Posts in category: Google AI

Posted by Zachary Nado, Research Engineer and Dustin Tran, Research Scientist, Google Research, Brain Team

Machine learning (ML) is increasingly being used in real-world applications, so understanding the uncertainty and robustness of a model is necessary to ensure performance in practice. For example, how do models behave when deployed on data that differs from the data on which they were trained? How do models signal when they are likely to make a mistake?

To get a handle on an ML model’s behavior, its performance is often measured against a baseline for the task of interest. With each baseline, researchers must try to reproduce results only using descriptions from the corresponding papers , which results in serious challenges for replication. Having access to the code for experiments may be more useful, assuming it is well-documented and maintained. But even this is not enough, because the baselines must be rigorously validated. For example, in retrospective analyses over a collection of works [1, 2, 3], authors often find that a simple well-tuned baseline outperforms more sophisticated methods. In order to truly understand how models perform relative to each other, and enable researchers to measure whether new ideas in fact yield meaningful progress, models of interest must be compared to a common baseline.

In “Uncertainty Baselines: Benchmarks for Uncertainty & Robustness in Deep Learning”, we introduce Uncertainty Baselines, a collection of high-quality implementations of standard and state-of-the-art deep learning methods for a variety of tasks, with the goal of making research on uncertainty and robustness more reproducible. The collection spans 19 methods across nine tasks, each with at least five metrics. Each baseline is a self-contained experiment pipeline with easily reusable and extendable components and with minimal dependencies outside of the framework in which it is written. The included pipelines are implemented in TensorFlow, PyTorch, and Jax. Additionally, the hyperparameters for each baseline have been extensively tuned over numerous iterations so as to provide even stronger results.

Uncertainty Baselines
As of this writing, Uncertainty Baselines provides a total of 83 baselines, comprising 19 methods encompassing standard and more recent strategies over nine datasets. Example methods include BatchEnsemble, Deep Ensembles, Rank-1 Bayesian Neural Nets, Monte Carlo Dropout, and Spectral-normalized Neural Gaussian Processes. It acts as a successor in merging several popular benchmarks in the community: Can You Trust Your Model’s Uncertainty?, BDL benchmarks, and Edward2’s baselines.

A subset of 5 out of 9 available datasets for which baselines are provided. The datasets span tabular, text, and image modalities.

Uncertainty Baselines sets up each baseline under a choice of base model, training dataset, and a suite of evaluation metrics. Each is then tuned over its hyperparameters to maximize performance on such metrics. The available baselines vary among these three axes:

• Base models (architectures) include Wide ResNet 28-10, ResNet-50, BERT, and simple fully-connected networks.
• Training datasets include standard machine learning datasets (CIFAR, ImageNet, and UCI) as well as more real-world problems (Clinc Intent Detection, Kaggle’s Diabetic Retinopathy Detection, and Wikipedia Toxicity).
• Evaluation includes predictive metrics (e.g., accuracy), uncertainty metrics (e.g., selective prediction and calibration error), compute metrics (inference latency), and performance on in- and out-of-distribution datasets.

Modularity and Reusability
In order for researchers to use and build on the baselines, we deliberately optimized them to be as modular and minimal as possible. As seen in the workflow figure below, Uncertainty Baselines introduces no new class abstractions, instead reusing classes that pre-exist in the ecosystem (e.g., TensorFlow’s tf.data.Dataset). The train/evaluation pipeline for each of the baselines is contained in a standalone Python file for that experiment, which can run on CPU, GPU, or Google Cloud TPUs. Because of this independence between baselines, we are able to develop baselines in any of TensorFlow, PyTorch or JAX.

Workflow diagram for how the different components of Uncertainty Baselines are structured. All datasets are subclasses of the BaseDataset class, which provides a simple API for use in baselines written with any of the supported frameworks. The outputs from any of the baselines can then be analyzed with the Robustness Metrics library.

One area of debate among research engineers is how to manage hyperparameters and other experiment configuration values, which can easily number in the dozens. Instead of using one of the many frameworks built for this, and risk users having to learn yet another library, we opted to simply use Python flags, i.e., flags defined using Abseil that follow Python conventions. This should be a familiar technique to most researchers, and is easy to extend and plug into other pipelines.

Reproducibility
In addition to being able to run each of our baselines using the documented commands and get the same reported results, we also aim to release hyperparameter tuning results and final model checkpoints for further reproducibility. Right now we only have these fully open-sourced for the Diabetic Retinopathy baselines, but we will continue to upload more results as we run them. Additionally, we have examples of baselines that are exactly reproducible up to hardware determinism.

Practical Impact
Each of the baselines included in our repository has gone through extensive hyperparameter tuning, and we hope that researchers can readily reuse this effort without the need for expensive retraining or retuning. Additionally, we hope to avoid minor differences in the pipeline implementations affecting baseline comparisons.

Uncertainty Baselines has already been used in numerous research projects. If you are a researcher with other methods or datasets you would like to contribute, please open a GitHub issue to start a discussion!

Acknowledgements
We would like to thank a number of folks who are codevelopers, provided guidance, and/or helped review this post: Neil Band, Mark Collier, Josip Djolonga, Michael W. Dusenberry, Sebastian Farquhar, Angelos Filos, Marton Havasi, Rodolphe Jenatton, Ghassen Jerfel, Jeremiah Liu, Zelda Mariet, Jeremy Nixon, Shreyas Padhy, Jie Ren, Tim G. J. Rudner, Yeming Wen, Florian Wenzel, Kevin Murphy, D. Sculley, Balaji Lakshminarayanan, Jasper Snoek, Yarin Gal.

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Posted by Joel Shor, Software Engineer, Google Research and Sercan Arik, Research Scientist, Google Research, Cloud AI Team

Over the past 20 months, the COVID-19 pandemic has had a profound impact on daily life, presented logistical challenges for businesses planning for supply and demand, and created difficulties for governments and organizations working to support communities with timely public health responses. While there have been well-studied epidemiology models that can help predict COVID-19 cases and deaths to help with these challenges, this pandemic has generated an unprecedented amount of real-time publicly-available data, which makes it possible to use more advanced machine learning techniques in order to improve results.

In “A prospective evaluation of AI-augmented epidemiology to forecast COVID-19 in the USA and Japan“, accepted to npj Digital Medicine, we continued our previous work [1, 2, 3, 4] and proposed a framework designed to simulate the effect of certain policy changes on COVID-19 deaths and cases, such as school closings or a state-of-emergency at a US-state, US-county, and Japan-prefecture level, using only publicly-available data. We conducted a 2-month prospective assessment of our public forecasts, during which our US model tied or outperformed all other 33 models on COVID19 Forecast Hub. We also released a fairness analysis of the performance on protected sub-groups in the US and Japan. Like other Google initiatives to help with COVID-19 [1, 2, 3], we are releasing daily forecasts based on this work to the public for free, on the web [us, ja] and through BigQuery.

Prospective forecasts for the USA and Japan models. Ground truth cumulative deaths counts (green lines) are shown alongside the forecasts for each day. Each daily forecast contains a predicted increase in deaths for each day during the prediction window of 4 weeks (shown as colored dots, where shading shifting to yellow indicates days further from the date of prediction in the forecasting horizon, up to 4 weeks). Predictions of deaths are shown for the USA (above) and Japan (below).

The Model
Models for infectious diseases have been studied by epidemiologists for decades. Compartmental models are the most common, as they are simple, interpretable, and can fit different disease phases effectively. In compartmental models, individuals are separated into mutually exclusive groups, or compartments, based on their disease status (such as susceptible, exposed, or recovered), and the rates of change between these compartments are modeled to fit the past data. A population is assigned to compartments representing disease states, with people flowing between states as their disease status changes.

In this work, we propose a few extensions to the Susceptible-Exposed-Infectious-Removed (SEIR) type compartmental model. For example, susceptible people becoming exposed causes the susceptible compartment to decrease and the exposed compartment to increase, with a rate that depends on disease spreading characteristics. Observed data for COVID-19 associated outcomes, such as confirmed cases, hospitalizations and deaths, are used for training of compartmental models.

Visual explanation of “compartmental” models in epidemiology. People “flow” between compartments. Real-world events, like policy changes and more ICU beds, change the rate of flow between compartments.

Our framework proposes a number of novel technical innovations:

1. Learned transition rates: Instead of using static rates for transitions between compartments across all locations and times, we use machine-learned rates to map them. This allows us to take advantage of the vast amount of available data with informative signals, such as Google’s COVID-19 Community Mobility Reports, healthcare supply, demographics, and econometrics features.
2. Explainability: Our framework provides explainability for decision makers, offering insights on disease propagation trends via its compartmental structure, and suggesting which factors may be most important for driving compartmental transitions.
3. Expanded compartments: We add hospitalization, ICU, ventilator, and vaccine compartments and demonstrate efficient training despite data sparsity.
4. Information sharing across locations: As opposed to fitting to an individual location, we have a single model for all locations in a country (e.g., >3000 US counties) with distinct dynamics and characteristics, and we show the benefit of transferring information across locations.
5. Seq2seq modeling: We use a sequence-to-sequence model with a novel partial teacher forcing approach that minimizes amplified growth of errors into the future.

Forecast Accuracy
Each day, we train models to predict COVID-19 associated outcomes (primarily deaths and cases) 28 days into the future. We report the mean absolute percentage error (MAPE) for both a country-wide score and a location-level score, with both cumulative values and weekly incremental values for COVID-19 associated outcomes.

We compare our framework with alternatives for the US from the COVID19 Forecast Hub. In MAPE, our models outperform all other 33 models except one — the ensemble forecast that also includes our model’s predictions, where the difference is not statistically significant.

We also used prediction uncertainty to estimate whether a forecast is likely to be accurate. If we reject forecasts that the model considers uncertain, we can improve the accuracy of the forecasts that we do release. This is possible because our model has well-calibrated uncertainty.

Mean average percentage error (MAPE, the lower the better) decreases as we remove uncertain forecasts, increasing accuracy.

What-If Tool to Simulate Pandemic Management Policies and Strategies
In addition to understanding the most probable scenario given past data, decision makers are interested in how different decisions could affect future outcomes, for example, understanding the impact of school closures, mobility restrictions and different vaccination strategies. Our framework allows counterfactual analysis by replacing the forecasted values for selected variables with their counterfactual counterparts. The results of our simulations reinforce the risk of prematurely relaxing non-pharmaceutical interventions (NPIs) until the rapid disease spreading is reduced. Similarly, the Japan simulations show that maintaining the State of Emergency while having a high vaccination rate greatly reduces infection rates.

What-if simulations on the percent change of predicted exposed individuals assuming different non-pharmaceutical interventions (NPIs) for the prediction date of March 1, 2021 in Texas, Washington and South Carolina. Increased NPI restrictions are associated with a larger % reduction in the number of exposed people.

What-if simulations on the percent change of predicted exposed individuals assuming different vaccination rates for the prediction date of March 1, 2021 in Texas, Washington and South Carolina. Increased vaccination rate also plays a key role to reduce exposed count in these cases.

Fairness Analysis
To ensure that our models do not create or reinforce unfairly biased decision making, in alignment with our AI Principles, we performed a fairness analysis separately for forecasts in the US and Japan by quantifying whether the model’s accuracy was worse on protected sub-groups. These categories include age, gender, income, and ethnicity in the US, and age, gender, income, and country of origin in Japan. In all cases, we demonstrated no consistent pattern of errors among these groups once we controlled for the number of COVID-19 deaths and cases that occur in each subgroup.

Normalized errors by median income. The comparison between the two shows that patterns of errors don’t persist once errors are normalized by cases. Left: Normalized errors by median income for the US. Right: Normalized errors by median income for Japan.

Real-World Use Cases
In addition to quantitative analyses to measure the performance of our models, we conducted a structured survey in the US and Japan to understand how organisations were using our model forecasts. In total, seven organisations responded with the following results on the applicability of the model.

• Organization type: Academia (3), Government (2), Private industry (2)
• Main user job role: Analyst/Scientist (3), Healthcare professional (1), Statistician (2), Managerial (1)
• Location: USA (4), Japan (3)
• Predictions used: Confirmed cases (7), Death (4), Hospitalizations (4), ICU (3), Ventilator (2), Infected (2)
• Model use case: Resource allocation (2), Business planning (2), scenario planning (1), General understanding of COVID spread (1), Confirm existing forecasts (1)
• Frequency of use: Daily (1), Weekly (1), Monthly (1)
• Was the model helpful?: Yes (7)

To share a few examples, in the US, the Harvard Global Health Institute and Brown School of Public Health used the forecasts to help create COVID-19 testing targets that were used by the media to help inform the public. The US Department of Defense used the forecasts to help determine where to allocate resources, and to help take specific events into account. In Japan, the model was used to make business decisions. One large, multi-prefecture company with stores in more than 20 prefectures used the forecasts to better plan their sales forecasting, and to adjust store hours.

Limitations and next steps
Our approach has a few limitations. First, it is limited by available data, and we are only able to release daily forecasts as long as there is reliable, high-quality public data. For instance, public transportation usage could be very useful but that information is not publicly available. Second, there are limitations due to the model capacity of compartmental models as they cannot model very complex dynamics of Covid-19 disease propagation. Third, the distribution of case counts and deaths are very different between the US and Japan. For example, most of Japan’s COVID-19 cases and deaths have been concentrated in a few of its 47 prefectures, with the others experiencing low values. This means that our per-prefecture models, which are trained to perform well across all Japanese prefectures, often have to strike a delicate balance between avoiding overfitting to noise while getting supervision from these relatively COVID-19-free prefectures.

We have updated our models to take into account large changes in disease dynamics, such as the increasing number of vaccinations. We are also expanding to new engagements with city governments, hospitals, and private organizations. We hope that our public releases continue to help public and policy-makers address the challenges of the ongoing pandemic, and we hope that our method will be useful to epidemiologists and public health officials in this and future health crises.

Acknowledgements
This paper was the result of hard work from a variety of teams within Google and collaborators around the globe. We’d especially like to thank our paper co-authors from the School of Medicine at Keio University, Graduate School of Public Health at St Luke’s International University, and Graduate School of Medicine at The University of Tokyo.

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Posted by Shekoofeh Azizi, AI Resident, Google Research

In recent years, there has been increasing interest in applying deep learning to medical imaging tasks, with exciting progress in various applications like radiology, pathology and dermatology. Despite the interest, it remains challenging to develop medical imaging models, because high-quality labeled data is often scarce due to the time-consuming effort needed to annotate medical images. Given this, transfer learning is a popular paradigm for building medical imaging models. With this approach, a model is first pre-trained using supervised learning on a large labeled dataset (like ImageNet) and then the learned generic representation is fine-tuned on in-domain medical data.

Other more recent approaches that have proven successful in natural image recognition tasks, especially when labeled examples are scarce, use self-supervised contrastive pre-training, followed by supervised fine-tuning (e.g., SimCLR and MoCo). In pre-training with contrastive learning, generic representations are learned by simultaneously maximizing agreement between differently transformed views of the same image and minimizing agreement between transformed views of different images. Despite their successes, these contrastive learning methods have received limited attention in medical image analysis and their efficacy is yet to be explored.

In “Big Self-Supervised Models Advance Medical Image Classification”, to appear at the International Conference on Computer Vision (ICCV 2021), we study the effectiveness of self-supervised contrastive learning as a pre-training strategy within the domain of medical image classification. We also propose Multi-Instance Contrastive Learning (MICLe), a novel approach that generalizes contrastive learning to leverage special characteristics of medical image datasets. We conduct experiments on two distinct medical image classification tasks: dermatology condition classification from digital camera images (27 categories) and multilabel chest X-ray classification (5 categories). We observe that self-supervised learning on ImageNet, followed by additional self-supervised learning on unlabeled domain-specific medical images, significantly improves the accuracy of medical image classifiers. Specifically, we demonstrate that self-supervised pre-training outperforms supervised pre-training, even when the full ImageNet dataset (14M images and 21.8K classes) is used for supervised pre-training.

SimCLR and Multi Instance Contrastive Learning (MICLe)
Our approach consists of three steps: (1) self-supervised pre-training on unlabeled natural images (using SimCLR); (2) further self-supervised pre-training using unlabeled medical data (using either SimCLR or MICLe); followed by (3) task-specific supervised fine-tuning using labeled medical data.

Our approach comprises three steps: (1) Self-supervised pre-training on unlabeled ImageNet using SimCLR (2) Additional self-supervised pre-training using unlabeled medical images. If multiple images of each medical condition are available, a novel Multi-Instance Contrastive Learning (MICLe) strategy is used to construct more informative positive pairs based on different images. (3) Supervised fine-tuning on labeled medical images. Note that unlike step (1), steps (2) and (3) are task and dataset specific.

After the initial pre-training with SimCLR on unlabeled natural images is complete, we train the model to capture the special characteristics of medical image datasets. This, too, can be done with SimCLR, but this method constructs positive pairs only through augmentation and does not readily leverage patients’ meta data for positive pair construction. Alternatively, we use MICLe, which uses multiple images of the underlying pathology for each patient case, when available, to construct more informative positive pairs for self-supervised learning. Such multi-instance data is often available in medical imaging datasets — e.g., frontal and lateral views of mammograms, retinal fundus images from each eye, etc.

Given multiple images of a given patient case, MICLe constructs a positive pair for self-supervised contrastive learning by drawing two crops from two distinct images from the same patient case. Such images may be taken from different viewing angles and show different body parts with the same underlying pathology. This presents a great opportunity for self-supervised learning algorithms to learn representations that are robust to changes of viewpoint, imaging conditions, and other confounding factors in a direct way. MICLe does not require class label information and only relies on different images of an underlying pathology, the type of which may be unknown.

MICLe generalizes contrastive learning to leverage special characteristics of medical image datasets (patient metadata) to create realistic augmentations, yielding further performance boost of image classifiers.

Combining these self-supervised learning strategies, we show that even in a highly competitive production setting we can achieve a sizable gain of 6.7% in top-1 accuracy on dermatology skin condition classification and an improvement of 1.1% in mean AUC on chest X-ray classification, outperforming strong supervised baselines pre-trained on ImageNet (the prevailing protocol for training medical image analysis models). In addition, we show that self-supervised models are robust to distribution shift and can learn efficiently with only a small number of labeled medical images.

Comparison of Supervised and Self-Supervised Pre-training
Despite its simplicity, we observe that pre-training with MICLe consistently improves the performance of dermatology classification over the original method of pre-training with SimCLR under different pre-training dataset and base network architecture choices. Using MICLe for pre-training, translates to (1.18 ± 0.09)% increase in top-1 accuracy for dermatology classification over using SimCLR. The results demonstrate the benefit accrued from utilizing additional metadata or domain knowledge to construct more semantically meaningful augmentations for contrastive pre-training. In addition, our results suggest that wider and deeper models yield greater performance gains, with ResNet-152 (2x width) models often outperforming ResNet-50 (1x width) models or smaller counterparts.

Comparison of supervised and self-supervised pre-training, followed by supervised fine-tuning using two architectures on dermatology and chest X-ray classification. Self-supervised learning utilizes unlabeled domain-specific medical images and significantly outperforms supervised ImageNet pre-training.

Improved Generalization with Self-Supervised Models
For each task we perform pretraining and fine-tuning using the in-domain unlabeled and labeled data respectively. We also use another dataset obtained in a different clinical setting as a shifted dataset to further evaluate the robustness of our method to out-of-domain data. For the chest X-ray task, we note that self-supervised pre-training with either ImageNet or CheXpert data improves generalization, but stacking them both yields further gains. As expected, we also note that when only using ImageNet for self-supervised pre-training, the model performs worse compared to using only in-domain data for pre-training.

To test the performance under distribution shift, for each task, we held out additional labeled datasets for testing that were collected under different clinical settings. We find that the performance improvement in the distribution-shifted dataset (ChestX-ray14) by using self-supervised pre-training (both using ImageNet and CheXpert data) is more pronounced than the original improvement on the CheXpert dataset. This is a valuable finding, as generalization under distribution shift is of paramount importance to clinical applications. On the dermatology task, we observe similar trends for a separate shifted dataset that was collected in skin cancer clinics and had a higher prevalence of malignant conditions. This demonstrates that the robustness of the self-supervised representations to distribution shifts is consistent across tasks.

Evaluation of models on distribution-shifted datasets for the chest-xray interpretation task. We use the model trained on in-domain data to make predictions on an additional shifted dataset without any further fine-tuning (zero-shot transfer learning). We observe that self-supervised pre-training leads to better representations that are more robust to distribution shifts.

Evaluation of models on distribution-shifted datasets for the dermatology task. Our results generally suggest that self-supervised pre-trained models can generalize better to distribution shifts with MICLe pre-training leading to the most gains.

Improved Label Efficiency
We further investigate the label-efficiency of the self-supervised models for medical image classification by fine-tuning the models on different fractions of labeled training data. We use label fractions ranging from 10% to 90% for both Derm and CheXpert training datasets and examine how the performance varies using the different available label fractions for the dermatology task. First, we observe that pre-training using self-supervised models can compensate for low label efficiency for medical image classification, and across the sampled label fractions, self-supervised models consistently outperform the supervised baseline. These results also suggest that MICLe yields proportionally higher gains when fine-tuning with fewer labeled examples. In fact, MICLe is able to match baselines using only 20% of the training data for ResNet-50 (4x) and 30% of the training data for ResNet152 (2x).

Top-1 accuracy for dermatology condition classification for MICLe, SimCLR, and supervised models under different unlabeled pre-training datasets and varied sizes of label fractions. MICLe is able to match baselines using only 20% of the training data for ResNet-50 (4x).

Conclusion
Supervised pre-training on natural image datasets is commonly used to improve medical image classification. We investigate an alternative strategy based on self-supervised pre-training on unlabeled natural and medical images and find that it can significantly improve upon supervised pre-training, the standard paradigm for training medical image analysis models. This approach can lead to models that are more accurate and label efficient and are robust to distribution shifts. In addition, our proposed Multi-Instance Contrastive Learning method (MICLe) enables the use of additional metadata to create realistic augmentations, yielding further performance boost of image classifiers.

Self-supervised pre-training is much more scalable than supervised pre-training because class label annotation is not required. We hope this paper will help popularize the use of self-supervised approaches in medical image analysis yielding label efficient and robust models suited for clinical deployment at scale in the real world.

Acknowledgements
This work involved collaborative efforts from a multidisciplinary team of researchers, software engineers, clinicians, and cross-functional contributors across Google Health and Google Brain. We thank our co-authors: Basil Mustafa, Fiona Ryan, Zach Beaver, Jan Freyberg, Jon Deaton, Aaron Loh, Alan Karthikesalingam, Simon Kornblith, Ting Chen, Vivek Natarajan, and Mohammad Norouzi. We also thank Yuan Liu from Google Health for valuable feedback and our partners for access to the datasets used in the research.

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