cuda.synchronize()
    if step == 0:
        gc.collect(); gc.freeze(); gc.disable()  # avoid ~500ms GC stalls
    step += 1

Key principles

• Gradient clipping: clip_grad_norm_(params, 1.0) — near-universal for Transformers.

Exception: Muon optimizer normalizes updates via orthogonalization, so clipping is optional.

• Tensor Core alignment: batch size, hidden dims should be multiples of 8 (bf16) or 64 (A100).
• Time-based budgets make experiments comparable across hardware.
• cudnn.benchmark = True for fixed-size vision inputs.

Optimizer Configuration

Modern LLM training uses different optimizers per parameter group:

| Parameter Type | Optimizer | LR (base) | Weight Decay |

|---------------|-----------|-----------|--------------|

| 2D weight matrices | Muon | 0.04 | 0.2 |

| Token embeddings | AdamW | 0.6 × scale | 0.0 |

| Unembedding (lm_head) | AdamW | 0.004 × scale | 0.0 |

| Per-layer scalars | AdamW | 0.005 × scale | 0.0 |

LR scaling by dimension: lr * (d_model / 768)^(-0.5) — keeps dynamics stable across sizes.

Rules of thumb

• Embeddings need higher LR (sparse updates). Never weight-decay embeddings.
• Weight decay scheduling: linearly decay WD to 0 over training.
• AdamW defaults: β1=0.9, β2=0.95, eps=1e-10 (not default 1e-8 — prevents stale updates in bf16).

For Muon details (polar express orthogonalization, NorMuon), see references/optimizers.md.

Learning Rate Scheduling

Time-based (autoresearch style)

def get_lr_multiplier(progress):  # progress = elapsed_time / time_budget
    if progress < warmup_ratio:
        return progress / warmup_ratio
    elif progress < 1.0 - warmdown_ratio:
        return 1.0
    else:
        cooldown = (1.0 - progress) / warmdown_ratio
        return cooldown + (1 - cooldown) * final_lr_frac

Cosine decay

def get_lr(step, total_steps, max_lr, min_lr, warmup_steps):
    if step < warmup_steps:
        return max_lr * step / warmup_steps
    progress = (step - warmup_steps) / (total_steps - warmup_steps)
    return min_lr + 0.5 * (max_lr - min_lr) * (1 + math.cos(math.pi * progress))

WSD (Warmup-Stable-Decay): gaining traction — easier to resume training mid-run.

Guidance

• Warmup: 1-5% of training. Zero warmup valid with Muon (autoresearch uses WARMUP_RATIO=0.0).
• Warmdown: 30-50% of training in LR decay. Matters more than warmup for final quality.
• Final LR: 0 or ~10% of peak. Zero is simpler.

Mixed Precision & Compilation

import os
os.environ["PYTORCH_ALLOC_CONF"] = "expandable_segments:True"  # before torch import

import torch
torch.set_float32_matmul_precision("high")
autocast_ctx = torch.amp.autocast(device_type="cuda", dtype=torch.bfloat16)
model = torch.compile(model, dynamic=False)

• bf16 (Ampere+): same exponent as fp32, no loss scaling needed. Preferred over fp16.
• fp16: needs GradScaler. Use only on V100 or older.
• dynamic=False enables max optimization. Add fullgraph=True if no graph breaks.
• First steps are slow (JIT) — exclude from timing.

Memory & Performance

Meta device init (large models)

with torch.device("meta"):
    model = GPT(config)          # zero memory
model.to_empty(device="cuda")
model.init_weights()

MFU (Model FLOPs Utilization)

achieved_flops = model_flops_per_token * batch_tokens / step_time
mfu = achieved_flops / gpu_peak_flops
# H100 SXM: 989.5 TFLOPS | A100: 312 | RTX 4090: 165

Good targets: >30% decent, >40% good, >50% excellent (single-GPU).

OOM solutions (in order)

• Reduce DEVICE_BATCH_SIZE, increase grad_accum_steps
• PYTORCH_ALLOC_CONF=expandable_segments:True
• model.zero_grad(set_to_none=True)
• Meta device init → to_empty
• Activation checkpointing: torch.utils.checkpoint.checkpoint()
• 8-bit optimizer (bitsandbytes): ~30% savings on optimizer states

Hyperparameter Search

Priority order (tune first → last)

• Learning rate — most impactful. Always tune first.
• Batch size — largest that fits. Speed knob, not quality knob.
• Weight decay — 0.01-0.1 for AdamW.
• Warmup steps — 1-5% of training.

The 2025 default recipe

| Setting | Value |

|---------|-------|

| Optimizer | AdamW (β1=0.9, β2=0.95, eps=1e-10) |

| Weight decay | 0.1 |

| LR schedule | Cosine decay or WSD |

| Peak LR | 3e-4 (scale down for larger models) |

| Precision | bf16 |

| Grad clipping | max_norm=1.0 |

| Normalization | RMSNorm (pre-norm) |

| Activation | SwiGLU |

| Position encoding | RoPE |

| Attention | Flash Attention, optionally GQA |

Debugging Checklist

Karpathy's recipe (still canonical)

• Become one with the data — visualize, check distributions, verify labels
• Get end-to-end running first — verify on a trivial case
• Overfit one batch — if you can't, you have a bug
• Then regularize — add regularization only after overfitting works
• Tune hyperparameters — start with known defaults

Loss exploding / NaN

• Reduce LR (3-10× smaller)
• Add gradient clipping: clip_grad_norm_(params, 1.0)
• Check for inf/nan in inputs
• Add logit soft capping: softcap * tanh(logits / softcap)
• Add QK-norm in attention
• Verify weight init (zero-init output projections?)
• Check loss reduction with gradient accumulation (loss / grad_accum_steps)

Slow training / Low MFU

• Verify torch.compile is active
• Check torch.set_float32_matmul_precision("high")
• Pin memory + non_blocking transfers
• Profile with torch.profiler
• GC stalls? gc.freeze(); gc.disable()
• Tensor Core alignment: dims multiples of 8/64

Loss plateau / Slow convergence

• LR too low — try 2-5× larger
• Warmup too long
• Weight decay too high
• Verify LR schedule is actually applied (print each step)
• Model too small for task

Silent failures

• Data leakage between train/val
• Wrong preprocessing at inference — augmentation mismatch
• Label errors — use cleanlab to detect
• Shuffling bugs — correlated batches
• Tokenizer mismatch with pretrained model

What to monitor

• Gradient norms — spike precedes loss spike
• Per-layer activation stats — reveals exploding/vanishing
• Dead neurons — >50% zero ReLU = dying ReLU problem
• Learning rate — verify schedule applied (common silent bug)

Experiment Management

Track experiments in TSV for easy comparison:

commit  val_bpb  memory_gb  status   description
a1b2c3d 0.9979   44.0       keep     baseline
b2c3d4e 0.9932   44.2       keep     increase matrix LR to 0.04
c3d4e5f 1.0050   44.0       discard  switch to GeLU (worse)

Simplicity criterion: all else equal, simpler is better. Removing something and getting equal

results is a great outcome. For systematic agent-driven experimentation, see references/experiment-loop.md.

Evaluation metrics by domain

| Domain | Primary Metric | Notes |

|--------|---------------|-------|

| LLM | BPB (bits per byte) | Vocab-size-independent |

| Classification | Accuracy / F1 | Macro-F1 for imbalanced |

| Segmentation | mIoU / Dice | Per-class IoU reveals weak spots |

| Generation | FID | Needs >10k samples |

| Regression | RMSE / MAE | Log-transform skewed targets |