Alphagenome Finetuning
genomicsxai/alphagenome-pytorch
Fine-tune or transfer-learn AlphaGenome-PyTorch on custom genomic data — pick a mode (linear probe, LoRA, Locon, full), train on BigWig tracks with agt finetune, use adapters, delta checkpoints…
Walks through nanoGPT, Karpathy's compact GPT implementation: training on Shakespeare, reproducing GPT-2, fine-tuning GPT-2 checkpoints and training on your own text.
$ npx skills add Orchestra-Research/AI-Research-SKILLs --skill nanogpt -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install Orchestra-Research/AI-Research-SKILLs nanogpt --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/Orchestra-Research/AI-Research-SKILLs.git skills-src && mkdir -p .claude/skills && cp -r skills-src/01-model-architecture/nanogpt .claude/skills/nanogpt && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "nanogpt" agent skill from https://github.com/Orchestra-Research/AI-Research-SKILLs/tree/main/01-model-architecture/nanogpt into .claude/skills/nanogpt/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "nanogpt", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/Orchestra-Research/AI-Research-SKILLs/tree/main/01-model-architecture/nanogptType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add Orchestra-Research/AI-Research-SKILLs --skill nanogpt -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install Orchestra-Research/AI-Research-SKILLs nanogpt --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Orchestra-Research/AI-Research-SKILLs.git skills-src && mkdir -p .agents/skills && cp -r skills-src/01-model-architecture/nanogpt .agents/skills/nanogpt && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "nanogpt" agent skill from https://github.com/Orchestra-Research/AI-Research-SKILLs/tree/main/01-model-architecture/nanogpt into .agents/skills/nanogpt/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "nanogpt", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add Orchestra-Research/AI-Research-SKILLs --skill nanogpt -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install Orchestra-Research/AI-Research-SKILLs nanogpt --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Orchestra-Research/AI-Research-SKILLs.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/01-model-architecture/nanogpt .cursor/skills/nanogpt && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "nanogpt" agent skill from https://github.com/Orchestra-Research/AI-Research-SKILLs/tree/main/01-model-architecture/nanogpt into .cursor/skills/nanogpt/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "nanogpt", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/Orchestra-Research/AI-Research-SKILLs.git --path 01-model-architecture/nanogpt--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add Orchestra-Research/AI-Research-SKILLs --skill nanogpt -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install Orchestra-Research/AI-Research-SKILLs nanogpt --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Orchestra-Research/AI-Research-SKILLs.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/01-model-architecture/nanogpt .gemini/skills/nanogpt && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "nanogpt" agent skill from https://github.com/Orchestra-Research/AI-Research-SKILLs/tree/main/01-model-architecture/nanogpt into .gemini/skills/nanogpt/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "nanogpt", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install Orchestra-Research/AI-Research-SKILLs nanogptInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add Orchestra-Research/AI-Research-SKILLs --skill nanogpt -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/Orchestra-Research/AI-Research-SKILLs.git skills-src && mkdir -p .github/skills && cp -r skills-src/01-model-architecture/nanogpt .github/skills/nanogpt && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "nanogpt" agent skill from https://github.com/Orchestra-Research/AI-Research-SKILLs/tree/main/01-model-architecture/nanogpt into .github/skills/nanogpt/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "nanogpt", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add Orchestra-Research/AI-Research-SKILLs --skill nanogpt -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install Orchestra-Research/AI-Research-SKILLs nanogpt --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/Orchestra-Research/AI-Research-SKILLs.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/01-model-architecture/nanogpt .opencode/skills/nanogpt && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "nanogpt" agent skill from https://github.com/Orchestra-Research/AI-Research-SKILLs/tree/main/01-model-architecture/nanogpt into .opencode/skills/nanogpt/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "nanogpt", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
nanogptWalks through nanoGPT, Karpathy's compact GPT implementation: training on Shakespeare, reproducing GPT-2, fine-tuning GPT-2 checkpoints and training on your own text.
nanoGPT is presented as a roughly 300-line model file plus a roughly 300-line training loop in plain PyTorch, meant for learning how GPT works and for experimenting with transformer variants. The quick start trains a character-level model on Shakespeare, which is light enough for a CPU, and the skill gives rough training times: about five minutes on CPU or about one minute on a GPU.
Other workflows reproduce GPT-2 at 124M parameters on OpenWebText with multi-GPU training, fine-tune a pretrained GPT-2 checkpoint by setting the init_from option, and train on a custom dataset through your own prepare script followed by train.py with a dataset flag. Data preparation for OpenWebText is said to take about an hour and the full run about four days on eight A100s. The skill points to Hugging Face Transformers, Megatron-LM and LitGPT as alternatives for production or large-scale work.
Read from SKILL.md and the folder at commit 773a529. It shows what the files ask for, not the result of running them.
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Shell commands in SKILL.md call:
pythonpipFrom the folder's file list and the shell code blocks in SKILL.md.
Links to these hosts (documentation or services it may open):
github.comhuggingface.coFrom URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
nanoGPT Training Guide loads about 1.7k tokens when it runs, and up to ~11k if it reads all its reference files. Until then it costs about 68 tokens; SKILL.md has 316 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
The full file from Orchestra-Research/AI-Research-SKILLs at commit 773a529, republished under its MIT licence (© Orchestra-Research). 316 words, ~1,686 tokens.
.claude/skills/nanogpt/SKILL.md (or your agent's skills folder). This skill also uses 3 other files; get the full folder from GitHub.nanoGPT is a simplified GPT implementation designed for learning and experimentation.
Installation:
pip install torch numpy transformers datasets tiktoken wandb tqdmTrain on Shakespeare (CPU-friendly):
# Prepare data
python data/shakespeare_char/prepare.py
# Train (5 minutes on CPU)
python train.py config/train_shakespeare_char.py
# Generate text
python sample.py --out_dir=out-shakespeare-charOutput:
ROMEO:
What say'st thou? Shall I speak, and be a man?
JULIET:
I am afeard, and yet I'll speak; for thou art
One that hath been a man, and yet I know not
What thou art.Complete training pipeline:
# Step 1: Prepare data (creates train.bin, val.bin)
python data/shakespeare_char/prepare.py
# Step 2: Train small model
python train.py config/train_shakespeare_char.py
# Step 3: Generate text
python sample.py --out_dir=out-shakespeare-charConfig (config/train_shakespeare_char.py):
# Model config
n_layer = 6 # 6 transformer layers
n_head = 6 # 6 attention heads
n_embd = 384 # 384-dim embeddings
block_size = 256 # 256 char context
# Training config
batch_size = 64
learning_rate = 1e-3
max_iters = 5000
eval_interval = 500
# Hardware
device = 'cpu' # Or 'cuda'
compile = False # Set True for PyTorch 2.0Training time: ~5 minutes (CPU), ~1 minute (GPU)
Multi-GPU training on OpenWebText:
# Step 1: Prepare OpenWebText (takes ~1 hour)
python data/openwebtext/prepare.py
# Step 2: Train GPT-2 124M with DDP (8 GPUs)
torchrun --standalone --nproc_per_node=8 \
train.py config/train_gpt2.py
# Step 3: Sample from trained model
python sample.py --out_dir=outConfig (config/train_gpt2.py):
# GPT-2 (124M) architecture
n_layer = 12
n_head = 12
n_embd = 768
block_size = 1024
dropout = 0.0
# Training
batch_size = 12
gradient_accumulation_steps = 5 * 8 # Total batch ~0.5M tokens
learning_rate = 6e-4
max_iters = 600000
lr_decay_iters = 600000
# System
compile = True # PyTorch 2.0Training time: ~4 days (8× A100)
Start from OpenAI checkpoint:
# In train.py or config
init_from = 'gpt2' # Options: gpt2, gpt2-medium, gpt2-large, gpt2-xl
# Model loads OpenAI weights automatically
python train.py config/finetune_shakespeare.pyExample config (config/finetune_shakespeare.py):
# Start from GPT-2
init_from = 'gpt2'
# Dataset
dataset = 'shakespeare_char'
batch_size = 1
block_size = 1024
# Fine-tuning
learning_rate = 3e-5 # Lower LR for fine-tuning
max_iters = 2000
warmup_iters = 100
# Regularization
weight_decay = 1e-1Train on your own text:
# data/custom/prepare.py
import numpy as np
# Load your data
with open('my_data.txt', 'r') as f:
text = f.read()
# Create character mappings
chars = sorted(list(set(text)))
stoi = {ch: i for i, ch in enumerate(chars)}
itos = {i: ch for i, ch in enumerate(chars)}
# Tokenize
data = np.array([stoi[ch] for ch in text], dtype=np.uint16)
# Split train/val
n = len(data)
train_data = data[:int(n*0.9)]
val_data = data[int(n*0.9):]
# Save
train_data.tofile('data/custom/train.bin')
val_data.tofile('data/custom/val.bin')Train:
python data/custom/prepare.py
python train.py --dataset=customUse nanoGPT when:
Simplicity advantages:
model.pytrain.pyUse alternatives instead:
Issue: CUDA out of memory
Reduce batch size or context length:
batch_size = 1 # Reduce from 12
block_size = 512 # Reduce from 1024
gradient_accumulation_steps = 40 # Increase to maintain effective batchIssue: Training too slow
Enable compilation (PyTorch 2.0+):
compile = True # 2× speedupUse mixed precision:
dtype = 'bfloat16' # Or 'float16'Issue: Poor generation quality
Train longer:
max_iters = 10000 # Increase from 5000Lower temperature:
# In sample.py
temperature = 0.7 # Lower from 1.0
top_k = 200 # Add top-k samplingIssue: Can't load GPT-2 weights
Install transformers:
pip install transformersCheck model name:
init_from = 'gpt2' # Valid: gpt2, gpt2-medium, gpt2-large, gpt2-xlModel architecture: See references/architecture.md for GPT block structure, multi-head attention, and MLP layers explained simply.
Training loop: See references/training.md for learning rate schedule, gradient accumulation, and distributed data parallel setup.
Data preparation: See references/data.md for tokenization strategies (character-level vs BPE) and binary format details.
Shakespeare (char-level):
GPT-2 (124M):
GPT-2 Medium (350M):
Performance:
compile=True: 2× speedupdtype=bfloat16: 50% memory reduction© Orchestra-Research, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
SKILL.md and 3 other files (references) in 01-model-architecture/nanogpt of Orchestra-Research/AI-Research-SKILLs.
Open the folder on GitHubat commit 773a529
We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in Orchestra-Research/AI-Research-SKILLs, which our catalogue first saw on October 7, 2026.
nanoGPT Training Guide next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| nanoGPT Training Guide this skillOrchestra-Research/AI-Research-SKILLs | 13k | 2 repos | ~1.7k | Automated safety check: Pass | MIT | |
| Alphagenome Finetuninggenomicsxai/alphagenome-pytorch | 162 | — | ~1k | Automated safety check: Pass | Apache-2.0 | |
| Deep Learningericrisco/rsc-harness | 180 | — | ~3.4k | Automated safety check: Pass | MIT | |
| Quaxnstarman/quax | 143 | — | ~5.5k | Automated safety check: Pass | Apache-2.0 | |
| ML Experiment IterationLeeroo-AI/superml | 195 | — | ~4.8k | Automated safety check: Pass | Apache-2.0 | |
| Alphagenome Predictionsgenomicsxai/alphagenome-pytorch | 162 | — | ~868 | Automated safety check: Pass | Apache-2.0 |
genomicsxai/alphagenome-pytorch
Fine-tune or transfer-learn AlphaGenome-PyTorch on custom genomic data — pick a mode (linear probe, LoRA, Locon, full), train on BigWig tracks with agt finetune, use adapters, delta checkpoints…
ericrisco/rsc-harness
A skill your agent uses when training or debugging a neural net in PyTorch — the forward/loss/backward/step loop and its silent bugs, mixed precision (AMP), AdamW/LR schedules, DDP/FSDP/ZeRO…
nstarman/quax
A skill your agent uses when writing, reviewing, or debugging JAX code that involves quax — custom array-ish objects (physical units, LoRA, sparse, symbolic zero, named axes), quax.quaxify…
Leeroo-AI/superml
Produces ranked, evidence-grounded next steps when an ML experiment has stalled, drawing on a Leeroopedia knowledge base or on fetched docs and issues.
genomicsxai/alphagenome-pytorch
Run AlphaGenome-PyTorch to get genomic track predictions — via the agt predict CLI (single locus, BED regions, whole chromosomes, raw FASTA sequences, or per-gene count tables/AnnData), variant…
pytorch/executorch
Export a PyTorch model to .pte format for ExecuTorch. Use when converting models, lowering to edge, or generating .pte files.
Orchestra-Research/AI-Research-SKILLs
Generates music from text descriptions with MusicGen and sound effects with AudioGen, using Meta's AudioCraft PyTorch library with melody and style conditioning.
Orchestra-Research/AI-Research-SKILLs
Runs lm-evaluation-harness to benchmark language models on academic suites such as MMLU, GSM8K and HumanEval, compare models and track training checkpoints.
Orchestra-Research/AI-Research-SKILLs
Guide to using Meta's Segment Anything Model for zero-shot image segmentation with point, box or mask prompts, or automatic mask generation.
Orchestra-Research/AI-Research-SKILLs
Shows how to store documents and embeddings in Chroma, query them by similarity with metadata filters, and persist them to disk for RAG and semantic search projects.
Orchestra-Research/AI-Research-SKILLs
Explains OpenAI's CLIP model for zero-shot image classification, image-text similarity, semantic image search and content moderation, with install steps and code patterns.
Orchestra-Research/AI-Research-SKILLs
Transcribes audio with OpenAI's Whisper: 99 languages, translation to English, language detection, six model sizes and word-level timestamps, from Python or the CLI.
Works with
Categories
Walks through nanoGPT, Karpathy's compact GPT implementation: training on Shakespeare, reproducing GPT-2, fine-tuning GPT-2 checkpoints and training on your own text. nanoGPT is presented as a roughly 300-line model file plus a roughly 300-line training loop in plain PyTorch, meant for learning how GPT works and for experimenting with transformer variants. The quick start trains a character-level model on Shakespeare, which is light enough for a CPU, and the skill gives rough training times: about five minutes on CPU or about one minute on a GPU.
nanoGPT Training Guide fits situations like: learning how a GPT model and its training loop work; training a small character-level model on a laptop CPU; fine-tuning a pretrained GPT-2 checkpoint on your own text; reproducing the GPT-2 124M run on OpenWebText.
Run `npx skills add Orchestra-Research/AI-Research-SKILLs --skill nanogpt -a claude-code`. Or copy the skill folder (01-model-architecture/nanogpt in Orchestra-Research/AI-Research-SKILLs) into .claude/skills/nanogpt in your project. Claude Code loads it when a task matches its description.
Run `npx skills add Orchestra-Research/AI-Research-SKILLs --skill nanogpt -a codex`. Or copy the skill folder (01-model-architecture/nanogpt in Orchestra-Research/AI-Research-SKILLs) into .agents/skills/nanogpt in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add Orchestra-Research/AI-Research-SKILLs --skill nanogpt -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/nanogpt, .gemini/skills/nanogpt, .github/skills/nanogpt and .opencode/skills/nanogpt in your project.
Going by SKILL.md and its folder, nanoGPT Training Guide needs the command-line tools its instructions call (python and pip). Our summary lists: Python with torch, numpy, transformers, datasets, tiktoken, wandb and tqdm; Multiple GPUs for the OpenWebText run.
SKILL.md names 2 domains. As links in the text: github.com and huggingface.co. This is read from the text; nothing was executed.
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
nanoGPT Training Guide is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
About 1.7k tokens (SKILL.md is roughly 6.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 9.1k tokens, read only when the agent opens those files.
Skills that share tags, products or a category with nanoGPT Training Guide: Alphagenome Finetuning (genomicsxai/alphagenome-pytorch, 162 stars), Deep Learning (ericrisco/rsc-harness, 180 stars), Quax (nstarman/quax, 143 stars) and ML Experiment Iteration (Leeroo-AI/superml, 195 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Orchestra-Research (a GitHub organization) maintains it in Orchestra-Research/AI-Research-SKILLs, which has 13,405 GitHub stars. The repository holds 96 skills in this directory. The repository was last updated on June 16, 2026.
Source: Orchestra-Research/AI-Research-SKILLs on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.