Text Generation
Transformers
Safetensors
PyTorch
English
gemma2
biology
scRNAseq
genomics
computational-biology
bioinformatics
gene-expression
cell-biology
cell-type-annotation
Question Answering
text-generation-inference
Instructions to use edward-google/C2S-Scale-Gemma-2-27B with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use edward-google/C2S-Scale-Gemma-2-27B with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("text-generation", model="edward-google/C2S-Scale-Gemma-2-27B")# Load model directly from transformers import AutoTokenizer, AutoModelForCausalLM tokenizer = AutoTokenizer.from_pretrained("edward-google/C2S-Scale-Gemma-2-27B") model = AutoModelForCausalLM.from_pretrained("edward-google/C2S-Scale-Gemma-2-27B", device_map="auto") - Notebooks
- Google Colab
- Kaggle
- Local Apps Settings
- vLLM
How to use edward-google/C2S-Scale-Gemma-2-27B with vLLM:
Install from pip and serve model
# Install vLLM from pip: pip install vllm # Start the vLLM server: vllm serve "edward-google/C2S-Scale-Gemma-2-27B" # Call the server using curl (OpenAI-compatible API): curl -X POST "http://localhost:8000/v1/completions" \ -H "Content-Type: application/json" \ --data '{ "model": "edward-google/C2S-Scale-Gemma-2-27B", "prompt": "Once upon a time,", "max_tokens": 512, "temperature": 0.5 }'Use Docker
docker model run hf.co/edward-google/C2S-Scale-Gemma-2-27B
- SGLang
How to use edward-google/C2S-Scale-Gemma-2-27B with SGLang:
Install from pip and serve model
# Install SGLang from pip: pip install sglang # Start the SGLang server: python3 -m sglang.launch_server \ --model-path "edward-google/C2S-Scale-Gemma-2-27B" \ --host 0.0.0.0 \ --port 30000 # Call the server using curl (OpenAI-compatible API): curl -X POST "http://localhost:30000/v1/completions" \ -H "Content-Type: application/json" \ --data '{ "model": "edward-google/C2S-Scale-Gemma-2-27B", "prompt": "Once upon a time,", "max_tokens": 512, "temperature": 0.5 }'Use Docker images
docker run --gpus all \ --shm-size 32g \ -p 30000:30000 \ -v ~/.cache/huggingface:/root/.cache/huggingface \ --env "HF_TOKEN=<secret>" \ --ipc=host \ lmsysorg/sglang:latest \ python3 -m sglang.launch_server \ --model-path "edward-google/C2S-Scale-Gemma-2-27B" \ --host 0.0.0.0 \ --port 30000 # Call the server using curl (OpenAI-compatible API): curl -X POST "http://localhost:30000/v1/completions" \ -H "Content-Type: application/json" \ --data '{ "model": "edward-google/C2S-Scale-Gemma-2-27B", "prompt": "Once upon a time,", "max_tokens": 512, "temperature": 0.5 }' - Docker Model Runner
How to use edward-google/C2S-Scale-Gemma-2-27B with Docker Model Runner:
docker model run hf.co/edward-google/C2S-Scale-Gemma-2-27B
Commit ·
eb727b6
0
Parent(s):
Duplicate from vandijklab/C2S-Scale-Gemma-2-27B
Browse filesCo-authored-by: Syed Rizvi <SyedA5688@users.noreply.huggingface.co>
- .gitattributes +35 -0
- LICENSE +396 -0
- README.md +250 -0
- config.json +80 -0
- generation_config.json +7 -0
- model-00001-of-00012.safetensors +3 -0
- model-00002-of-00012.safetensors +3 -0
- model-00003-of-00012.safetensors +3 -0
- model-00004-of-00012.safetensors +3 -0
- model-00005-of-00012.safetensors +3 -0
- model-00006-of-00012.safetensors +3 -0
- model-00007-of-00012.safetensors +3 -0
- model-00008-of-00012.safetensors +3 -0
- model-00009-of-00012.safetensors +3 -0
- model-00010-of-00012.safetensors +3 -0
- model-00011-of-00012.safetensors +3 -0
- model-00012-of-00012.safetensors +3 -0
- model.safetensors.index.json +516 -0
- special_tokens_map.json +30 -0
- tokenizer.model +3 -0
- tokenizer_config.json +49 -0
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| 79 |
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synched in timed relation with a moving image.
|
| 80 |
+
|
| 81 |
+
b. Adapter's License means the license You apply to Your Copyright
|
| 82 |
+
and Similar Rights in Your contributions to Adapted Material in
|
| 83 |
+
accordance with the terms and conditions of this Public License.
|
| 84 |
+
|
| 85 |
+
c. Copyright and Similar Rights means copyright and/or similar rights
|
| 86 |
+
closely related to copyright including, without limitation,
|
| 87 |
+
performance, broadcast, sound recording, and Sui Generis Database
|
| 88 |
+
Rights, without regard to how the rights are labeled or
|
| 89 |
+
categorized. For purposes of this Public License, the rights
|
| 90 |
+
specified in Section 2(b)(1)-(2) are not Copyright and Similar
|
| 91 |
+
Rights.
|
| 92 |
+
|
| 93 |
+
d. Effective Technological Measures means those measures that, in the
|
| 94 |
+
absence of proper authority, may not be circumvented under laws
|
| 95 |
+
fulfilling obligations under Article 11 of the WIPO Copyright
|
| 96 |
+
Treaty adopted on December 20, 1996, and/or similar international
|
| 97 |
+
agreements.
|
| 98 |
+
|
| 99 |
+
e. Exceptions and Limitations means fair use, fair dealing, and/or
|
| 100 |
+
any other exception or limitation to Copyright and Similar Rights
|
| 101 |
+
that applies to Your use of the Licensed Material.
|
| 102 |
+
|
| 103 |
+
f. Licensed Material means the artistic or literary work, database,
|
| 104 |
+
or other material to which the Licensor applied this Public
|
| 105 |
+
License.
|
| 106 |
+
|
| 107 |
+
g. Licensed Rights means the rights granted to You subject to the
|
| 108 |
+
terms and conditions of this Public License, which are limited to
|
| 109 |
+
all Copyright and Similar Rights that apply to Your use of the
|
| 110 |
+
Licensed Material and that the Licensor has authority to license.
|
| 111 |
+
|
| 112 |
+
h. Licensor means the individual(s) or entity(ies) granting rights
|
| 113 |
+
under this Public License.
|
| 114 |
+
|
| 115 |
+
i. Share means to provide material to the public by any means or
|
| 116 |
+
process that requires permission under the Licensed Rights, such
|
| 117 |
+
as reproduction, public display, public performance, distribution,
|
| 118 |
+
dissemination, communication, or importation, and to make material
|
| 119 |
+
available to the public including in ways that members of the
|
| 120 |
+
public may access the material from a place and at a time
|
| 121 |
+
individually chosen by them.
|
| 122 |
+
|
| 123 |
+
j. Sui Generis Database Rights means rights other than copyright
|
| 124 |
+
resulting from Directive 96/9/EC of the European Parliament and of
|
| 125 |
+
the Council of 11 March 1996 on the legal protection of databases,
|
| 126 |
+
as amended and/or succeeded, as well as other essentially
|
| 127 |
+
equivalent rights anywhere in the world.
|
| 128 |
+
|
| 129 |
+
k. You means the individual or entity exercising the Licensed Rights
|
| 130 |
+
under this Public License. Your has a corresponding meaning.
|
| 131 |
+
|
| 132 |
+
|
| 133 |
+
Section 2 -- Scope.
|
| 134 |
+
|
| 135 |
+
a. License grant.
|
| 136 |
+
|
| 137 |
+
1. Subject to the terms and conditions of this Public License,
|
| 138 |
+
the Licensor hereby grants You a worldwide, royalty-free,
|
| 139 |
+
non-sublicensable, non-exclusive, irrevocable license to
|
| 140 |
+
exercise the Licensed Rights in the Licensed Material to:
|
| 141 |
+
|
| 142 |
+
a. reproduce and Share the Licensed Material, in whole or
|
| 143 |
+
in part; and
|
| 144 |
+
|
| 145 |
+
b. produce, reproduce, and Share Adapted Material.
|
| 146 |
+
|
| 147 |
+
2. Exceptions and Limitations. For the avoidance of doubt, where
|
| 148 |
+
Exceptions and Limitations apply to Your use, this Public
|
| 149 |
+
License does not apply, and You do not need to comply with
|
| 150 |
+
its terms and conditions.
|
| 151 |
+
|
| 152 |
+
3. Term. The term of this Public License is specified in Section
|
| 153 |
+
6(a).
|
| 154 |
+
|
| 155 |
+
4. Media and formats; technical modifications allowed. The
|
| 156 |
+
Licensor authorizes You to exercise the Licensed Rights in
|
| 157 |
+
all media and formats whether now known or hereafter created,
|
| 158 |
+
and to make technical modifications necessary to do so. The
|
| 159 |
+
Licensor waives and/or agrees not to assert any right or
|
| 160 |
+
authority to forbid You from making technical modifications
|
| 161 |
+
necessary to exercise the Licensed Rights, including
|
| 162 |
+
technical modifications necessary to circumvent Effective
|
| 163 |
+
Technological Measures. For purposes of this Public License,
|
| 164 |
+
simply making modifications authorized by this Section 2(a)
|
| 165 |
+
(4) never produces Adapted Material.
|
| 166 |
+
|
| 167 |
+
5. Downstream recipients.
|
| 168 |
+
|
| 169 |
+
a. Offer from the Licensor -- Licensed Material. Every
|
| 170 |
+
recipient of the Licensed Material automatically
|
| 171 |
+
receives an offer from the Licensor to exercise the
|
| 172 |
+
Licensed Rights under the terms and conditions of this
|
| 173 |
+
Public License.
|
| 174 |
+
|
| 175 |
+
b. No downstream restrictions. You may not offer or impose
|
| 176 |
+
any additional or different terms or conditions on, or
|
| 177 |
+
apply any Effective Technological Measures to, the
|
| 178 |
+
Licensed Material if doing so restricts exercise of the
|
| 179 |
+
Licensed Rights by any recipient of the Licensed
|
| 180 |
+
Material.
|
| 181 |
+
|
| 182 |
+
6. No endorsement. Nothing in this Public License constitutes or
|
| 183 |
+
may be construed as permission to assert or imply that You
|
| 184 |
+
are, or that Your use of the Licensed Material is, connected
|
| 185 |
+
with, or sponsored, endorsed, or granted official status by,
|
| 186 |
+
the Licensor or others designated to receive attribution as
|
| 187 |
+
provided in Section 3(a)(1)(A)(i).
|
| 188 |
+
|
| 189 |
+
b. Other rights.
|
| 190 |
+
|
| 191 |
+
1. Moral rights, such as the right of integrity, are not
|
| 192 |
+
licensed under this Public License, nor are publicity,
|
| 193 |
+
privacy, and/or other similar personality rights; however, to
|
| 194 |
+
the extent possible, the Licensor waives and/or agrees not to
|
| 195 |
+
assert any such rights held by the Licensor to the limited
|
| 196 |
+
extent necessary to allow You to exercise the Licensed
|
| 197 |
+
Rights, but not otherwise.
|
| 198 |
+
|
| 199 |
+
2. Patent and trademark rights are not licensed under this
|
| 200 |
+
Public License.
|
| 201 |
+
|
| 202 |
+
3. To the extent possible, the Licensor waives any right to
|
| 203 |
+
collect royalties from You for the exercise of the Licensed
|
| 204 |
+
Rights, whether directly or through a collecting society
|
| 205 |
+
under any voluntary or waivable statutory or compulsory
|
| 206 |
+
licensing scheme. In all other cases the Licensor expressly
|
| 207 |
+
reserves any right to collect such royalties.
|
| 208 |
+
|
| 209 |
+
|
| 210 |
+
Section 3 -- License Conditions.
|
| 211 |
+
|
| 212 |
+
Your exercise of the Licensed Rights is expressly made subject to the
|
| 213 |
+
following conditions.
|
| 214 |
+
|
| 215 |
+
a. Attribution.
|
| 216 |
+
|
| 217 |
+
1. If You Share the Licensed Material (including in modified
|
| 218 |
+
form), You must:
|
| 219 |
+
|
| 220 |
+
a. retain the following if it is supplied by the Licensor
|
| 221 |
+
with the Licensed Material:
|
| 222 |
+
|
| 223 |
+
i. identification of the creator(s) of the Licensed
|
| 224 |
+
Material and any others designated to receive
|
| 225 |
+
attribution, in any reasonable manner requested by
|
| 226 |
+
the Licensor (including by pseudonym if
|
| 227 |
+
designated);
|
| 228 |
+
|
| 229 |
+
ii. a copyright notice;
|
| 230 |
+
|
| 231 |
+
iii. a notice that refers to this Public License;
|
| 232 |
+
|
| 233 |
+
iv. a notice that refers to the disclaimer of
|
| 234 |
+
warranties;
|
| 235 |
+
|
| 236 |
+
v. a URI or hyperlink to the Licensed Material to the
|
| 237 |
+
extent reasonably practicable;
|
| 238 |
+
|
| 239 |
+
b. indicate if You modified the Licensed Material and
|
| 240 |
+
retain an indication of any previous modifications; and
|
| 241 |
+
|
| 242 |
+
c. indicate the Licensed Material is licensed under this
|
| 243 |
+
Public License, and include the text of, or the URI or
|
| 244 |
+
hyperlink to, this Public License.
|
| 245 |
+
|
| 246 |
+
2. You may satisfy the conditions in Section 3(a)(1) in any
|
| 247 |
+
reasonable manner based on the medium, means, and context in
|
| 248 |
+
which You Share the Licensed Material. For example, it may be
|
| 249 |
+
reasonable to satisfy the conditions by providing a URI or
|
| 250 |
+
hyperlink to a resource that includes the required
|
| 251 |
+
information.
|
| 252 |
+
|
| 253 |
+
3. If requested by the Licensor, You must remove any of the
|
| 254 |
+
information required by Section 3(a)(1)(A) to the extent
|
| 255 |
+
reasonably practicable.
|
| 256 |
+
|
| 257 |
+
4. If You Share Adapted Material You produce, the Adapter's
|
| 258 |
+
License You apply must not prevent recipients of the Adapted
|
| 259 |
+
Material from complying with this Public License.
|
| 260 |
+
|
| 261 |
+
|
| 262 |
+
Section 4 -- Sui Generis Database Rights.
|
| 263 |
+
|
| 264 |
+
Where the Licensed Rights include Sui Generis Database Rights that
|
| 265 |
+
apply to Your use of the Licensed Material:
|
| 266 |
+
|
| 267 |
+
a. for the avoidance of doubt, Section 2(a)(1) grants You the right
|
| 268 |
+
to extract, reuse, reproduce, and Share all or a substantial
|
| 269 |
+
portion of the contents of the database;
|
| 270 |
+
|
| 271 |
+
b. if You include all or a substantial portion of the database
|
| 272 |
+
contents in a database in which You have Sui Generis Database
|
| 273 |
+
Rights, then the database in which You have Sui Generis Database
|
| 274 |
+
Rights (but not its individual contents) is Adapted Material; and
|
| 275 |
+
|
| 276 |
+
c. You must comply with the conditions in Section 3(a) if You Share
|
| 277 |
+
all or a substantial portion of the contents of the database.
|
| 278 |
+
|
| 279 |
+
For the avoidance of doubt, this Section 4 supplements and does not
|
| 280 |
+
replace Your obligations under this Public License where the Licensed
|
| 281 |
+
Rights include other Copyright and Similar Rights.
|
| 282 |
+
|
| 283 |
+
|
| 284 |
+
Section 5 -- Disclaimer of Warranties and Limitation of Liability.
|
| 285 |
+
|
| 286 |
+
a. UNLESS OTHERWISE SEPARATELY UNDERTAKEN BY THE LICENSOR, TO THE
|
| 287 |
+
EXTENT POSSIBLE, THE LICENSOR OFFERS THE LICENSED MATERIAL AS-IS
|
| 288 |
+
AND AS-AVAILABLE, AND MAKES NO REPRESENTATIONS OR WARRANTIES OF
|
| 289 |
+
ANY KIND CONCERNING THE LICENSED MATERIAL, WHETHER EXPRESS,
|
| 290 |
+
IMPLIED, STATUTORY, OR OTHER. THIS INCLUDES, WITHOUT LIMITATION,
|
| 291 |
+
WARRANTIES OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR
|
| 292 |
+
PURPOSE, NON-INFRINGEMENT, ABSENCE OF LATENT OR OTHER DEFECTS,
|
| 293 |
+
ACCURACY, OR THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT
|
| 294 |
+
KNOWN OR DISCOVERABLE. WHERE DISCLAIMERS OF WARRANTIES ARE NOT
|
| 295 |
+
ALLOWED IN FULL OR IN PART, THIS DISCLAIMER MAY NOT APPLY TO YOU.
|
| 296 |
+
|
| 297 |
+
b. TO THE EXTENT POSSIBLE, IN NO EVENT WILL THE LICENSOR BE LIABLE
|
| 298 |
+
TO YOU ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION,
|
| 299 |
+
NEGLIGENCE) OR OTHERWISE FOR ANY DIRECT, SPECIAL, INDIRECT,
|
| 300 |
+
INCIDENTAL, CONSEQUENTIAL, PUNITIVE, EXEMPLARY, OR OTHER LOSSES,
|
| 301 |
+
COSTS, EXPENSES, OR DAMAGES ARISING OUT OF THIS PUBLIC LICENSE OR
|
| 302 |
+
USE OF THE LICENSED MATERIAL, EVEN IF THE LICENSOR HAS BEEN
|
| 303 |
+
ADVISED OF THE POSSIBILITY OF SUCH LOSSES, COSTS, EXPENSES, OR
|
| 304 |
+
DAMAGES. WHERE A LIMITATION OF LIABILITY IS NOT ALLOWED IN FULL OR
|
| 305 |
+
IN PART, THIS LIMITATION MAY NOT APPLY TO YOU.
|
| 306 |
+
|
| 307 |
+
c. The disclaimer of warranties and limitation of liability provided
|
| 308 |
+
above shall be interpreted in a manner that, to the extent
|
| 309 |
+
possible, most closely approximates an absolute disclaimer and
|
| 310 |
+
waiver of all liability.
|
| 311 |
+
|
| 312 |
+
|
| 313 |
+
Section 6 -- Term and Termination.
|
| 314 |
+
|
| 315 |
+
a. This Public License applies for the term of the Copyright and
|
| 316 |
+
Similar Rights licensed here. However, if You fail to comply with
|
| 317 |
+
this Public License, then Your rights under this Public License
|
| 318 |
+
terminate automatically.
|
| 319 |
+
|
| 320 |
+
b. Where Your right to use the Licensed Material has terminated under
|
| 321 |
+
Section 6(a), it reinstates:
|
| 322 |
+
|
| 323 |
+
1. automatically as of the date the violation is cured, provided
|
| 324 |
+
it is cured within 30 days of Your discovery of the
|
| 325 |
+
violation; or
|
| 326 |
+
|
| 327 |
+
2. upon express reinstatement by the Licensor.
|
| 328 |
+
|
| 329 |
+
For the avoidance of doubt, this Section 6(b) does not affect any
|
| 330 |
+
right the Licensor may have to seek remedies for Your violations
|
| 331 |
+
of this Public License.
|
| 332 |
+
|
| 333 |
+
c. For the avoidance of doubt, the Licensor may also offer the
|
| 334 |
+
Licensed Material under separate terms or conditions or stop
|
| 335 |
+
distributing the Licensed Material at any time; however, doing so
|
| 336 |
+
will not terminate this Public License.
|
| 337 |
+
|
| 338 |
+
d. Sections 1, 5, 6, 7, and 8 survive termination of this Public
|
| 339 |
+
License.
|
| 340 |
+
|
| 341 |
+
|
| 342 |
+
Section 7 -- Other Terms and Conditions.
|
| 343 |
+
|
| 344 |
+
a. The Licensor shall not be bound by any additional or different
|
| 345 |
+
terms or conditions communicated by You unless expressly agreed.
|
| 346 |
+
|
| 347 |
+
b. Any arrangements, understandings, or agreements regarding the
|
| 348 |
+
Licensed Material not stated herein are separate from and
|
| 349 |
+
independent of the terms and conditions of this Public License.
|
| 350 |
+
|
| 351 |
+
|
| 352 |
+
Section 8 -- Interpretation.
|
| 353 |
+
|
| 354 |
+
a. For the avoidance of doubt, this Public License does not, and
|
| 355 |
+
shall not be interpreted to, reduce, limit, restrict, or impose
|
| 356 |
+
conditions on any use of the Licensed Material that could lawfully
|
| 357 |
+
be made without permission under this Public License.
|
| 358 |
+
|
| 359 |
+
b. To the extent possible, if any provision of this Public License is
|
| 360 |
+
deemed unenforceable, it shall be automatically reformed to the
|
| 361 |
+
minimum extent necessary to make it enforceable. If the provision
|
| 362 |
+
cannot be reformed, it shall be severed from this Public License
|
| 363 |
+
without affecting the enforceability of the remaining terms and
|
| 364 |
+
conditions.
|
| 365 |
+
|
| 366 |
+
c. No term or condition of this Public License will be waived and no
|
| 367 |
+
failure to comply consented to unless expressly agreed to by the
|
| 368 |
+
Licensor.
|
| 369 |
+
|
| 370 |
+
d. Nothing in this Public License constitutes or may be interpreted
|
| 371 |
+
as a limitation upon, or waiver of, any privileges and immunities
|
| 372 |
+
that apply to the Licensor or You, including from the legal
|
| 373 |
+
processes of any jurisdiction or authority.
|
| 374 |
+
|
| 375 |
+
|
| 376 |
+
=======================================================================
|
| 377 |
+
|
| 378 |
+
Creative Commons is not a party to its public
|
| 379 |
+
licenses. Notwithstanding, Creative Commons may elect to apply one of
|
| 380 |
+
its public licenses to material it publishes and in those instances
|
| 381 |
+
will be considered the “Licensor.” The text of the Creative Commons
|
| 382 |
+
public licenses is dedicated to the public domain under the CC0 Public
|
| 383 |
+
Domain Dedication. Except for the limited purpose of indicating that
|
| 384 |
+
material is shared under a Creative Commons public license or as
|
| 385 |
+
otherwise permitted by the Creative Commons policies published at
|
| 386 |
+
creativecommons.org/policies, Creative Commons does not authorize the
|
| 387 |
+
use of the trademark "Creative Commons" or any other trademark or logo
|
| 388 |
+
of Creative Commons without its prior written consent including,
|
| 389 |
+
without limitation, in connection with any unauthorized modifications
|
| 390 |
+
to any of its public licenses or any other arrangements,
|
| 391 |
+
understandings, or agreements concerning use of licensed material. For
|
| 392 |
+
the avoidance of doubt, this paragraph does not form part of the
|
| 393 |
+
public licenses.
|
| 394 |
+
|
| 395 |
+
Creative Commons may be contacted at creativecommons.org.
|
| 396 |
+
|
README.md
ADDED
|
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|
|
| 1 |
+
---
|
| 2 |
+
license: cc-by-4.0
|
| 3 |
+
language:
|
| 4 |
+
- en
|
| 5 |
+
base_model: google/gemma-2-27b
|
| 6 |
+
library_name: transformers
|
| 7 |
+
pipeline_tag: text-generation
|
| 8 |
+
tags:
|
| 9 |
+
- biology
|
| 10 |
+
- scRNAseq
|
| 11 |
+
- gemma2
|
| 12 |
+
- genomics
|
| 13 |
+
- computational-biology
|
| 14 |
+
- bioinformatics
|
| 15 |
+
- gene-expression
|
| 16 |
+
- cell-biology
|
| 17 |
+
- transformers
|
| 18 |
+
- pytorch
|
| 19 |
+
- cell-type-annotation
|
| 20 |
+
- Question Answering
|
| 21 |
+
---
|
| 22 |
+
|
| 23 |
+
# C2S-Scale-Gemma-27B model card
|
| 24 |
+
|
| 25 |
+
**GitHub homepage:** [Cell2Sentence GitHub](https://github.com/vandijklab/cell2sentence)
|
| 26 |
+
|
| 27 |
+
**Model documentation:** [Cell2Sentence Documentation](https://vandijklab-cell2sentence.readthedocs.io/en/latest/)
|
| 28 |
+
|
| 29 |
+
**Resources:**
|
| 30 |
+
|
| 31 |
+
* C2S-Scale Paper: [Scaling Large Language Models for Next-Generation Single-Cell Analysis](https://www.biorxiv.org/content/10.1101/2025.04.14.648850v1)
|
| 32 |
+
* HuggingFace C2S Collection: [C2S-Scale Models](https://huggingface.co/collections/vandijklab/c2s-scale-gemma-models-68ed5e4d3b55c8c29682d842)
|
| 33 |
+
* GitHub Repository: [vandijklab/cell2sentence](https://github.com/vandijklab/cell2sentence) (for code, tutorials, and discussions)
|
| 34 |
+
* Google Research Blog Post: [Teaching machines the language of biology](https://research.google/blog/teaching-machines-the-language-of-biology-scaling-large-language-models-for-next-generation-single-cell-analysis/)
|
| 35 |
+
|
| 36 |
+
**Author:** van Dijk Lab (Yale), Google Research, Google DeepMind
|
| 37 |
+
|
| 38 |
+
|
| 39 |
+
## Model information
|
| 40 |
+
|
| 41 |
+
This section describes the C2S-Scale model and how to use it.
|
| 42 |
+
|
| 43 |
+
### Description
|
| 44 |
+
|
| 45 |
+
C2S-Scale-Gemma-27B is a state-of-the-art, open language model built upon the Gemma-2 27B
|
| 46 |
+
architecture and fine-tuned for single-cell biology. Developed through the Cell2Sentence
|
| 47 |
+
(C2S) framework, the model processes and understands single-cell RNA sequencing
|
| 48 |
+
(scRNA-seq) data by treating it as a language. It converts high-dimensional scRNA-seq
|
| 49 |
+
expression data into "cell sentences" - ordered sequences of gene names - enabling a
|
| 50 |
+
wide range of biological analyses.
|
| 51 |
+
|
| 52 |
+
This work is the result of a collaboration between Yale University, Google Research,
|
| 53 |
+
and Google DeepMind to scale up C2S models. The C2S-Scale models were trained on
|
| 54 |
+
Google's TPU v5s, which allowed for a significant increase in model size and
|
| 55 |
+
capability. These models excel at tasks such as cell type prediction, tissue
|
| 56 |
+
classification, and generating biologically meaningful cell representations.
|
| 57 |
+
|
| 58 |
+
**Key Features**
|
| 59 |
+
|
| 60 |
+
* Versatility: Demonstrates strong performance across a diverse set of single-cell and multi-cell tasks.
|
| 61 |
+
* Scalability: Trained on a massive dataset of over 57 million cells, showcasing the power of scaling LLMs for biological data.
|
| 62 |
+
* Generative Power: Capable of generating realistic single-cell gene expression profiles.
|
| 63 |
+
* Foundation for Fine-tuning: Can serve as a powerful pretrained foundation for specialized, domain-specific single-cell analysis tasks.
|
| 64 |
+
|
| 65 |
+
**Potential Applications**
|
| 66 |
+
|
| 67 |
+
C2S-Scale can be a valuable tool for researchers in the following areas:
|
| 68 |
+
|
| 69 |
+
* In Silico Experiments: Generate cells under specific conditions or predict perturbational changes to form and test new biological hypotheses.
|
| 70 |
+
* Cell Atlas Annotation: Streamline the process of annotating large-scale single-cell datasets by predicting cell types and tissues.
|
| 71 |
+
* Biomarker Discovery: Analyze gene patterns within cell sentences to identify potential markers for specific cell states or diseases.
|
| 72 |
+
|
| 73 |
+
### How to use
|
| 74 |
+
|
| 75 |
+
Below are code snippets to help you get started running the model locally on a GPU.
|
| 76 |
+
The model can be used for various tasks, further described in the C2S-Scale paper.
|
| 77 |
+
|
| 78 |
+
#### Formatting prompts for cell type prediction
|
| 79 |
+
|
| 80 |
+
To perform cell type prediction, the model expects a prompt containing the cell sentence followed by a query.
|
| 81 |
+
|
| 82 |
+
```python
|
| 83 |
+
# A "cell sentence" is a space-separated string of gene names
|
| 84 |
+
# ordered by expression level, from highest to lowest.
|
| 85 |
+
cell_sentence = "MALAT1 TMSB4X B2M EEF1A1 H3F3B ACTB FTL RPL13 ..." # Truncated for example purposes
|
| 86 |
+
num_genes = 1000
|
| 87 |
+
organism = "Homo sapiens"
|
| 88 |
+
|
| 89 |
+
# Construct the prompt for cell type prediction
|
| 90 |
+
prompt = f"""The following is a list of {num_genes} gene names ordered by descending expression level in a {organism} cell. Your task is to give the cell type which this cell belongs to based on its gene expression.
|
| 91 |
+
Cell sentence: {cell_sentence}.
|
| 92 |
+
The cell type corresponding to these genes is:"""
|
| 93 |
+
|
| 94 |
+
print(prompt)
|
| 95 |
+
```
|
| 96 |
+
|
| 97 |
+
The resulting prompt is in the format expected by the model for this task:
|
| 98 |
+
```none
|
| 99 |
+
The following is a list of 1000 gene names ordered by descending expression level in a Homo sapiens cell. Your task is to give the cell type which this cell belongs to based on its gene expression.
|
| 100 |
+
Cell sentence: MALAT1 TMSB4X B2M EEF1A1 H3F3B ACTB FTL RPL13 ... .
|
| 101 |
+
The cell type corresponding to these genes is:
|
| 102 |
+
```
|
| 103 |
+
|
| 104 |
+
#### Running the model on predictive tasks
|
| 105 |
+
|
| 106 |
+
```python
|
| 107 |
+
# pip install accelerate transformers sentencepiece
|
| 108 |
+
from transformers import AutoTokenizer, AutoModelForCausalLM
|
| 109 |
+
import torch
|
| 110 |
+
|
| 111 |
+
device = "cuda" if torch.cuda.is_available() else "cpu"
|
| 112 |
+
|
| 113 |
+
# Load model directly from Hugging Face Hub
|
| 114 |
+
model_id = "vandijklab/C2S-Scale-Gemma-2-27B"
|
| 115 |
+
|
| 116 |
+
# Load tokenizer; requires sentencepiece to be installed
|
| 117 |
+
tokenizer = AutoTokenizer.from_pretrained(model_id)
|
| 118 |
+
model = AutoModelForCausalLM.from_pretrained(
|
| 119 |
+
model_id,
|
| 120 |
+
).to(device)
|
| 121 |
+
|
| 122 |
+
# Format prompt (see previous section)
|
| 123 |
+
cell_sentence = "MALAT1 TMSB4X B2M EEF1A1 H3F3B ACTB FTL RPL13 ..." # Truncated for example, use at least 200 genes for inference
|
| 124 |
+
num_genes = 1000
|
| 125 |
+
organism = "Homo sapiens"
|
| 126 |
+
|
| 127 |
+
prompt = f"""The following is a list of {num_genes} gene names ordered by descending expression level in a {organism} cell. Your task is to give the cell type which this cell belongs to based on its gene expression.
|
| 128 |
+
Cell sentence: {cell_sentence}.
|
| 129 |
+
The cell type corresponding to these genes is:"""
|
| 130 |
+
|
| 131 |
+
# Prepare tokenized inputs
|
| 132 |
+
input_ids = tokenizer(prompt, return_tensors="pt").to(device)
|
| 133 |
+
|
| 134 |
+
# Generate response
|
| 135 |
+
outputs = model.generate(**input_ids, max_new_tokens=20)
|
| 136 |
+
response = tokenizer.decode(outputs[0], skip_special_tokens=True)
|
| 137 |
+
|
| 138 |
+
# The predicted cell type will be the text immediately following the prompt
|
| 139 |
+
predicted_cell_type = response.split("The cell type corresponding to these genes is:")[1].strip()
|
| 140 |
+
print(f"Predicted Cell Type: {predicted_cell_type}")
|
| 141 |
+
```
|
| 142 |
+
|
| 143 |
+
### Examples
|
| 144 |
+
|
| 145 |
+
See the following Colab notebooks in our GitHub repository for examples of how to use C2S-Scale models:
|
| 146 |
+
|
| 147 |
+
* To quickly get started with the model for tasks like cell type prediction and generation: [C2S Tutorials](https://github.com/vandijklab/cell2sentence/tree/master/tutorials)
|
| 148 |
+
|
| 149 |
+
### Model architecture overview
|
| 150 |
+
|
| 151 |
+
* C2S-Scale is based on the Gemma 2 family of lightweight, state-of-the-art open LLMs, which utilizes a decoder-only transformer architecture.
|
| 152 |
+
* Base Model: Gemma-2 27B.
|
| 153 |
+
* Fine-tuning Data: A comprehensive collection of over 800 datasets from CellxGene and the Human Cell Atlas, totaling over 57 million human and mouse cells.
|
| 154 |
+
* Training Approach: Instruction fine-tuning using the Cell2Sentence framework, which converts scRNA-seq expression data into sequences of gene tokens.
|
| 155 |
+
|
| 156 |
+
|
| 157 |
+
### Technical Specifications
|
| 158 |
+
|
| 159 |
+
* Model type: Decoder-only Transformer (based on Gemma-2)
|
| 160 |
+
* Key publication: [Scaling Large Language Models for Next-Generation Single-Cell Analysis](https://www.biorxiv.org/content/10.1101/2025.04.14.648850v1)
|
| 161 |
+
|
| 162 |
+
|
| 163 |
+
### Performance & Validation
|
| 164 |
+
|
| 165 |
+
The performance of C2S-Scale models was validated on a wide range of single-cell and multi-cell
|
| 166 |
+
tasks, including advanced downstream tasks such as cluster captioning, question answering,
|
| 167 |
+
and perturbation prediction. C2S-Scale models demonstrated significant improvements over
|
| 168 |
+
other open and closed-source models, establishing new state-of-the-art benchmarks for LLMs
|
| 169 |
+
in single-cell biology. Please see our preprint for a full breakdown of performance metrics.
|
| 170 |
+
|
| 171 |
+
### Inputs and outputs
|
| 172 |
+
|
| 173 |
+
* Input: Text. For best performance, prompts should be structured according to the specific task (e.g., cell type prediction, conditioned generation). Inputs are "cell sentences"—ordered, space-separated lists of gene names.
|
| 174 |
+
* Output: Text. The model generates text as a response, which can be a predicted label (like a cell type or tissue), a full cell sentence, or a natural language abstract.
|
| 175 |
+
|
| 176 |
+
## Dataset details
|
| 177 |
+
|
| 178 |
+
### Training dataset
|
| 179 |
+
|
| 180 |
+
**CellxGene and Human Cell Atlas:** The model was trained on a curated collection of over 800
|
| 181 |
+
public scRNA-seq datasets, encompassing more than 57 million cells. This data covers a broad
|
| 182 |
+
range of tissues, cell types, and experimental conditions from both human and mouse, ensuring
|
| 183 |
+
the model learns a robust and generalizable representation of cellular states.
|
| 184 |
+
|
| 185 |
+
### Evaluation dataset
|
| 186 |
+
|
| 187 |
+
Evaluation was performed using held-out datasets and standardized benchmarks designed to
|
| 188 |
+
test the model's capabilities on the tasks listed above. All evaluation methodologies followed
|
| 189 |
+
established best practices for splitting data to ensure robust and unbiased assessment.
|
| 190 |
+
|
| 191 |
+
## License
|
| 192 |
+
|
| 193 |
+
The model weights shared on Huggingface are CC-by-4.0.
|
| 194 |
+
|
| 195 |
+
## Implementation information
|
| 196 |
+
|
| 197 |
+
### Software
|
| 198 |
+
|
| 199 |
+
The model was trained using [JAX](https://github.com/jax-ml/jax), leveraging Google's TPU v5
|
| 200 |
+
hardware for efficient and large-scale training.
|
| 201 |
+
|
| 202 |
+
## Use and limitations
|
| 203 |
+
|
| 204 |
+
### Intended use
|
| 205 |
+
|
| 206 |
+
* Research in single-cell genomics and computational biology.
|
| 207 |
+
* As a foundational model for fine-tuning on specific biological domains or datasets.
|
| 208 |
+
* To aid in the annotation and interpretation of large-scale scRNA-seq experiments.
|
| 209 |
+
|
| 210 |
+
### Benefits
|
| 211 |
+
|
| 212 |
+
C2S-Scale provides a powerful, versatile, and scalable tool for single-cell analysis. It offers:
|
| 213 |
+
* State-of-the-art performance on a wide range of scRNA-seq tasks.
|
| 214 |
+
* A unified framework for handling diverse single-cell analysis challenges.
|
| 215 |
+
* A foundation for building more specialized models from private or proprietary data.
|
| 216 |
+
* The ability to perform in silico generation of cellular data to explore biological hypotheses.
|
| 217 |
+
|
| 218 |
+
### Limitations
|
| 219 |
+
|
| 220 |
+
* The model is trained on public data and its knowledge is limited to the genes, cell types, and conditions present in that data.
|
| 221 |
+
* Performance on out-of-distribution data (e.g., completely novel cell types or technologies) is not guaranteed and requires validation.
|
| 222 |
+
* Performance of the models on input prompt formats that greatly deviate from training prompt formatting is not guaranteed.
|
| 223 |
+
|
| 224 |
+
## Citation
|
| 225 |
+
|
| 226 |
+
```bibtex
|
| 227 |
+
@article{Rizvi2025.04.14.648850,
|
| 228 |
+
abstract = {Single-cell RNA sequencing has transformed our understanding of cellular diversity, yet current single-cell foundation models (scFMs) remain limited in their scalability, flexibility across diverse tasks, and ability to natively integrate textual information. In this work, we build upon the Cell2Sentence (C2S) framework, which represents scRNA-seq profiles as textual {\textquotedblleft}cell sentences,{\textquotedblright} to train Large Language Models (LLMs) on a corpus comprising over one billion tokens of transcriptomic data, biological text, and metadata. By scaling model size to 27 billion parameters, we observe consistent improvements in predictive and generative capabilities, as well as the capacity for advanced downstream tasks requiring synthesis of information across multicellular contexts. Through targeted fine-tuning supported by modern reinforcement learning techniques, our approach excels in tasks such as perturbation response prediction, natural language interpretation, and complex biological reasoning. By unifying transcriptomic and textual data at unprecedented scales, this approach not only surpasses both specialized single-cell models and general-purpose LLMs, but also establishes a powerful platform for next-generation single-cell analysis, paving the way for the development of {\textquotedblleft}virtual cells.{\textquotedblright}Competing Interest StatementThe authors have declared no competing interest.},
|
| 229 |
+
author = {Rizvi, Syed Asad and Levine, Daniel and Patel, Aakash and Zhang, Shiyang and Wang, Eric and He, Sizhuang and Zhang, David and Tang, Cerise and Lyu, Zhuoyang and Darji, Rayyan and Li, Chang and Sun, Emily and Jeong, David and Zhao, Lawrence and Kwan, Jennifer and Braun, David and Hafler, Brian and Ishizuka, Jeffrey and Dhodapkar, Rahul M. and Chung, Hattie and Azizi, Shekoofeh and Perozzi, Bryan and van Dijk, David},
|
| 230 |
+
doi = {10.1101/2025.04.14.648850},
|
| 231 |
+
elocation-id = {2025.04.14.648850},
|
| 232 |
+
eprint = {https://www.biorxiv.org/content/early/2025/04/17/2025.04.14.648850.full.pdf},
|
| 233 |
+
journal = {bioRxiv},
|
| 234 |
+
publisher = {Cold Spring Harbor Laboratory},
|
| 235 |
+
title = {Scaling Large Language Models for Next-Generation Single-Cell Analysis},
|
| 236 |
+
url = {https://www.biorxiv.org/content/early/2025/04/17/2025.04.14.648850},
|
| 237 |
+
year = {2025},
|
| 238 |
+
Bdsk-Url-1 = {https://www.biorxiv.org/content/early/2025/04/17/2025.04.14.648850},
|
| 239 |
+
Bdsk-Url-2 = {https://doi.org/10.1101/2025.04.14.648850}}
|
| 240 |
+
```
|
| 241 |
+
|
| 242 |
+
# C2S-Scale Links
|
| 243 |
+
- Paper: [Scaling Large Language Models for Next-Generation Single-Cell Analysis](https://www.biorxiv.org/content/10.1101/2025.04.14.648850v1)
|
| 244 |
+
- Google Research Blog Post: [Teaching machines the language of biology: Scaling large language models for next-generation single-cell analysis](https://research.google/blog/teaching-machines-the-language-of-biology-scaling-large-language-models-for-next-generation-single-cell-analysis/)
|
| 245 |
+
- GitHub: https://github.com/vandijklab/cell2sentence (Note: Codebase has Apache 2.0 license, weights shared on HuggingFace are CC-by-4.0)
|
| 246 |
+
|
| 247 |
+
# Gemma-2 Links
|
| 248 |
+
- HuggingFace: https://huggingface.co/google/gemma-2-27b
|
| 249 |
+
- Gemma-2 Blog Post: [Gemma explained: What's new in Gemma 2](https://developers.googleblog.com/en/gemma-explained-new-in-gemma-2/)
|
| 250 |
+
- Technical report: https://storage.googleapis.com/deepmind-media/gemma/gemma-2-report.pdf
|
config.json
ADDED
|
@@ -0,0 +1,80 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"architectures": [
|
| 3 |
+
"Gemma2ForCausalLM"
|
| 4 |
+
],
|
| 5 |
+
"attention_bias": false,
|
| 6 |
+
"attention_dropout": 0.0,
|
| 7 |
+
"attn_logit_softcapping": 50.0,
|
| 8 |
+
"bos_token_id": 2,
|
| 9 |
+
"dtype": "bfloat16",
|
| 10 |
+
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| 11 |
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"single_word": false
|
| 22 |
+
},
|
| 23 |
+
"unk_token": {
|
| 24 |
+
"content": "<unk>",
|
| 25 |
+
"lstrip": false,
|
| 26 |
+
"normalized": false,
|
| 27 |
+
"rstrip": false,
|
| 28 |
+
"single_word": false
|
| 29 |
+
}
|
| 30 |
+
}
|
tokenizer.model
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:a343c33e9f5cd740f55625b7fc556d71599c239ada13f6308387d6ce79b3a9d6
|
| 3 |
+
size 4945541
|
tokenizer_config.json
ADDED
|
@@ -0,0 +1,49 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"add_bos_token": true,
|
| 3 |
+
"add_eos_token": false,
|
| 4 |
+
"added_tokens_decoder": {
|
| 5 |
+
"0": {
|
| 6 |
+
"content": "<pad>",
|
| 7 |
+
"lstrip": false,
|
| 8 |
+
"normalized": false,
|
| 9 |
+
"rstrip": false,
|
| 10 |
+
"single_word": false,
|
| 11 |
+
"special": true
|
| 12 |
+
},
|
| 13 |
+
"1": {
|
| 14 |
+
"content": "<eos>",
|
| 15 |
+
"lstrip": false,
|
| 16 |
+
"normalized": false,
|
| 17 |
+
"rstrip": false,
|
| 18 |
+
"single_word": false,
|
| 19 |
+
"special": true
|
| 20 |
+
},
|
| 21 |
+
"2": {
|
| 22 |
+
"content": "<bos>",
|
| 23 |
+
"lstrip": false,
|
| 24 |
+
"normalized": false,
|
| 25 |
+
"rstrip": false,
|
| 26 |
+
"single_word": false,
|
| 27 |
+
"special": true
|
| 28 |
+
},
|
| 29 |
+
"3": {
|
| 30 |
+
"content": "<unk>",
|
| 31 |
+
"lstrip": false,
|
| 32 |
+
"normalized": false,
|
| 33 |
+
"rstrip": false,
|
| 34 |
+
"single_word": false,
|
| 35 |
+
"special": true
|
| 36 |
+
}
|
| 37 |
+
},
|
| 38 |
+
"bos_token": "<bos>",
|
| 39 |
+
"clean_up_tokenization_spaces": false,
|
| 40 |
+
"eos_token": "<eos>",
|
| 41 |
+
"extra_special_tokens": {},
|
| 42 |
+
"model_max_length": 1000000000000000019884624838656,
|
| 43 |
+
"pad_token": "<pad>",
|
| 44 |
+
"sp_model_kwargs": {},
|
| 45 |
+
"spaces_between_special_tokens": false,
|
| 46 |
+
"tokenizer_class": "GemmaTokenizer",
|
| 47 |
+
"unk_token": "<unk>",
|
| 48 |
+
"use_default_system_prompt": false
|
| 49 |
+
}
|