Category: Offsites

Posted by Dave Steiner, Clinical Research Scientist, Google Health, and Rory Pilgrim, Product Manager, Google Research

There’s a worldwide shortage of access to medical imaging expert interpretation across specialties including radiology, dermatology and pathology. Machine learning (ML) technology can help ease this burden by powering tools that enable doctors to interpret these images more accurately and efficiently. However, the development and implementation of such ML tools are often limited by the availability of high-quality data, ML expertise, and computational resources.

One way to catalyze the use of ML for medical imaging is via domain-specific models that utilize deep learning (DL) to capture the information in medical images as compressed numerical vectors (called embeddings). These embeddings represent a type of pre-learned understanding of the important features in an image. Identifying patterns in the embeddings reduces the amount of data, expertise, and compute needed to train performant models as compared to working with high-dimensional data, such as images, directly. Indeed, these embeddings can be used to perform a variety of downstream tasks within the specialized domain (see animated graphic below). This framework of leveraging pre-learned understanding to solve related tasks is similar to that of a seasoned guitar player quickly learning a new song by ear. Because the guitar player has already built up a foundation of skill and understanding, they can quickly pick up the patterns and groove of a new song.

Path Foundation is used to convert a small dataset of (image, label) pairs into (embedding, label) pairs. These pairs can then be used to train a task-specific classifier using a linear probe, (i.e., a lightweight linear classifier) as represented in this graphic, or other types of models using the embeddings as input.

Once the linear probe is trained, it can be used to make predictions on embeddings from new images. These predictions can be compared to ground truth information in order to evaluate the linear probe’s performance.

In order to make this type of embedding model available and drive further development of ML tools in medical imaging, we are excited to release two domain-specific tools for research use: Derm Foundation and Path Foundation. This follows on the strong response we’ve already received from researchers using the CXR Foundation embedding tool for chest radiographs and represents a portion of our expanding research offerings across multiple medical-specialized modalities. These embedding tools take an image as input and produce a numerical vector (the embedding) that is specialized to the domains of dermatology and digital pathology images, respectively. By running a dataset of chest X-ray, dermatology, or pathology images through the respective embedding tool, researchers can obtain embeddings for their own images, and use these embeddings to quickly develop new models for their applications.

Path Foundation

In “Domain-specific optimization and diverse evaluation of self-supervised models for histopathology”, we showed that self-supervised learning (SSL) models for pathology images outperform traditional pre-training approaches and enable efficient training of classifiers for downstream tasks. This effort focused on hematoxylin and eosin (H&E) stained slides, the principal tissue stain in diagnostic pathology that enables pathologists to visualize cellular features under a microscope. The performance of linear classifiers trained using the output of the SSL models matched that of prior DL models trained on orders of magnitude more labeled data.

Due to substantial differences between digital pathology images and “natural image” photos, this work involved several pathology-specific optimizations during model training. One key element is that whole-slide images (WSIs) in pathology can be 100,000 pixels across (thousands of times larger than typical smartphone photos) and are analyzed by experts at multiple magnifications (zoom levels). As such, the WSIs are typically broken down into smaller tiles or patches for computer vision and DL applications. The resulting images are information dense with cells or tissue structures distributed throughout the frame instead of having distinct semantic objects or foreground vs. background variations, thus creating unique challenges for robust SSL and feature extraction. Additionally, physical (e.g., cutting) and chemical (e.g., fixing and staining) processes used to prepare the samples can influence image appearance dramatically.

Taking these important aspects into consideration, pathology-specific SSL optimizations included helping the model learn stain-agnostic features, generalizing the model to patches from multiple magnifications, augmenting the data to mimic scanning and image post processing, and custom data balancing to improve input heterogeneity for SSL training. These approaches were extensively evaluated using a broad set of benchmark tasks involving 17 different tissue types over 12 different tasks.

Utilizing the vision transformer (ViT-S/16) architecture, Path Foundation was selected as the best performing model from the optimization and evaluation process described above (and illustrated in the figure below). This model thus provides an important balance between performance and model size to enable valuable and scalable use in generating embeddings over the many individual image patches of large pathology WSIs.

SSL training with pathology-specific optimizations for Path Foundation.

The value of domain-specific image representations can also be seen in the figure below, which shows the linear probing performance improvement of Path Foundation (as measured by AUROC) compared to traditional pre-training on natural images (ImageNet-21k). This includes evaluation for tasks such as metastatic breast cancer detection in lymph nodes, prostate cancer grading, and breast cancer grading, among others.

Path Foundation embeddings significantly outperform traditional ImageNet embeddings as evaluated by linear probing across multiple evaluation tasks in histopathology.

Derm Foundation

Derm Foundation is an embedding tool derived from our research in applying DL to interpret images of dermatology conditions and includes our recent work that adds improvements to generalize better to new datasets. Due to its dermatology-specific pre-training it has a latent understanding of features present in images of skin conditions and can be used to quickly develop models to classify skin conditions. The model underlying the API is a BiT ResNet-101×3 trained in two stages. The first pre-training stage uses contrastive learning, similar to ConVIRT, to train on a large number of image-text pairs from the internet. In the second stage, the image component of this pre-trained model is then fine-tuned for condition classification using clinical datasets, such as those from teledermatology services.

Unlike histopathology images, dermatology images more closely resemble the real-world images used to train many of today’s computer vision models. However, for specialized dermatology tasks, creating a high-quality model may still require a large dataset. With Derm Foundation, researchers can use their own smaller dataset to retrieve domain-specific embeddings, and use those to build smaller models (e.g., linear classifiers or other small non-linear models) that enable them to validate their research or product ideas. To evaluate this approach, we trained models on a downstream task using teledermatology data. Model training involved varying dataset sizes (12.5%, 25%, 50%, 100%) to compare embedding-based linear classifiers against fine-tuning.

The modeling variants considered were:

• A linear classifier on frozen embeddings from BiT-M (a standard pre-trained image model)
• Fine-tuned version of BiT-M with an extra dense layer for the downstream task
• A linear classifier on frozen embeddings from the Derm Foundation API
• Fine-tuned version of the model underlying the Derm Foundation API with an extra layer for the downstream task

We found that models built on top of the Derm Foundation embeddings for dermatology-related tasks achieved significantly higher quality than those built solely on embeddings or fine tuned from BiT-M. This advantage was found to be most pronounced for smaller training dataset sizes.

These results demonstrate that the Derm Foundation tooI can serve as a useful starting point to accelerate skin-related modeling tasks. We aim to enable other researchers to build on the underlying features and representations of dermatology that the model has learned.

However, there are limitations with this analysis. We’re still exploring how well these embeddings generalize across task types, patient populations, and image settings. Downstream models built using Derm Foundation still require careful evaluation to understand their expected performance in the intended setting.

Access Path and Derm Foundation

We envision that the Derm Foundation and Path Foundation embedding tools will enable a range of use cases, including efficient development of models for diagnostic tasks, quality assurance and pre-analytical workflow improvements, image indexing and curation, and biomarker discovery and validation. We are releasing both tools to the research community so they can explore the utility of the embeddings for their own dermatology and pathology data.

To get access, please sign up to each tool’s terms of service using the following Google Forms.

• Derm Foundation Access Form
• Path Foundation Access Form

After gaining access to each tool, you can use the API to retrieve embeddings from dermatology images or digital pathology images stored in Google Cloud. Approved users who are just curious to see the model and embeddings in action can use the provided example Colab notebooks to train models using public data for classifying six common skin conditions or identifying tumors in histopathology patches. We look forward to seeing the range of use-cases these tools can unlock.

Acknowledgements

We would like to thank the many collaborators who helped make this work possible including Yun Liu, Can Kirmizi, Fereshteh Mahvar, Bram Sterling, Arman Tajback, Kenneth Philbrik, Arnav Agharwal, Aurora Cheung, Andrew Sellergren, Boris Babenko, Basil Mustafa, Jan Freyberg, Terry Spitz, Yuan Liu, Pinal Bavishi, Ayush Jain, Amit Talreja, Rajeev Rikhye, Abbi Ward, Jeremy Lai, Faruk Ahmed, Supriya Vijay,Tiam Jaroensri, Jessica Loo, Saurabh Vyawahare, Saloni Agarwal, Ellery Wulczyn, Jonathan Krause, Fayaz Jamil, Tom Small, Annisah Um’rani, Lauren Winer, Sami Lachgar, Yossi Matias, Greg Corrado, and Dale Webster.

Posted by Pooja Rao, Research Scientist, Google Research

Health datasets play a crucial role in research and medical education, but it can be challenging to create a dataset that represents the real world. For example, dermatology conditions are diverse in their appearance and severity and manifest differently across skin tones. Yet, existing dermatology image datasets often lack representation of everyday conditions (like rashes, allergies and infections) and skew towards lighter skin tones. Furthermore, race and ethnicity information is frequently missing, hindering our ability to assess disparities or create solutions.

To address these limitations, we are releasing the Skin Condition Image Network (SCIN) dataset in collaboration with physicians at Stanford Medicine. We designed SCIN to reflect the broad range of concerns that people search for online, supplementing the types of conditions typically found in clinical datasets. It contains images across various skin tones and body parts, helping to ensure that future AI tools work effectively for all. We’ve made the SCIN dataset freely available as an open-access resource for researchers, educators, and developers, and have taken careful steps to protect contributor privacy.

Example set of images and metadata from the SCIN dataset.

Dataset composition

The SCIN dataset currently contains over 10,000 images of skin, nail, or hair conditions, directly contributed by individuals experiencing them. All contributions were made voluntarily with informed consent by individuals in the US, under an institutional-review board approved study. To provide context for retrospective dermatologist labeling, contributors were asked to take images both close-up and from slightly further away. They were given the option to self-report demographic information and tanning propensity (self-reported Fitzpatrick Skin Type, i.e., sFST), and to describe the texture, duration and symptoms related to their concern.

One to three dermatologists labeled each contribution with up to five dermatology conditions, along with a confidence score for each label. The SCIN dataset contains these individual labels, as well as an aggregated and weighted differential diagnosis derived from them that could be useful for model testing or training. These labels were assigned retrospectively and are not equivalent to a clinical diagnosis, but they allow us to compare the distribution of dermatology conditions in the SCIN dataset with existing datasets.

The SCIN dataset contains largely allergic, inflammatory and infectious conditions while datasets from clinical sources focus on benign and malignant neoplasms.

While many existing dermatology datasets focus on malignant and benign tumors and are intended to assist with skin cancer diagnosis, the SCIN dataset consists largely of common allergic, inflammatory, and infectious conditions. The majority of images in the SCIN dataset show early-stage concerns — more than half arose less than a week before the photo, and 30% arose less than a day before the image was taken. Conditions within this time window are seldom seen within the health system and therefore are underrepresented in existing dermatology datasets.

We also obtained dermatologist estimates of Fitzpatrick Skin Type (estimated FST or eFST) and layperson labeler estimates of Monk Skin Tone (eMST) for the images. This allowed comparison of the skin condition and skin type distributions to those in existing dermatology datasets. Although we did not selectively target any skin types or skin tones, the SCIN dataset has a balanced Fitzpatrick skin type distribution (with more of Types 3, 4, 5, and 6) compared to similar datasets from clinical sources.

Self-reported and dermatologist-estimated Fitzpatrick Skin Type distribution in the SCIN dataset compared with existing un-enriched dermatology datasets (Fitzpatrick17k, PH², SKINL2, and PAD-UFES-20).

The Fitzpatrick Skin Type scale was originally developed as a photo-typing scale to measure the response of skin types to UV radiation, and it is widely used in dermatology research. The Monk Skin Tone scale is a newer 10-shade scale that measures skin tone rather than skin phototype, capturing more nuanced differences between the darker skin tones. While neither scale was intended for retrospective estimation using images, the inclusion of these labels is intended to enable future research into skin type and tone representation in dermatology. For example, the SCIN dataset provides an initial benchmark for the distribution of these skin types and tones in the US population.

The SCIN dataset has a high representation of women and younger individuals, likely reflecting a combination of factors. These could include differences in skin condition incidence, propensity to seek health information online, and variations in willingness to contribute to research across demographics.

Crowdsourcing method

To create the SCIN dataset, we used a novel crowdsourcing method, which we describe in the accompanying research paper co-authored with investigators at Stanford Medicine. This approach empowers individuals to play an active role in healthcare research. It allows us to reach people at earlier stages of their health concerns, potentially before they seek formal care. Crucially, this method uses advertisements on web search result pages — the starting point for many people’s health journey — to connect with participants.

Our results demonstrate that crowdsourcing can yield a high-quality dataset with a low spam rate. Over 97.5% of contributions were genuine images of skin conditions. After performing further filtering steps to exclude images that were out of scope for the SCIN dataset and to remove duplicates, we were able to release nearly 90% of the contributions received over the 8-month study period. Most images were sharp and well-exposed. Approximately half of the contributions include self-reported demographics, and 80% contain self-reported information relating to the skin condition, such as texture, duration, or other symptoms. We found that dermatologists’ ability to retrospectively assign a differential diagnosis depended more on the availability of self-reported information than on image quality.

Dermatologist confidence in their labels (scale from 1-5) depended on the availability of self-reported demographic and symptom information.

While perfect image de-identification can never be guaranteed, protecting the privacy of individuals who contributed their images was a top priority when creating the SCIN dataset. Through informed consent, contributors were made aware of potential re-identification risks and advised to avoid uploading images with identifying features. Post-submission privacy protection measures included manual redaction or cropping to exclude potentially identifying areas, reverse image searches to exclude publicly available copies and metadata removal or aggregation. The SCIN Data Use License prohibits attempts to re-identify contributors.

We hope the SCIN dataset will be a helpful resource for those working to advance inclusive dermatology research, education, and AI tool development. By demonstrating an alternative to traditional dataset creation methods, SCIN paves the way for more representative datasets in areas where self-reported data or retrospective labeling is feasible.

Acknowledgements

We are grateful to all our co-authors Abbi Ward, Jimmy Li, Julie Wang, Sriram Lakshminarasimhan, Ashley Carrick, Bilson Campana, Jay Hartford, Pradeep Kumar S, Tiya Tiyasirisokchai, Sunny Virmani, Renee Wong, Yossi Matias, Greg S. Corrado, Dale R. Webster, Dawn Siegel (Stanford Medicine), Steven Lin (Stanford Medicine), Justin Ko (Stanford Medicine), Alan Karthikesalingam and Christopher Semturs. We also thank Yetunde Ibitoye, Sami Lachgar, Lisa Lehmann, Javier Perez, Margaret Ann Smith (Stanford Medicine), Rachelle Sico, Amit Talreja, Annisah Um’rani and Wayne Westerlind for their essential contributions to this work. Finally, we are grateful to Heather Cole-Lewis, Naama Hammel, Ivor Horn, Michael Howell, Yun Liu, and Eric Teasley for their insightful comments on the study design and manuscript.

Posted by Mark Matthews, Senior Software Engineer, and Dmitry Lagun, Research Scientist, Google Research

A person’s prior experience and understanding of the world generally enables them to easily infer what an object looks like in whole, even if only looking at a few 2D pictures of it. Yet the capacity for a computer to reconstruct the shape of an object in 3D given only a few images has remained a difficult algorithmic problem for years. This fundamental computer vision task has applications ranging from the creation of e-commerce 3D models to autonomous vehicle navigation.

A key part of the problem is how to determine the exact positions from which images were taken, known as pose inference. If camera poses are known, a range of successful techniques — such as neural radiance fields (NeRF) or 3D Gaussian Splatting — can reconstruct an object in 3D. But if these poses are not available, then we face a difficult “chicken and egg” problem where we could determine the poses if we knew the 3D object, but we can’t reconstruct the 3D object until we know the camera poses. The problem is made harder by pseudo-symmetries — i.e., many objects look similar when viewed from different angles. For example, square objects like a chair tend to look similar every 90° rotation. Pseudo-symmetries of an object can be revealed by rendering it on a turntable from various angles and plotting its photometric self-similarity map.

Self-Similarity map of a toy truck model. Left: The model is rendered on a turntable from various azimuthal angles, θ. Right: The average L2 RGB similarity of a rendering from θ with that of θ*. The pseudo-similarities are indicated by the dashed red lines.

The diagram above only visualizes one dimension of rotation. It becomes even more complex (and difficult to visualize) when introducing more degrees of freedom. Pseudo-symmetries make the problem ill-posed, with naïve approaches often converging to local minima. In practice, such an approach might mistake the back view as the front view of an object, because they share a similar silhouette. Previous techniques (such as BARF or SAMURAI) side-step this problem by relying on an initial pose estimate that starts close to the global minima. But how can we approach this if those aren’t available?

Methods, such as GNeRF and VMRF leverage generative adversarial networks (GANs) to overcome the problem. These techniques have the ability to artificially “amplify” a limited number of training views, aiding reconstruction. GAN techniques, however, often have complex, sometimes unstable, training processes, making robust and reliable convergence difficult to achieve in practice. A range of other successful methods, such as SparsePose or RUST, can infer poses from a limited number views, but require pre-training on a large dataset of posed images, which aren’t always available, and can suffer from “domain-gap” issues when inferring poses for different types of images.

In “MELON: NeRF with Unposed Images in SO(3)”, spotlighted at 3DV 2024, we present a technique that can determine object-centric camera poses entirely from scratch while reconstructing the object in 3D. MELON (Modulo Equivalent Latent Optimization of NeRF) is one of the first techniques that can do this without initial pose camera estimates, complex training schemes or pre-training on labeled data. MELON is a relatively simple technique that can easily be integrated into existing NeRF methods. We demonstrate that MELON can reconstruct a NeRF from unposed images with state-of-the-art accuracy while requiring as few as 4–6 images of an object.

MELON

We leverage two key techniques to aid convergence of this ill-posed problem. The first is a very lightweight, dynamically trained convolutional neural network (CNN) encoder that regresses camera poses from training images. We pass a downscaled training image to a four layer CNN that infers the camera pose. This CNN is initialized from noise and requires no pre-training. Its capacity is so small that it forces similar looking images to similar poses, providing an implicit regularization greatly aiding convergence.

The second technique is a modulo loss that simultaneously considers pseudo symmetries of an object. We render the object from a fixed set of viewpoints for each training image, backpropagating the loss only through the view that best fits the training image. This effectively considers the plausibility of multiple views for each image. In practice, we find N=2 views (viewing an object from the other side) is all that’s required in most cases, but sometimes get better results with N=4 for square objects.

These two techniques are integrated into standard NeRF training, except that instead of fixed camera poses, poses are inferred by the CNN and duplicated by the modulo loss. Photometric gradients back-propagate through the best-fitting cameras into the CNN. We observe that cameras generally converge quickly to globally optimal poses (see animation below). After training of the neural field, MELON can synthesize novel views using standard NeRF rendering methods.

We simplify the problem by using the NeRF-Synthetic dataset, a popular benchmark for NeRF research and common in the pose-inference literature. This synthetic dataset has cameras at precisely fixed distances and a consistent “up” orientation, requiring us to infer only the polar coordinates of the camera. This is the same as an object at the center of a globe with a camera always pointing at it, moving along the surface. We then only need the latitude and longitude (2 degrees of freedom) to specify the camera pose.

MELON uses a dynamically trained lightweight CNN encoder that predicts a pose for each image. Predicted poses are replicated by the modulo loss, which only penalizes the smallest L2 distance from the ground truth color. At evaluation time, the neural field can be used to generate novel views.

Results

We compute two key metrics to evaluate MELON’s performance on the NeRF Synthetic dataset. The error in orientation between the ground truth and inferred poses can be quantified as a single angular error that we average across all training images, the pose error. We then test the accuracy of MELON’s rendered objects from novel views by measuring the peak signal-to-noise ratio (PSNR) against held out test views. We see that MELON quickly converges to the approximate poses of most cameras within the first 1,000 steps of training, and achieves a competitive PSNR of 27.5 dB after 50k steps.

Convergence of MELON on a toy truck model during optimization. Left: Rendering of the NeRF. Right: Polar plot of predicted (blue x), and ground truth (red dot) cameras.

MELON achieves similar results for other scenes in the NeRF Synthetic dataset.

Reconstruction quality comparison between ground-truth (GT) and MELON on NeRF-Synthetic scenes after 100k training steps.

Noisy images

MELON also works well when performing novel view synthesis from extremely noisy, unposed images. We add varying amounts, σ, of white Gaussian noise to the training images. For example, the object in σ=1.0 below is impossible to make out, yet MELON can determine the pose and generate novel views of the object.

Novel view synthesis from noisy unposed 128×128 images. Top: Example of noise level present in training views. Bottom: Reconstructed model from noisy training views and mean angular pose error.

This perhaps shouldn’t be too surprising, given that techniques like RawNeRF have demonstrated NeRF’s excellent de-noising capabilities with known camera poses. The fact that MELON works for noisy images of unknown camera poses so robustly was unexpected.

Conclusion

We present MELON, a technique that can determine object-centric camera poses to reconstruct objects in 3D without the need for approximate pose initializations, complex GAN training schemes or pre-training on labeled data. MELON is a relatively simple technique that can easily be integrated into existing NeRF methods. Though we only demonstrated MELON on synthetic images we are adapting our technique to work in real world conditions. See the paper and MELON site to learn more.

Acknowledgements

We would like to thank our paper co-authors Axel Levy, Matan Sela, and Gordon Wetzstein, as well as Florian Schroff and Hartwig Adam for continuous help in building this technology. We also thank Matthew Brown, Ricardo Martin-Brualla and Frederic Poitevin for their helpful feedback on the paper draft. We also acknowledge the use of the computational resources at the SLAC Shared Scientific Data Facility (SDF).