Upload folder using huggingface_hub

0161e74 verified 6 months ago

31.2 kB

	Metadata-Version: 2.4
	Name: arc-stack
	Version: 0.1.2
	Summary: Stack is a single-cell foundation model that enables in-context learning at inference time.
	Author-email: Mingze Dong <mingze.dong@arcinstitute.org>, Yusuf Roohani <yusuf.roohani@arcinstitute.org>
	License: Attribution-NonCommercial-ShareAlike 4.0 International

	=======================================================================

	Creative Commons Corporation ("Creative Commons") is not a law firm and
	does not provide legal services or legal advice. Distribution of
	Creative Commons public licenses does not create a lawyer-client or
	other relationship. Creative Commons makes its licenses and related
	information available on an "as-is" basis. Creative Commons gives no
	warranties regarding its licenses, any material licensed under their
	terms and conditions, or any related information. Creative Commons
	disclaims all liability for damages resulting from their use to the
	fullest extent possible.

	Using Creative Commons Public Licenses

	Creative Commons public licenses provide a standard set of terms and
	conditions that creators and other rights holders may use to share
	original works of authorship and other material subject to copyright
	and certain other rights specified in the public license below. The
	following considerations are for informational purposes only, are not
	exhaustive, and do not form part of our licenses.

	Considerations for licensors: Our public licenses are
	intended for use by those authorized to give the public
	permission to use material in ways otherwise restricted by
	copyright and certain other rights. Our licenses are
	irrevocable. Licensors should read and understand the terms
	and conditions of the license they choose before applying it.
	Licensors should also secure all rights necessary before
	applying our licenses so that the public can reuse the
	material as expected. Licensors should clearly mark any
	material not subject to the license. This includes other CC-
	licensed material, or material used under an exception or
	limitation to copyright. More considerations for licensors:
	wiki.creativecommons.org/Considerations_for_licensors

	Considerations for the public: By using one of our public
	licenses, a licensor grants the public permission to use the
	licensed material under specified terms and conditions. If
	the licensor's permission is not necessary for any reason--for
	example, because of any applicable exception or limitation to
	copyright--then that use is not regulated by the license. Our
	licenses grant only permissions under copyright and certain
	other rights that a licensor has authority to grant. Use of
	the licensed material may still be restricted for other
	reasons, including because others have copyright or other
	rights in the material. A licensor may make special requests,
	such as asking that all changes be marked or described.
	Although not required by our licenses, you are encouraged to
	respect those requests where reasonable. More considerations
	for the public:
	wiki.creativecommons.org/Considerations_for_licensees

	=======================================================================

	Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
	Public License

	By exercising the Licensed Rights (defined below), You accept and agree
	to be bound by the terms and conditions of this Creative Commons
	Attribution-NonCommercial-ShareAlike 4.0 International Public License
	("Public License"). To the extent this Public License may be
	interpreted as a contract, You are granted the Licensed Rights in
	consideration of Your acceptance of these terms and conditions, and the
	Licensor grants You such rights in consideration of benefits the
	Licensor receives from making the Licensed Material available under
	these terms and conditions.


	Section 1 -- Definitions.

	a. Adapted Material means material subject to Copyright and Similar
	Rights that is derived from or based upon the Licensed Material
	and in which the Licensed Material is translated, altered,
	arranged, transformed, or otherwise modified in a manner requiring
	permission under the Copyright and Similar Rights held by the
	Licensor. For purposes of this Public License, where the Licensed
	Material is a musical work, performance, or sound recording,
	Adapted Material is always produced where the Licensed Material is
	synched in timed relation with a moving image.

	b. Adapter's License means the license You apply to Your Copyright
	and Similar Rights in Your contributions to Adapted Material in
	accordance with the terms and conditions of this Public License.

	c. BY-NC-SA Compatible License means a license listed at
	creativecommons.org/compatiblelicenses, approved by Creative
	Commons as essentially the equivalent of this Public License.

	d. Copyright and Similar Rights means copyright and/or similar rights
	closely related to copyright including, without limitation,
	performance, broadcast, sound recording, and Sui Generis Database
	Rights, without regard to how the rights are labeled or
	categorized. For purposes of this Public License, the rights
	specified in Section 2(b)(1)-(2) are not Copyright and Similar
	Rights.

	e. Effective Technological Measures means those measures that, in the
	absence of proper authority, may not be circumvented under laws
	fulfilling obligations under Article 11 of the WIPO Copyright
	Treaty adopted on December 20, 1996, and/or similar international
	agreements.

	f. Exceptions and Limitations means fair use, fair dealing, and/or
	any other exception or limitation to Copyright and Similar Rights
	that applies to Your use of the Licensed Material.

	g. License Elements means the license attributes listed in the name
	of a Creative Commons Public License. The License Elements of this
	Public License are Attribution, NonCommercial, and ShareAlike.

	h. Licensed Material means the artistic or literary work, database,
	or other material to which the Licensor applied this Public
	License.

	i. Licensed Rights means the rights granted to You subject to the
	terms and conditions of this Public License, which are limited to
	all Copyright and Similar Rights that apply to Your use of the
	Licensed Material and that the Licensor has authority to license.

	j. Licensor means the individual(s) or entity(ies) granting rights
	under this Public License.

	k. NonCommercial means not primarily intended for or directed towards
	commercial advantage or monetary compensation. For purposes of
	this Public License, the exchange of the Licensed Material for
	other material subject to Copyright and Similar Rights by digital
	file-sharing or similar means is NonCommercial provided there is
	no payment of monetary compensation in connection with the
	exchange.

	l. Share means to provide material to the public by any means or
	process that requires permission under the Licensed Rights, such
	as reproduction, public display, public performance, distribution,
	dissemination, communication, or importation, and to make material
	available to the public including in ways that members of the
	public may access the material from a place and at a time
	individually chosen by them.

	m. Sui Generis Database Rights means rights other than copyright
	resulting from Directive 96/9/EC of the European Parliament and of
	the Council of 11 March 1996 on the legal protection of databases,
	as amended and/or succeeded, as well as other essentially
	equivalent rights anywhere in the world.

	n. You means the individual or entity exercising the Licensed Rights
	under this Public License. Your has a corresponding meaning.


	Section 2 -- Scope.

	a. License grant.

	1. Subject to the terms and conditions of this Public License,
	the Licensor hereby grants You a worldwide, royalty-free,
	non-sublicensable, non-exclusive, irrevocable license to
	exercise the Licensed Rights in the Licensed Material to:

	a. reproduce and Share the Licensed Material, in whole or
	in part, for NonCommercial purposes only; and

	b. produce, reproduce, and Share Adapted Material for
	NonCommercial purposes only.

	2. Exceptions and Limitations. For the avoidance of doubt, where
	Exceptions and Limitations apply to Your use, this Public
	License does not apply, and You do not need to comply with
	its terms and conditions.

	3. Term. The term of this Public License is specified in Section
	6(a).

	4. Media and formats; technical modifications allowed. The
	Licensor authorizes You to exercise the Licensed Rights in
	all media and formats whether now known or hereafter created,
	and to make technical modifications necessary to do so. The
	Licensor waives and/or agrees not to assert any right or
	authority to forbid You from making technical modifications
	necessary to exercise the Licensed Rights, including
	technical modifications necessary to circumvent Effective
	Technological Measures. For purposes of this Public License,
	simply making modifications authorized by this Section 2(a)
	(4) never produces Adapted Material.

	5. Downstream recipients.

	a. Offer from the Licensor -- Licensed Material. Every
	recipient of the Licensed Material automatically
	receives an offer from the Licensor to exercise the
	Licensed Rights under the terms and conditions of this
	Public License.

	b. Additional offer from the Licensor -- Adapted Material.
	Every recipient of Adapted Material from You
	automatically receives an offer from the Licensor to
	exercise the Licensed Rights in the Adapted Material
	under the conditions of the Adapter's License You apply.

	c. No downstream restrictions. You may not offer or impose
	any additional or different terms or conditions on, or
	apply any Effective Technological Measures to, the
	Licensed Material if doing so restricts exercise of the
	Licensed Rights by any recipient of the Licensed
	Material.

	6. No endorsement. Nothing in this Public License constitutes or
	may be construed as permission to assert or imply that You
	are, or that Your use of the Licensed Material is, connected
	with, or sponsored, endorsed, or granted official status by,
	the Licensor or others designated to receive attribution as
	provided in Section 3(a)(1)(A)(i).

	b. Other rights.

	1. Moral rights, such as the right of integrity, are not
	licensed under this Public License, nor are publicity,
	privacy, and/or other similar personality rights; however, to
	the extent possible, the Licensor waives and/or agrees not to
	assert any such rights held by the Licensor to the limited
	extent necessary to allow You to exercise the Licensed
	Rights, but not otherwise.

	2. Patent and trademark rights are not licensed under this
	Public License.

	3. To the extent possible, the Licensor waives any right to
	collect royalties from You for the exercise of the Licensed
	Rights, whether directly or through a collecting society
	under any voluntary or waivable statutory or compulsory
	licensing scheme. In all other cases the Licensor expressly
	reserves any right to collect such royalties, including when
	the Licensed Material is used other than for NonCommercial
	purposes.


	Section 3 -- License Conditions.

	Your exercise of the Licensed Rights is expressly made subject to the
	following conditions.

	a. Attribution.

	1. If You Share the Licensed Material (including in modified
	form), You must:

	a. retain the following if it is supplied by the Licensor
	with the Licensed Material:

	i. identification of the creator(s) of the Licensed
	Material and any others designated to receive
	attribution, in any reasonable manner requested by
	the Licensor (including by pseudonym if
	designated);

	ii. a copyright notice;

	iii. a notice that refers to this Public License;

	iv. a notice that refers to the disclaimer of
	warranties;

	v. a URI or hyperlink to the Licensed Material to the
	extent reasonably practicable;

	b. indicate if You modified the Licensed Material and
	retain an indication of any previous modifications; and

	c. indicate the Licensed Material is licensed under this
	Public License, and include the text of, or the URI or
	hyperlink to, this Public License.

	2. You may satisfy the conditions in Section 3(a)(1) in any
	reasonable manner based on the medium, means, and context in
	which You Share the Licensed Material. For example, it may be
	reasonable to satisfy the conditions by providing a URI or
	hyperlink to a resource that includes the required
	information.
	3. If requested by the Licensor, You must remove any of the
	information required by Section 3(a)(1)(A) to the extent
	reasonably practicable.

	b. ShareAlike.

	In addition to the conditions in Section 3(a), if You Share
	Adapted Material You produce, the following conditions also apply.

	1. The Adapter's License You apply must be a Creative Commons
	license with the same License Elements, this version or
	later, or a BY-NC-SA Compatible License.

	2. You must include the text of, or the URI or hyperlink to, the
	Adapter's License You apply. You may satisfy this condition
	in any reasonable manner based on the medium, means, and
	context in which You Share Adapted Material.

	3. You may not offer or impose any additional or different terms
	or conditions on, or apply any Effective Technological
	Measures to, Adapted Material that restrict exercise of the
	rights granted under the Adapter's License You apply.


	Section 4 -- Sui Generis Database Rights.

	Where the Licensed Rights include Sui Generis Database Rights that
	apply to Your use of the Licensed Material:

	a. for the avoidance of doubt, Section 2(a)(1) grants You the right
	to extract, reuse, reproduce, and Share all or a substantial
	portion of the contents of the database for NonCommercial purposes
	only;

	b. if You include all or a substantial portion of the database
	contents in a database in which You have Sui Generis Database
	Rights, then the database in which You have Sui Generis Database
	Rights (but not its individual contents) is Adapted Material,
	including for purposes of Section 3(b); and

	c. You must comply with the conditions in Section 3(a) if You Share
	all or a substantial portion of the contents of the database.

	For the avoidance of doubt, this Section 4 supplements and does not
	replace Your obligations under this Public License where the Licensed
	Rights include other Copyright and Similar Rights.


	Section 5 -- Disclaimer of Warranties and Limitation of Liability.

	a. UNLESS OTHERWISE SEPARATELY UNDERTAKEN BY THE LICENSOR, TO THE
	EXTENT POSSIBLE, THE LICENSOR OFFERS THE LICENSED MATERIAL AS-IS
	AND AS-AVAILABLE, AND MAKES NO REPRESENTATIONS OR WARRANTIES OF
	ANY KIND CONCERNING THE LICENSED MATERIAL, WHETHER EXPRESS,
	IMPLIED, STATUTORY, OR OTHER. THIS INCLUDES, WITHOUT LIMITATION,
	WARRANTIES OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR
	PURPOSE, NON-INFRINGEMENT, ABSENCE OF LATENT OR OTHER DEFECTS,
	ACCURACY, OR THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT
	KNOWN OR DISCOVERABLE. WHERE DISCLAIMERS OF WARRANTIES ARE NOT
	ALLOWED IN FULL OR IN PART, THIS DISCLAIMER MAY NOT APPLY TO YOU.

	b. TO THE EXTENT POSSIBLE, IN NO EVENT WILL THE LICENSOR BE LIABLE
	TO YOU ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION,
	NEGLIGENCE) OR OTHERWISE FOR ANY DIRECT, SPECIAL, INDIRECT,
	INCIDENTAL, CONSEQUENTIAL, PUNITIVE, EXEMPLARY, OR OTHER LOSSES,
	COSTS, EXPENSES, OR DAMAGES ARISING OUT OF THIS PUBLIC LICENSE OR
	USE OF THE LICENSED MATERIAL, EVEN IF THE LICENSOR HAS BEEN
	ADVISED OF THE POSSIBILITY OF SUCH LOSSES, COSTS, EXPENSES, OR
	DAMAGES. WHERE A LIMITATION OF LIABILITY IS NOT ALLOWED IN FULL OR
	IN PART, THIS LIMITATION MAY NOT APPLY TO YOU.

	c. The disclaimer of warranties and limitation of liability provided
	above shall be interpreted in a manner that, to the extent
	possible, most closely approximates an absolute disclaimer and
	waiver of all liability.


	Section 6 -- Term and Termination.

	a. This Public License applies for the term of the Copyright and
	Similar Rights licensed here. However, if You fail to comply with
	this Public License, then Your rights under this Public License
	terminate automatically.

	b. Where Your right to use the Licensed Material has terminated under
	Section 6(a), it reinstates:

	1. automatically as of the date the violation is cured, provided
	it is cured within 30 days of Your discovery of the
	violation; or

	2. upon express reinstatement by the Licensor.

	For the avoidance of doubt, this Section 6(b) does not affect any
	right the Licensor may have to seek remedies for Your violations
	of this Public License.

	c. For the avoidance of doubt, the Licensor may also offer the
	Licensed Material under separate terms or conditions or stop
	distributing the Licensed Material at any time; however, doing so
	will not terminate this Public License.

	d. Sections 1, 5, 6, 7, and 8 survive termination of this Public
	License.


	Section 7 -- Other Terms and Conditions.

	a. The Licensor shall not be bound by any additional or different
	terms or conditions communicated by You unless expressly agreed.

	b. Any arrangements, understandings, or agreements regarding the
	Licensed Material not stated herein are separate from and
	independent of the terms and conditions of this Public License.


	Section 8 -- Interpretation.

	a. For the avoidance of doubt, this Public License does not, and
	shall not be interpreted to, reduce, limit, restrict, or impose
	conditions on any use of the Licensed Material that could lawfully
	be made without permission under this Public License.

	b. To the extent possible, if any provision of this Public License is
	deemed unenforceable, it shall be automatically reformed to the
	minimum extent necessary to make it enforceable. If the provision
	cannot be reformed, it shall be severed from this Public License
	without affecting the enforceability of the remaining terms and
	conditions.

	c. No term or condition of this Public License will be waived and no
	failure to comply consented to unless expressly agreed to by the
	Licensor.

	d. Nothing in this Public License constitutes or may be interpreted
	as a limitation upon, or waiver of, any privileges and immunities
	that apply to the Licensor or You, including from the legal
	processes of any jurisdiction or authority.

	=======================================================================

	Creative Commons is not a party to its public
	licenses. Notwithstanding, Creative Commons may elect to apply one of
	its public licenses to material it publishes and in those instances
	will be considered the “Licensor.” The text of the Creative Commons
	public licenses is dedicated to the public domain under the CC0 Public
	Domain Dedication. Except for the limited purpose of indicating that
	material is shared under a Creative Commons public license or as
	otherwise permitted by the Creative Commons policies published at
	creativecommons.org/policies, Creative Commons does not authorize the
	use of the trademark "Creative Commons" or any other trademark or logo
	of Creative Commons without its prior written consent including,
	without limitation, in connection with any unauthorized modifications
	to any of its public licenses or any other arrangements,
	understandings, or agreements concerning use of licensed material. For
	the avoidance of doubt, this paragraph does not form part of the
	public licenses.

	Creative Commons may be contacted at creativecommons.org.

	Project-URL: Homepage, https://github.com/ArcInstitute/stack
	Project-URL: Source, https://github.com/ArcInstitute/stack
	Requires-Python: >=3.9
	Description-Content-Type: text/markdown
	License-File: LICENSE
	Requires-Dist: anndata>=0.9
	Requires-Dist: h5py>=3.8
	Requires-Dist: geomloss>=0.2.6
	Requires-Dist: numpy>=1.22
	Requires-Dist: pandas>=1.5
	Requires-Dist: psutil>=5.9
	Requires-Dist: pytorch-lightning>=2.1
	Requires-Dist: PyYAML>=6.0
	Requires-Dist: scipy>=1.8
	Requires-Dist: scvi-tools>=1.0
	Requires-Dist: torch>=2.0
	Requires-Dist: wandb>=0.15
	Dynamic: license-file


	# Stack: In-context learning of single-cell biology

	Stack is a large-scale encoder-decoder foundation model trained on 150 million uniformly-preprocessed single cells. It introduces a novel tabular attention architecture that enables both intra- and inter-cellular information flow, setting cell-by-gene matrix chunks as the basic input data unit. Through in-context learning, Stack offers substantial performance improvements in generalizing biological effects and enables generation of unseen cell profiles in novel contexts.

	## Installation

	### Using pip
	```bash
	# Install from PyPI
	pip install arc-stack

	# Or install from source for development
	git clone https://github.com/ArcInstitute/stack.git
	cd stack
	pip install -e .
	```

	### Using uv
	```bash
	# Install from PyPI
	uv pip install arc-stack

	# Or install from source for development
	git clone https://github.com/ArcInstitute/stack.git
	cd stack
	uv pip install -e .
	```


	## Quick Start

	- Use Stack to embed your single-cell data: [Notebook](notebooks/tutorial-embed.ipynb)
	- Use Stack to zero-shot predict unseen perturbation/observation profiles: [Notebook](notebooks/tutorial-predict.ipynb)

	### Training Stack from Scratch

	```bash
	# Once installed, the console entry point becomes available
	stack-train \
	--dataset_configs "/path/to/data:false:gene_symbols" \
	--genelist_path "hvg_genes.pkl" \
	--save_dir "./checkpoints" \
	--sample_size 256 \
	--batch_size 32 \
	--n_hidden 100 \
	--token_dim 16 \
	--n_layers 9 \
	--max_epochs 10

	# Alternatively, invoke the module directly when working from a cloned repo
	python -m stack.cli.launch_training [args...]
	```

	### Fine-tuning Stack with Frozen Teacher

	```bash
	stack-finetune \
	--checkpoint_path "./checkpoints/pretrained.ckpt" \
	--dataset_configs "human:/path/to/data:donor_id:cell_type:false" \
	--genelist_path "hvg_genes.pkl" \
	--save_dir "./finetuned_checkpoints" \
	--sample_size 512 \
	--batch_size 8 \
	--replacement_ratio 0.75 \
	--max_epochs 8

	# Or use uv run
	uv run stack-finetune [args...]

	# Repository wrapper remains available for local development
	python -m stack.cli.launch_finetuning [args...]
	```

	### Running Stack with configuration files

	Both `launch_training.py` and `launch_finetuning.py` accept a `--config` flag that points to a YAML or JSON file. Any command line
	arguments omitted after `--config` inherit their values from the file, while flags provided on the command line override the
	configuration. Example configs mirroring the provided Slurm scripts live under `configs/`:

	```bash
	# Train with the preset configuration
	stack-train --config configs/training/bc_large.yaml

	# Override a single hyperparameter without editing the file
	stack-train --config configs/training/bc_large.yaml --learning_rate 5e-5

	# Fine-tune using a config file
	stack-finetune --config configs/finetuning/ft_parsecg.yaml

	# Direct module invocation is still supported if you prefer python -m
	python -m stack.cli.launch_training --config configs/training/bc_large.yaml
	```

	> Note: YAML configs require [`pyyaml`](https://pyyaml.org/). Install it with `pip install pyyaml` or use a JSON config file.

	### Extracting Stack Embeddings

	```bash
	stack-embedding \
	--checkpoint "./checkpoints/pretrained.ckpt" \
	--adata "data.h5ad" \
	--genelist "hvg_genes.pkl" \
	--output "embeddings.h5ad" \
	--batch-size 32

	# Or use uv run
	uv run stack-embedding \
	--checkpoint "./checkpoints/pretrained.ckpt" \
	--adata "data.h5ad" \
	--genelist "hvg_genes.pkl" \
	--output "embeddings.h5ad" \
	--batch-size 32
	```

	### In-Context Generation with Stack

	```bash
	stack-generation \
	--checkpoint "./checkpoints/pretrained.ckpt" \
	--base-adata "base_data.h5ad" \
	--test-adata "test_data.h5ad" \
	--genelist "hvg_genes.pkl" \
	--output-dir "./generations" \
	--split-column "donor_id"

	# Or use uv run
	uv run stack-generation \
	--checkpoint "./checkpoints/pretrained.ckpt" \
	--base-adata "base_data.h5ad" \
	--test-adata "test_data.h5ad" \
	--genelist "hvg_genes.pkl" \
	--output-dir "./generations" \
	--split-column "donor_id"
	```

	## Model Architecture

	- Tabular Attention: Alternating cell-wise and gene-wise attention layers
	- Token Dimension: Configurable token embedding dimension (default: 16)
	- Hidden Dimension: Gene dimension reduction (default: 100)
	- Masking Strategy: Rectangular masking with variable rates (0.1-0.8)

	## Data Preparation

	### Computing Highly Variable Genes (HVGs)
	```python
	from stack.data.datasets import DatasetConfig, compute_hvg_union

	configs = [DatasetConfig(path="/data/path", filter_organism=True)]
	hvg_genes = compute_hvg_union(configs, n_top_genes=1000, output_path="hvg.pkl")
	```

	### Dataset Configuration Format
	- Human datasets: `human:/path:donor_col:cell_type_col[:filter_organism[:gene_col]]`
	- Drug datasets: `drug:/path:condition_col:cell_line_col:control_condition[:filter_organism[:gene_col]]`

	## Key Features

	- In-Context Learning: Zero-shot generalization to new biological contexts
	- Multi-Dataset Training: Simultaneous training on multiple single-cell datasets
	- Frozen Teacher Fine-tuning: Novel fine-tuning procedure with stable teacher targets
	- Efficient Data Loading: Optimized HDF5 loading with sparse matrix support

	> Note: `scShiftAttentionModel` remains available as an alias for backward compatibility.

	## Citation

	If you use Stack in your research, please cite the Stack [paper](https://www.biorxiv.org/content/10.64898/2026.01.09.698608v1).

	## Licenses
	Stack code is [licensed](LICENSE) under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 (CC BY-NC-SA 4.0).

	The model weights and output are licensed under the [Arc Research Institute Stack Model Non-Commercial License](MODEL_LICENSE.md) and subject to the [Arc Research Institute Stack Model Acceptable Use Policy](MODEL_ACCEPTABLE_USE_POLICY.md).