PRISM2: Unlocking Multi-Modal General Pathology AI with Clinical Dialogue
Paper • 2506.13063 • Published
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This model and associated code are released under the CC-BY-NC-ND 4.0 license and may only be used for non-commercial, academic research purposes with proper attribution. Any commercial use, sale, or other monetization of the Prism2-survival Model and its derivatives, which include models trained on outputs from the Prism2-survival Model or datasets created from the Prism2-survival Model, is prohibited and requires prior approval. Please note that the primary email used to sign up for your Hugging Face account must match your institutional email to receive approval. By downloading the Prism2-survival Model, you attest that all information (affiliation, research use) is correct and up-to-date. Downloading the Prism2-survival Model requires prior registration on Hugging Face and agreeing to the terms of use. By downloading the Prism2-survival model, you agree not to distribute, publish or reproduce a copy of the Prism2-survival Model. If another user within your organization wishes to use the Prism2-survival Model, they must register as an individual user and agree to comply with the terms of use. Requests from commercial entities will be rejected by default if no statement of use received separately. If you are a commercial entity, please contact the corresponding author of this paper.
Further, by downloading the Prism2-survival model, you agree you will only use the Prism2-survival model for academic research purposes and will not use, or allow others to use, the Prism2-survival model to:
Diagnose, cure, mitigate, treat, or prevent disease or any other conditions, including for Investigational Use Only (“IUO”), Research Use Only (“RUO”), commercial, clinical or other similar use, and including as a substitute for professional medical advice, a healthcare opinion, a diagnosis, treatment, or the clinical judgment of a healthcare professional, as no license or right is granted for any such purposes.
Re-identify the deidentified data used to develop the Prism2-survival Model;
Violate the law or others’ rights, including to:
a. Engage in, promote, generate, contribute to, encourage, plan, incite, or further illegal or unlawful activity or content;
b. Engage in, promote, incite, or facilitate the harassment, abuse, threatening, or bullying of individuals or groups of individuals;
c. Engage in, promote, incite, or facilitate discrimination or other unlawful or harmful conduct in the provision of employment, employment benefits, credit, housing, other economic benefits, or other essential goods and services;
d. Engage in the unauthorized or unlicensed practice of any profession including, but not limited to, financial, legal, medical/health, or related professional practices;
e. Collect, process, disclose, generate, or infer the identity of individuals or the health, demographic, or other sensitive personal or private information about individuals without rights and consents required by applicable laws;
f. Engage in or facilitate any action or generate any content that infringes, misappropriates, or otherwise violates any third-party rights, including the outputs or results of any products or services using the Prism2-survival Model or any related materials; and
g. Create, generate, or facilitate the creation of malicious code, malware, computer viruses or do anything else that could disable, overburden, interfere with or impair the proper working, integrity, operation or appearance of a website or computer system.
Engage in, promote, incite, facilitate, or assist in the planning or development of activities that present a risk of death or bodily harm to individuals, including the use of the Prism2-survival Model as a medical device, clinical support, diagnostic tool, or other technology intended to be used in the diagnosis, cure, mitigation, treatment, or prevention of disease or other conditions, including for Investigational Use Only (“IUO”), Research Use Only (“RUO”), commercial, clinical or similar use; and
Intentionally deceive or mislead others, including representing that the use of the Prism2-survival Model or its outputs is human-generated.
Further, you agree that you will appropriately disclose to end users any known dangers of your AI system.
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The full base PRISM2 model is published at
paige-ai/Prism2.
Model card for PRISM2-survival
PRISM2-survival is a survival-finetuned variant of the PRISM2 perceiver for slide-level analysis of H&E-stained histopathology images. It produces a survival-tuned, slide-level embedding from pre-extracted Virchow2 tile embeddings. This release ships only the WSI perceiver encoder weights — the Phi-3 text decoder and projection from PRISM2 are not included. Train your own downstream linear head (Cox / DeepHit / etc.) on the returned embeddings to produce survival predictions.
Model Usage
Requirements
Using Python 3.10 or newer and a CUDA-capable GPU:
torch>=2.3
transformers>=4.51
safetensors
flash-attn>=2.6.3
flash-attn is required — the perceiver's cross-attention uses
flash_attn_varlen_func to match the training-time kernel.
Get the model
After gaining access to the model here, you will need to login to HuggingFace in the environment you wish to use the model. This can be done from the command line:
python -m pip install huggingface_hub
huggingface-cli login
or in your Python code:
from huggingface_hub import login
login()
Please refer to official HuggingFace documentation for more details.
Test model access:
from transformers import AutoModel
AutoModel.from_pretrained("paige-ai/Prism2-survival", trust_remote_code=True)
Inference
PRISM2-survival requires Virchow2 tile embeddings with the following constraints:
- Class token only (not Class + Mean)
- 20x magnification (0.5 mpp)
- 224x224 tile size
- Foreground tissue tiles selected (with background/glass tiles removed)
See https://huggingface.co/paige-ai/Virchow2 for tile embedding.
PRISM2-survival takes pre-extracted tile embeddings, not raw slides. Per slide, you
should provide a (N, 1280) tensor produced by Virchow2 where N is that slide's
tile count. The processor pads + masks across a batch of slides with
different N.
import torch
from transformers import AutoModel, AutoProcessor
model = AutoModel.from_pretrained(
"paige-ai/Prism2-survival", trust_remote_code=True, torch_dtype="auto",
).cuda().eval()
processor = AutoProcessor.from_pretrained("paige-ai/Prism2-survival", trust_remote_code=True)
# Each slide is its own (N_i, 1280) tensor of Virchow2 tile embeddings.
slides = [tile_emb_slide_1, tile_emb_slide_2] # list of (N_i, 1280) tensors
batch = processor(tile_embeddings=slides).to("cuda")
Creating a multi-slide embedding: PRISM2-survival can embed both single-slide and multi-slide (specimen-level) inputs. If you want to produce a single embedding for multiple whole slide images (eg. a patient embedding), you can simply concatenate all tile embeddings across the slides. Note that PRISM2-survival was trained on the part-specimen level which typically contains multiple whole slide images all sharing the same tissue type.
Survival embedding
with torch.autocast("cuda", torch.bfloat16):
emb = model.get_survival_embedding(**batch)
print(emb.shape) # torch.Size([B, 2560])
Use emb as the input to whatever survival head you train downstream (Cox PH,
DeepHit, etc.). Common libraries: torchsurv, scikit-survival, lifelines.
Validation
To validate the extracted survival embeddings, you can use the resources provided in the accompanying Zenodo page to run linear probe evaluations:
https://zenodo.org/records/19056118
Note that bitwise reproducibilty of embeddings and linear probe results is not expected due to differences in foreground filtering, floating point error accumulation, and hardware/software.
Model Details
- Developed by: Paige, NYC, USA and Microsoft Research, Cambridge, MA USA
- Model Type: Vision Encoder (perceiver) finetuned for survival
- Model Stats:
- Params (M): ~620
- Model Architecture:
- WSI Encoder: Perceiver (https://doi.org/10.48550/arXiv.2103.03206)
- Model inputs: tile image embeddings
- Tile image encoder: Virchow2 (https://huggingface.co/paige-ai/Virchow2)
- Training Details:
- Initialized from a PRISM2 stage-2 checkpoint, then finetuned with a Cox
partial-log-likelihood survival objective on slide-level survival labels.
The perceiver pool token is renamed
survival. - Precision: Mixed precision (
bf16)
- Initialized from a PRISM2 stage-2 checkpoint, then finetuned with a Cox
partial-log-likelihood survival objective on slide-level survival labels.
The perceiver pool token is renamed
- Paper:
- PRISM2: Unlocking Multi-Modal General Pathology AI with Clinical Dialogue: https://arxiv.org/abs/2506.13063
- Pretraining Dataset: Internal dataset of 2.3 million whole slide images from 685,507 specimens (200,692 patients) and 14 million question-answer pairs derived from clinical reports at Memorial Sloan Kettering Cancer Center.
- Survival Finetuning Dataset: Internal dataset of 225,597 cases (~100,000 patients) with 69,114 death events at Memorial Sloan Kettering Cancer Center.
- License: CC-BY-NC-ND-4.0
Terms of use
This model and associated code are released under the CC-BY-NC-ND 4.0 license and may only be used for non-commercial, academic research purposes with proper attribution. Any commercial use, sale, or other monetization of the Prism2-survival Model and its derivatives, which include models trained on outputs from the Prism2-survival Model or datasets created from the Prism2-survival Model, is prohibited and requires prior approval. Please note that the primary email used to sign up for your Hugging Face account must match your institutional email to receive approval. By downloading the Prism2-survival Model, you attest that all information (affiliation, research use) is correct and up-to-date. Downloading the Prism2-survival Model requires prior registration on Hugging Face and agreeing to the terms of use. By downloading the Prism2-survival model, you agree not to distribute, publish or reproduce a copy of the Prism2-survival Model. If another user within your organization wishes to use the Prism2-survival Model, they must register as an individual user and agree to comply with the terms of use. If you are a commercial entity, please contact the corresponding author.
Further, by downloading the Prism2-survival model, you agree you will only use the Prism2-survival model for academic research purposes and will not use, or allow others to use, the Prism2-survival model to:
Diagnose, cure, mitigate, treat, or prevent disease or any other conditions, including for Investigational Use Only ("IUO"), Research Use Only ("RUO"), commercial, clinical or other similar use, and including as a substitute for professional medical advice, a healthcare opinion, a diagnosis, treatment, or the clinical judgment of a healthcare professional, as no license or right is granted for any such purposes.
Re-identify the deidentified data used to develop the Prism2-survival Model;
Violate the law or others' rights, including to:
a. Engage in, promote, generate, contribute to, encourage, plan, incite, or further illegal or unlawful activity or content;
b. Engage in, promote, incite, or facilitate the harassment, abuse, threatening, or bullying of individuals or groups of individuals;
c. Engage in, promote, incite, or facilitate discrimination or other unlawful or harmful conduct in the provision of employment, employment benefits, credit, housing, other economic benefits, or other essential goods and services;
d. Engage in the unauthorized or unlicensed practice of any profession including, but not limited to, financial, legal, medical/health, or related professional practices;
e. Collect, process, disclose, generate, or infer the identity of individuals or the health, demographic, or other sensitive personal or private information about individuals without rights and consents required by applicable laws;
f. Engage in or facilitate any action or generate any content that infringes, misappropriates, or otherwise violates any third-party rights, including the outputs or results of any products or services using the Prism2-survival Model or any related materials; and
g. Create, generate, or facilitate the creation of malicious code, malware, computer viruses or do anything else that could disable, overburden, interfere with or impair the proper working, integrity, operation or appearance of a website or computer system.
Engage in, promote, incite, facilitate, or assist in the planning or development of activities that present a risk of death or bodily harm to individuals, including the use of the Prism2-survival Model as a medical device, clinical support, diagnostic tool, or other technology intended to be used in the diagnosis, cure, mitigation, treatment, or prevention of disease or other conditions, including for Investigational Use Only ("IUO"), Research Use Only ("RUO"), commercial, clinical or similar use; and
Intentionally deceive or mislead others, including representing that the use of the Prism2-survival model or its outputs is human-generated.
Further, you agree that you will appropriately disclose to end users any known dangers of your AI system.
Citation
@article{vorontsov2025prism2,
title={PRISM2: Unlocking Multi-Modal General Pathology AI with Clinical Dialogue},
author={Vorontsov, Eugene and Shaikovski, George and Casson, Adam and Viret, Julian and Zimmermann, Eric and Tenenholtz, Neil and Wang, Yi Kan and Bernhard, Jan H. and Godrich, Ran A. and Retamero, Juan A. and Shia, Jinru and Gonen, Mithat and Weiser, Martin R. and Klimstra, David S. and Yousfi, Razik and Fusi, Nicolo and Fuchs, Thomas J. and Severson, Kristen and Liu, Siqi},
journal={arXiv preprint arXiv:2506.13063},
year={2025}
}
Disclaimer
PRISM2-survival has been developed for research purposes and is not intended for diagnosis or prognostication of real patients or projection/prediction of future disease possibilities.
Fairness evaluation cannot be completed due to limitations in the metadata. Underlying biases of the training datasets may not be well characterized and may not be representative of all demographics.
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