Tag Archives: deep learning

DeepVariant Accuracy Improvements for Genetic Datatypes



Last December we released DeepVariant, a deep learning model that has been trained to analyze genetic sequences and accurately identify the differences, known as variants, that make us all unique. Our initial post focused on how DeepVariant approaches “variant calling” as an image classification problem, and is able to achieve greater accuracy than previous methods.

Today we are pleased to announce the launch of DeepVariant v0.6, which includes some major accuracy improvements. In this post we describe how we train DeepVariant, and how we were able to improve DeepVariant's accuracy for two common sequencing scenarios, whole exome sequencing and polymerase chain reaction sequencing, simply by adding representative data into DeepVariant's training process.

Many Types of Sequencing Data
Approaches to genomic sequencing vary depending on the type of DNA sample (e.g., from blood or saliva), how the DNA was processed (e.g., amplification techniques), which technology was used to sequence the data (e.g., instruments can vary even within the same manufacturer) and what section or how much of the genome was sequenced. These differences result in a very large number of sequencing "datatypes".

Typically, variant calling tools have been tuned for one specific datatype and perform relatively poorly on others. Given the extensive time and expertise involved in tuning variant callers for new datatypes, it seemed infeasible to customize each tool for every one. In contrast, with DeepVariant we are able to improve accuracy for new datatypes simply by including representative data in the training process, without negatively impacting overall performance.

Truth Sets for Variant Calling
Deep learning models depend on having high quality data for training and evaluation. In the field of genomics, the Genome in a Bottle (GIAB) consortium, which is hosted by the National Institute of Standards and Technology (NIST), produces human genomes for use in technology development, evaluation, and optimization. The benefit of working with GIAB benchmarking genomes is that their true sequence is known (at least to the extent currently possible). To achieve this, GIAB takes a single person's DNA and repeatedly sequences it using a wide variety of laboratory methods and sequencing technologies (i.e. many datatypes) and analyzes the resulting data using many different variant calling tools. A tremendous amount of work then follows to evaluate and adjudicate discrepancies to produce a high-confidence "truth set" for each genome.

The majority of DeepVariant’s training data is from the first benchmarking genome released by GIAB, HG001. The sample, from a woman of northern European ancestry, was made available as part of the International HapMap Project, the first large-scale effort to identify common patterns of human genetic variation. Because DNA from HG001 is commercially available and so well characterized, it is often the first sample used to test new sequencing technologies and variant calling tools. By using many replicates and different datatypes of HG001, we can generate millions of training examples which helps DeepVariant learn to accurately classify many datatypes, and even generalize to datatypes it has never seen before.

Improved Exome Model in v0.5
In the v0.5 release we formalized a benchmarking-compatible training strategy to withhold from training a complete sample, HG002, as well as any data from chromosome 20. HG002, the second benchmarking genome released by GIAB, is from a male of Ashkenazi Jewish ancestry. Testing on this sample, which differs in both sex and ethnicity from HG001, helps to ensure that DeepVariant is performing well for diverse populations. Additionally reserving chromosome 20 for testing guarantees that we can evaluate DeepVariant's accuracy for any datatype that has truth data available.

In v0.5 we also focused on exome data, which is the subset of the genome that directly codes for proteins. The exome is only ~1% of the whole human genome, so whole exome sequencing (WES) costs less than whole genome sequencing (WGS). The exome also harbors many variants of clinical significance which makes it useful for both researchers and clinicians. To increase exome accuracy we added a variety of WES datatypes, provided by DNAnexus, to DeepVariant's training data. The v0.5 WES model shows 43% fewer indel (insertion-deletion) errors and a 22% reduction in single nucleotide polymorphism (SNP) errors.
The total number of exome errors for HG002 across DeepVariant versions, broken down by indel errors (left) and SNP errors (right). Errors are either false positive (FP), colored yellow, or false negative (FN), colored blue. The largest accuracy jump is between v0.4 and v0.5, largely attributable to a reduction in indel FPs.
Improved Whole Genome Sequencing Model for PCR+ data in v0.6
Our newest release of DeepVariant, v0.6, focuses on improved accuracy for data that has undergone DNA amplification via polymerase chain reaction (PCR) prior to sequencing. PCR is an easy and inexpensive way to amplify very small quantities of DNA, and once sequenced results in what is known as PCR positive (PCR+) sequencing data. It is well known, however, that PCR can be prone to bias and errors, and non-PCR-based (or PCR-free) DNA preparation methods are increasingly common. DeepVariant's training data prior to the v0.6 release was exclusively PCR-free data, and PCR+ was one of the few datatypes for which DeepVariant had underperformed in external evaluations. By adding PCR+ examples to DeepVariant's training data, also provided by DNAnexus, we have seen significant accuracy improvements for this datatype, including a 60% reduction in indel errors.
DeepVariant v0.6 shows major accuracy improvements for PCR+ data, largely attributable to a reduction in indel errors. Here we re-analyze two PCR+ samples that were used in external evaluations, including DNAnexus on the left (see details in figure 10) and bcbio on the right, showing how indel accuracy improves with each DeepVariant version.
Independent evaluations of DeepVariant v0.6 from both DNAnexus and bcbio are also available. Their analyses support our findings of improved indel accuracy, and also include comparisons to other variant calling tools.

Looking Forward
We released DeepVariant as open source software to encourage collaboration and to accelerate the use of this technology to solve real world problems. As the pace of innovation in sequencing technologies continues to grow, including more clinical applications, we are optimistic that DeepVariant can be further extended to produce consistent and highly accurate results. We hope that researchers will use DeepVariant v0.6 to accelerate discoveries, and if there is a sequencing datatype that you would like to see us prioritize, please let us know.

An Augmented Reality Microscope for Cancer Detection



Applications of deep learning to medical disciplines including ophthalmology, dermatology, radiology, and pathology have recently shown great promise to increase both the accuracy and availability of high-quality healthcare to patients around the world. At Google, we have also published results showing that a convolutional neural network is able to detect breast cancer metastases in lymph nodes at a level of accuracy comparable to a trained pathologist. However, because direct tissue visualization using a compound light microscope remains the predominant means by which a pathologist diagnoses illness, a critical barrier to the widespread adoption of deep learning in pathology is the dependence on having a digital representation of the microscopic tissue.

Today, in a talk delivered at the Annual Meeting of the American Association for Cancer Research (AACR), with an accompanying paper “An Augmented Reality Microscope for Real-time Automated Detection of Cancer” (under review), we describe a prototype Augmented Reality Microscope (ARM) platform that we believe can possibly help accelerate and democratize the adoption of deep learning tools for pathologists around the world. The platform consists of a modified light microscope that enables real-time image analysis and presentation of the results of machine learning algorithms directly into the field of view. Importantly, the ARM can be retrofitted into existing light microscopes found in hospitals and clinics around the world using low-cost, readily-available components, and without the need for whole slide digital versions of the tissue being analyzed.
Modern computational components and deep learning models, such as those built upon TensorFlow, will allow a wide range of pre-trained models to run on this platform. As in a traditional analog microscope, the user views the sample through the eyepiece. A machine learning algorithm projects its output back into the optical path in real-time. This digital projection is visually superimposed on the original (analog) image of the specimen to assist the viewer in localizing or quantifying features of interest. Importantly, the computation and visual feedback updates quickly — our present implementation runs at approximately 10 frames per second, so the model output updates seamlessly as the user scans the tissue by moving the slide and/or changing magnification.
Left: Schematic overview of the ARM. A digital camera captures the same field of view (FoV) as the user and passes the image to an attached compute unit capable of running real-time inference of a machine learning model. The results are fed back into a custom AR display which is inline with the ocular lens and projects the model output on the same plane as the slide. Right: A picture of our prototype which has been retrofitted into a typical clinical-grade light microscope.
In principle, the ARM can provide a wide variety of visual feedback, including text, arrows, contours, heatmaps, or animations, and is capable of running many types of machine learning algorithms aimed at solving different problems such as object detection, quantification, or classification.

As a demonstration of the potential utility of the ARM, we configured it to run two different cancer detection algorithms: one that detects breast cancer metastases in lymph node specimens, and another that detects prostate cancer in prostatectomy specimens. These models can run at magnifications between 4-40x, and the result of a given model is displayed by outlining detected tumor regions with a green contour. These contours help draw the pathologist’s attention to areas of interest without obscuring the underlying tumor cell appearance.
Example view through the lens of the ARM. These images show examples of the lymph node metastasis model with 4x, 10x, 20x, and 40x microscope objectives.
While both cancer models were originally trained on images from a whole slide scanner with a significantly different optical configuration, the models performed remarkably well on the ARM with no additional re-training. For example, the lymph node metastasis model had an area-under-the-curve (AUC) of 0.98 and our prostate cancer model had an AUC of 0.96 for cancer detection in the field of view (FoV) when run on the ARM, only slightly decreased performance than obtained on WSI. We believe it is likely that the performance of these models can be further improved by additional training on digital images captured directly from the ARM itself.

We believe that the ARM has potential for a large impact on global health, particularly for the diagnosis of infectious diseases, including tuberculosis and malaria, in developing countries. Furthermore, even in hospitals that will adopt a digital pathology workflow in the near future, ARM could be used in combination with the digital workflow where scanners still face major challenges or where rapid turnaround is required (e.g. cytology, fluorescent imaging, or intra-operative frozen sections). Of course, light microscopes have proven useful in many industries other than pathology, and we believe the ARM can be adapted for a broad range of applications across healthcare, life sciences research, and material science. We’re excited to continue to explore how the ARM can help accelerate the adoption of machine learning for positive impact around the world.


Introducing Semantic Experiences with Talk to Books and Semantris



Natural language understanding has evolved substantially in the past few years, in part due to the development of word vectors that enable algorithms to learn about the relationships between words, based on examples of actual language usage. These vector models map semantically similar phrases to nearby points based on equivalence, similarity or relatedness of ideas and language. Last year, we used hierarchical vector models of language to make improvements to Smart Reply for Gmail. More recently, we’ve been exploring other applications of these methods.

Today, we are proud to share Semantic Experiences, a website showing two examples of how these new capabilities can drive applications that weren’t possible before. Talk to Books is an entirely new way to explore books by starting at the sentence level, rather than the author or topic level. Semantris is a word association game powered by machine learning, where you type out words associated with a given prompt. We have also published “Universal Sentence Encoder”, which describes the models used for these examples in more detail. Lastly, we’ve provided a pretrained semantic TensorFlow module for the community to experiment with their own sentence and phrase encoding.

Modeling approach
Our approach extends the idea of representing language in a vector space by creating vectors for larger chunks of language such as full sentences and small paragraphs. Since language is composed of hierarchies of concepts, we create the vectors using a hierarchy of modules, each of which considers features that correspond to sequences at different temporal scales. Relatedness, synonymy, antonymy, meronymy, holonymy, and many other types of relationships may all be represented in vector space language models if we train them in the right way and then pose the right “questions”. We describe this method in our paper, “Efficient Natural Language Response for Smart Reply.”

Talk to Books
With Talk to Books, we provide an entirely new way to explore books. You make a statement or ask a question, and the tool finds sentences in books that respond, with no dependence on keyword matching. In a sense you are talking to the books, getting responses which can help you determine if you’re interested in reading them or not.
Talk to Books
The models driving this experience were trained on a billion conversation-like pairs of sentences, learning to identify what a good response might look like. Once you ask your question (or make a statement), the tools searches all the sentences in over 100,000 books to find the ones that respond to your input based on semantic meaning at the sentence level; there are no predefined rules bounding the relationship between what you put in and the results you get.

This capability is unique and can help you find interesting books that a keyword search might not surface, but there’s still room for improvement. For example, this experiment works at the sentence level (rather than at the paragraph level, as in Smart Reply for Gmail) so a “good” matching sentence can still be taken out of context. You might find books and passages that you didn’t expect, or the reason a particular passage was highlighted might not be obvious. You may also notice that being well-known does not make a book sort to the top; this experiment looks only at how well the individual sentences match up. However, one benefit of this is that the tool may help people discover unexpected authors and titles, and surface books in a way that is fresh and innovative.

Semantris
We are also providing Semantris, a word association game that is powered by this technology. When you enter a word or phrase, the game ranks all of the words on-screen, scoring them based on how well they respond to what you typed. Again, similarity, opposites and neighboring concepts are all fair-game using this semantic model. Try it out yourself to see what we mean! The time pressure in the Arcade version (shown below) will tempt you to enter in single words as prompts. The Blocks version has no time pressure, which makes it a great place to try out entering in phrases and sentences. You may enjoy exploring how obscure you can be with your hints.
Semantris Arcade
The examples we’re sharing today are just a few of the possible ways to think about experience and application design using these new tools. Other potential applications include classification, semantic similarity, semantic clustering, whitelist applications (selecting the right response from many alternatives), and semantic search (of which Talk to Books is an example). We hope you’ll come up with many more, inspired by these example applications. We look forward to seeing original and innovative uses of our TensorFlow models by the developer community.

Acknowledgements
Talk to Books was developed by Aaron Phillips, Amin Ahmad, Rachel Bernstein, Aaron Cohen, Noah Constant, Ray Kurzweil, Igor Krivokon, Vladimir Magay, Peter McKenzie, Bryan Richter, Chris Tar, and Dave Uthus. Semantris was developed by Ben Pietrzak, RJ Mical, Steve Pucci, Maria Voitovich, Mo Adeleye, Diana Huang, Catherine McCurry, Tomomi Sohn, and Connor Moore. We'd also like to acknowledge Hallie Benjamin, Eric Breck, Mario Guajardo-Céspedes, Yoni Halpern, Margaret Mitchell, Ben Packer, Andrew Smart and Lucy Vasserman.

Seeing More with In Silico Labeling of Microscopy Images



In the fields of biology and medicine, microscopy allows researchers to observe details of cells and molecules which are unavailable to the naked eye. Transmitted light microscopy, where a biological sample is illuminated on one side and imaged, is relatively simple and well-tolerated by living cultures but produces images which can be difficult to properly assess. Fluorescence microscopy, in which biological objects of interest (such as cell nuclei) are specifically targeted with fluorescent molecules, simplifies analysis but requires complex sample preparation. With the increasing application of machine learning to the field of microscopy, including algorithms used to automatically assess the quality of images and assist pathologists diagnosing cancerous tissue, we wondered if we could develop a deep learning system that could combine the benefits of both microscopy techniques while minimizing the downsides.

With “In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images”, appearing today in Cell, we show that a deep neural network can predict fluorescence images from transmitted light images, generating labeled, useful, images without modifying cells and potentially enabling longitudinal studies in unmodified cells, minimally invasive cell screening for cell therapies, and investigations using large numbers of simultaneous labels. We also open sourced our network, along with the complete training and test data, a trained model checkpoint, and example code.

Background
Transmitted light microscopy techniques are easy to use, but can produce images in which it can be hard to tell what’s going on. An example is the following image from a phase-contrast microscope, in which the intensity of a pixel indicates the degree to which light was phase-shifted as it passed through the sample.
Transmitted light (phase-contrast) image of a human motor neuron culture derived from induced pluripotent stem cells. Outset 1 shows a cluster of cells, possibly neurons. Outset 2 shows a flaw in the image obscuring underlying cells. Outset 3 shows neurites. Outset 4 shows what appear to be dead cells. Scale bar is 40 μm. Source images for this and the following figures come from the Finkbeiner lab at the Gladstone Institutes.
In the above figure, it’s difficult to tell how many cells are in the cluster in Outset 1, or the locations and states of the cells in Outset 4 (hint: there’s a barely-visible flat cell in the upper-middle). It’s also difficult to get fine structures consistently in focus, such as the neurites in Outset 3.

We can get more information out of transmitted light microscopy by acquiring images in z-stacks: sets of images registered in (x, y) where z (the distance from the camera) is systematically varied. This causes different parts of the cells to come in and out of focus, which provides information about a sample’s 3D structure. Unfortunately, it often takes a trained eye to make sense of the z-stack, and analysis of such z-stacks has largely defied automation. An example z-stack is shown below.
A phase-contrast z-stack of the same cells. Note how the appearance changes as the focus is shifted. Now we can see that the fuzzy shape in the lower right of Outset 1 is a single oblong cell, and that the rightmost cell in Outset 4 is taller than the uppermost cell, possibly indicating that it has undergone programmed cell death.
In contrast, fluorescence microscopy images are easier to analyze, because samples are prepared with carefully engineered fluorescent labels which light up just what the researchers want to see. For example, most human cells have exactly one nucleus, so a nuclear label (such as the blue one below) makes it possible for simple tools to find and count cells in an image.
Fluorescence microscopy image of the same cells. The blue fluorescent label localizes to DNA, highlighting cell nuclei. The green fluorescent label localizes to a protein found only in dendrites, a neural substructure. The red fluorescent label localizes to a protein found only in axons, another neural substructure. With these labels it is much easier to understand what’s happening in the sample. For example, the green and red labels in Outset 1 confirm this is a neural cluster. The red label in Outset 3 shows that the neurites are axons, not dendrites. The upper-left blue dot in Outset 4 reveals a previously hard-to-see nucleus, and the lack of a blue dot for the cell at the left shows it to be DNA-free cellular debris.
However, fluorescence microscopy can have significant downsides. First, there is the complexity and variability introduced by the sample preparation and fluorescent labels themselves. Second, when there are many different fluorescent labels in a sample, spectral overlap can make it hard to tell which color belongs to which label, typically limiting researchers to three or four simultaneous labels in a sample. Third, fluorescence labeling may be toxic to cells and sometimes involves protocols that outright kill them, which makes labeling difficult to use in longitudinal studies where the same cells are followed through time.

Seeing more with deep learning
In our paper, we show that a deep neural network can predict fluorescence images from transmitted light z-stacks. To do this, we created a dataset of transmitted light z-stacks matched to fluorescence images and trained a neural network to predict the fluorescence images from the z-stacks. The following diagram explains the process.
Overview of our system. (A) The dataset of training examples: pairs of transmitted light images from z-stacks with pixel-registered sets of fluorescence images of the same scene. Several different fluorescent labels were used to generate fluorescence images and were varied between training examples; the checkerboard images indicate fluorescent labels which were not acquired for a given example. (B) The untrained deep network was (C) trained on the data A. (D) A z-stack of images of a novel scene. (E) The trained network, C, is used to predict fluorescence labels learned from A for each pixel in the novel images, D.
In the course of this work we developed a new neural network composed of three kinds of basic building-blocks, inspired by the modular design of Inception: an in-scale configuration which does not change the spatial scaling of the features, a down-scale configuration which doubles the spatial scaling, and an up-scale configuration which halves it. This lets us break the hard problem of network architecture design into two easier problems: the arrangement of the building-blocks (macro-architecture), and the design of the building-blocks themselves (micro-architecture). We solved the first problem using design principles discussed in the paper, and the second via an automated search powered by Google Hypertune.

To make sure our method was sound, we validated our model using data from an Alphabet lab as well as two external partners: Steve Finkbeiner's lab at the Gladstone Institutes, and the Rubin Lab at Harvard. These data spanned three transmitted light imaging modalities (bright-field, phase-contrast, and differential interference contrast) and three culture types (human motor neurons derived from induced pluripotent stem cells, rat cortical cultures, and human breast cancer cells). We found that our method can accurately predict several labels including those for nuclei, cell type (e.g. neural), and cell state (e.g. cell death). The following figure shows the model’s predictions alongside the transmitted light input and fluorescence ground-truth for our motor neuron example.
Animation showing the same cells in transmitted light and fluorescence imaging, along with predicted fluorescence labels from our model. Outset 2 shows the model predicts the correct labels despite the artifact in the input image. Outset 3 shows the model infers these processes are axons, possibly because of their distance from the nearest cells. Outset 4 shows the model sees the hard-to-see cell at the top, and correctly identifies the object at the left as DNA-free cell debris.
Try it for yourself!
We’ve open sourced our model, along with our full dataset, code for training and inference, and an example. We’re pleased to report that new labels can be learned with minimal additional training data: in the paper and example code, we show a new label may be learned from a single image. This is due to a phenomenon called transfer learning, where a model can learn a new task more quickly and using less training data if it has already mastered similar tasks.

We hope the ability to generate labeled, useful, images without modifying cells will open up completely new kinds of experiments in biology and medicine. If you’re excited to try this technology in your own work, please read the paper or check out the code!

Acknowledgements
We thank the Google Accelerated Science team for originating and developing this project and its publication, and additionally Kevin P. Murphy for supporting its publication. We thank Mike Ando, Youness Bennani, Amy Chung-Yu Chou, Jason Freidenfelds, Jason Miller, Kevin P. Murphy, Philip Nelson, Patrick Riley, and Samuel Yang for ideas and editing help with this post. This study was supported by NINDS (NS091046, NS083390, NS101995), the NIH’s National Institute on Aging (AG065151, AG058476), the NIH’s National Human Genome Research Institute (HG008105), Google, the ALS Association, and the Michael J. Fox Foundation.

Looking to Listen: Audio-Visual Speech Separation



People are remarkably good at focusing their attention on a particular person in a noisy environment, mentally “muting” all other voices and sounds. Known as the cocktail party effect, this capability comes natural to us humans. However, automatic speech separation — separating an audio signal into its individual speech sources — while a well-studied problem, remains a significant challenge for computers.

In “Looking to Listen at the Cocktail Party”, we present a deep learning audio-visual model for isolating a single speech signal from a mixture of sounds such as other voices and background noise. In this work, we are able to computationally produce videos in which speech of specific people is enhanced while all other sounds are suppressed. Our method works on ordinary videos with a single audio track, and all that is required from the user is to select the face of the person in the video they want to hear, or to have such a person be selected algorithmically based on context. We believe this capability can have a wide range of applications, from speech enhancement and recognition in videos, through video conferencing, to improved hearing aids, especially in situations where there are multiple people speaking.
A unique aspect of our technique is in combining both the auditory and visual signals of an input video to separate the speech. Intuitively, movements of a person’s mouth, for example, should correlate with the sounds produced as that person is speaking, which in turn can help identify which parts of the audio correspond to that person. The visual signal not only improves the speech separation quality significantly in cases of mixed speech (compared to speech separation using audio alone, as we demonstrate in our paper), but, importantly, it also associates the separated, clean speech tracks with the visible speakers in the video.
The input to our method is a video with one or more people speaking, where the speech of interest is interfered by other speakers and/or background noise. The output is a decomposition of the input audio track into clean speech tracks, one for each person detected in the video.
An Audio-Visual Speech Separation Model
To generate training examples, we started by gathering a large collection of 100,000 high-quality videos of lectures and talks from YouTube. From these videos, we extracted segments with a clean speech (e.g. no mixed music, audience sounds or other speakers) and with a single speaker visible in the video frames. This resulted in roughly 2000 hours of video clips, each of a single person visible to the camera and talking with no background interference. We then used this clean data to generate “synthetic cocktail parties” -- mixtures of face videos and their corresponding speech from separate video sources, along with non-speech background noise we obtained from AudioSet.

Using this data, we were able to train a multi-stream convolutional neural network-based model to split the synthetic cocktail mixture into separate audio streams for each speaker in the video. The input to the network are visual features extracted from the face thumbnails of detected speakers in each frame, and a spectrogram representation of the video’s soundtrack. During training, the network learns (separate) encodings for the visual and auditory signals, then it fuses them together to form a joint audio-visual representation. With that joint representation, the network learns to output a time-frequency mask for each speaker. The output masks are multiplied by the noisy input spectrogram and converted back to a time-domain waveform to obtain an isolated, clean speech signal for each speaker. For full details, see our paper.
Our multi-stream, neural network-based model architecture.
Here are some more speech separation and enhancement results by our method. Sound by others than the selected speakers can be entirely suppressed or suppressed to the desired level.
To highlight the utilization of visual information by our model, we took two different parts from the same video of Google’s CEO, Sundar Pichai, and placed them side by side. It is very difficult to perform speech separation in this scenario using only characteristic speech frequencies contained in the audio, however our audio-visual model manages to properly separate the speech even in this challenging case.
Application to Speech Recognition
Our method can also potentially be used as a pre-process for speech recognition and automatic video captioning. Handling overlapping speakers is a known challenge for automatic captioning systems, and separating the audio to the different sources could help in presenting more accurate and easy-to-read captions.
You can similarly see and compare the captions before and after speech separation in all the other videos in this post and on our website, by turning on closed captions in the YouTube player when playing the videos (“cc” button at the lower right corner of the player).

On our project web page you can find more results, as well as comparisons with state-of-the-art audio-only speech separation and with other recent audio-visual speech separation work.
We envision a wide range of applications for this technology. We are currently exploring opportunities for incorporating it into various Google products. Stay tuned!

Acknowledgements
The research described in this post was done by Ariel Ephrat (as an intern), Inbar Mosseri, Oran Lang, Tali Dekel, Kevin Wilson, Avinatan Hassidim, Bill Freeman and Michael Rubinstein. We would like to thank Yossi Matias and Google Research Israel for their support for the project, and John Hershey for his valuable feedback. We also thank Arkady Ziefman for his help with animations and figures, and Rachel Soh for helping us procure permissions for video content in our results.

Using Machine Learning to Discover Neural Network Optimizers



Deep learning models have been deployed in numerous Google products, such as Search, Translate and Photos. The choice of optimization method plays a major role when training deep learning models. For example, stochastic gradient descent works well in many situations, but more advanced optimizers can be faster, especially for training very deep networks. Coming up with new optimizers for neural networks, however, is challenging due to to the non-convex nature of the optimization problem. On the Google Brain team, we wanted to see if it could be possible to automate the discovery of new optimizers, in a way that is similar to how AutoML has been used to discover new competitive neural network architectures.

In “Neural Optimizer Search with Reinforcement Learning”, we present a method to discover optimization methods with a focus on deep learning architectures. Using this method we found two new optimizers, PowerSign and AddSign, that are competitive on a variety of different tasks and architectures, including ImageNet classification and Google’s neural machine translation system. To help others benefit from this work we have made the optimizers available in Tensorflow.

Neural Optimizer Search makes use of a recurrent neural network controller which is given access to a list of simple primitives that are typically relevant for optimization. These primitives include, for example, the gradient or the running average of the gradient and lead to search spaces with over 1010 possible combinations. The controller then generates the computation graph for a candidate optimizer or update rule in that search space.

In our paper, proposed candidate update rules (U) are used to train a child convolutional neural network on CIFAR10 for a few epochs and the final validation accuracy (R) is fed as a reward to the controller. The controller is trained with reinforcement learning to maximize the validation accuracies of the sampled update rules. This process is illustrated below.
An overview of Neural Optimizer Search using an iterative process to discover new optimizers.
Interestingly, the optimizers we have found are interpretable. For example, in the PowerSign optimizer we are releasing, each update compares the sign of the gradient and its running average, adjusting the step size according to whether those two values agree. The intuition behind this is that if these values agree, one is more confident in the direction of the update, and thus the step size can be larger. We also discovered a simple learning rate decay scheme, linear cosine decay, which we found can lead to faster convergence.
Graph comparing learning rate decay functions for linear cosine decay, stepwise decay and cosine decay.
Neural Optimizer Search found several optimizers that outperform commonly used optimizers on the small ConvNet model. Among the ones that transfer well to other tasks, we found that PowerSign and AddSign improve top-1 and top-5 accuracy of a state-of-the-art ImageNet mobile-sized model by up to 0.4%. They also work well on Google’s Neural Machine Translation system, giving an improvement of up to 0.7 using bilingual evaluation metrics (BLEU) on an English to German translation task.

We are excited that Neural Optimizer Search can not only improve the performance of machine learning models but also potentially lead to new, interpretable equations and discoveries. It is our hope that open sourcing these optimizers in Tensorflow will be useful to machine learning practitioners.

Expressive Speech Synthesis with Tacotron



At Google, we're excited about the recent rapid progress of neural network-based text-to-speech (TTS) research. In particular, end-to-end architectures, such as the Tacotron systems we announced last year, can both simplify voice building pipelines and produce natural-sounding speech. This will help us build better human-computer interfaces, like conversational assistants, audiobook narration, news readers, or voice design software. To deliver a truly human-like voice, however, a TTS system must learn to model prosody, the collection of expressive factors of speech, such as intonation, stress, and rhythm. Most current end-to-end systems, including Tacotron, don't explicitly model prosody, meaning they can't control exactly how the generated speech should sound. This may lead to monotonous-sounding speech, even when models are trained on very expressive datasets like audiobooks, which often contain character voices with significant variation. Today, we are excited to share two new papers that address these problems.

Our first paper, “Towards End-to-End Prosody Transfer for Expressive Speech Synthesis with Tacotron”, introduces the concept of a prosody embedding. We augment the Tacotron architecture with an additional prosody encoder that computes a low-dimensional embedding from a clip of human speech (the reference audio).
We augment Tacotron with a prosody encoder. The lower half of the image is the original Tacotron sequence-to-sequence model. For technical details, please refer to the paper.
This embedding captures characteristics of the audio that are independent of phonetic information and idiosyncratic speaker traits — these are attributes like stress, intonation, and timing. At inference time, we can use this embedding to perform prosody transfer, generating speech in the voice of a completely different speaker, but exhibiting the prosody of the reference.

Text: *Is* that Utah travel agency?
Reference prosody (Australian)
Synthesized without prosody embedding (American)
Synthesized with prosody embedding (American)

The embedding can also transfer fine time-aligned prosody from one phrase to a slightly different phrase, though this technique works best when the reference and target phrases are similar in length and structure.

Reference Text: For the first time in her life she had been danced tired.
Synthesized Text: For the last time in his life he had been handily embarrassed.
Reference prosody (American)
Synthesized without prosody embedding (American)
Synthesized with prosody embedding (American)

Excitingly, we observe prosody transfer even when the reference audio comes from a speaker whose voice is not in Tacotron's training data.

Text: I've Swallowed a Pollywog.
Reference prosody (Unseen American Speaker)
Synthesized without prosody embedding (British)
Synthesized with prosody embedding (British)

This is a promising result, as it paves the way for voice interaction designers to use their own voice to customize speech synthesis. You can listen to the full set of audio demos for “Towards End-to-End Prosody Transfer for Expressive Speech Synthesis with Tacotron” on this web page.

Despite their ability to transfer prosody with high fidelity, the embeddings from the paper above don't completely disentangle prosody from the content of a reference audio clip. (This explains why they transfer prosody best to phrases of similar structure and length.) Furthermore, they require a clip of reference audio at inference time. A natural question then arises: can we develop a model of expressive speech that alleviates these problems?

In our second paper, “Style Tokens: Unsupervised Style Modeling, Control and Transfer in End-to-End Speech Synthesis”, we do just that. Building upon the architecture in our first paper, we propose a new unsupervised method for modeling latent "factors" of speech. The key to this model is that, rather than learning fine time-aligned prosodic elements, it learns higher-level speaking style patterns that can be transferred across arbitrarily different phrases.

The model works by adding an extra attention mechanism to Tacotron, forcing it to represent the prosody embedding of any speech clip as the linear combination of a fixed set of basis embeddings. We call these embeddings Global Style Tokens (GSTs), and find that they learn text-independent variations in a speaker's style (soft, high-pitch, intense, etc.), without the need for explicit style labels.
Model architecture of Global Style Tokens. The prosody embedding is decomposed into “style tokens” to enable unsupervised style control and transfer. For technical details, please refer to the paper.
At inference time, we can select or modify the combination weights for the tokens, allowing us to force Tacotron to use a specific speaking style without needing a reference audio clip. Using GSTs, for example, we can make different sentences of varying lengths sound more "lively", "angry", "lamenting", etc:

Text: United Airlines five six three from Los Angeles to New Orleans has Landed.
Style 1
Style 2
Style 3
Style 4
Style 5
The text-independent nature of GSTs make them ideal for style transfer, which takes a reference audio clip spoken in a specific style and transfers its style to any target phrase we choose. To achieve this, we first run inference to predict the GST combination weights for an utterance whose style we want to imitate. We can then feed those combination weights to the model to synthesize completely different phrases — even those with very different lengths and structure — in the same style.

Finally, our paper shows that Global Style Tokens can model more than just speaking style. When trained on noisy YouTube audio from unlabeled speakers, a GST-enabled Tacotron learns to represent noise sources and distinct speakers as separate tokens. This means that by selecting the GSTs we use in inference, we can synthesize speech free of background noise, or speech in the voice of a specific unlabeled speaker from the dataset. This exciting result provides a path towards highly scalable but robust speech synthesis. You can listen to the full set of demos for "Style Tokens: Unsupervised Style Modeling, Control and Transfer in End-to-End Speech Synthesis" on this web page.

We are excited about the potential applications and opportunities that these two bodies of research enable. In the meantime, there are new important research problems to be addressed. We'd like to extend the techniques of the first paper to support prosody transfer in the natural pitch range of the target speaker. We'd also like to develop techniques to select appropriate prosody or speaking style automatically from context, using, for example, the integration of natural language understanding with TTS. Finally, while our first paper proposes an initial set of objective and subjective metrics for prosody transfer, we'd like to develop these further to help establish generally-accepted methods for prosodic evaluation.

Acknowledgements
These projects were done jointly between multiple Google teams. Contributors include RJ Skerry-Ryan, Yuxuan Wang, Daisy Stanton, Eric Battenberg, Ying Xiao, Joel Shor, Rif A. Saurous, Yu Zhang, Ron J. Weiss, Rob Clark, Fei Ren and Ye Jia.


Using Deep Learning to Facilitate Scientific Image Analysis



Many scientific imaging applications, especially microscopy, can produce terabytes of data per day. These applications can benefit from recent advances in computer vision and deep learning. In our work with biologists on robotic microscopy applications (e.g., to distinguish cellular phenotypes) we've learned that assembling high quality image datasets that separate signal from noise is a difficult but important task. We've also learned that there are many scientists who may not write code, but who are still excited to utilize deep learning in their image analysis work. A particular challenge we can help address involves dealing with out-of-focus images. Even with the autofocus systems on state-of-the-art microscopes, poor configuration or hardware incompatibility may result in image quality issues. Having an automated way to rate focus quality can enable the detection, troubleshooting and removal of such images.

Deep Learning to the Rescue
In “Assessing Microscope Image Focus Quality with Deep Learning”, we trained a deep neural network to rate the focus quality of microscopy images with higher accuracy than previous methods. We also integrated the pre-trained TensorFlow model with plugins in Fiji (ImageJ) and CellProfiler, two leading open source scientific image analysis tools that can be used with either a graphical user interface or invoked via scripts.
A pre-trained TensorFlow model rates focus quality for a montage of microscope image patches of cells in Fiji (ImageJ). Hue and lightness of the borders denote predicted focus quality and prediction uncertainty, respectively.
Our publication and source code (TensorFlow, Fiji, CellProfiler) illustrate the basics of a machine learning project workflow: assembling a training dataset (we synthetically defocused 384 in-focus images of cells, avoiding the need for a hand-labeled dataset), training a model using data augmentation, evaluating generalization (in our case, on unseen cell types acquired by an additional microscope) and deploying the pre-trained model. Previous tools for identifying image focus quality often require a user to manually review images for each dataset to determine a threshold between in and out-of-focus images; our pre-trained model requires no user set parameters to use, and can rate focus quality more accurately as well. To help improve interpretability, our model evaluates focus quality on 84×84 pixel patches which can be visualized with colored patch borders.

What about Images without Objects?
An interesting challenge we overcame was that there are often "blank" image patches with no objects, a scenario where no notion of focus quality exists. Instead of explicitly labeling these "blank" patches and teaching our model to recognize them as a separate category, we configured our model to predict a probability distribution across defocus levels, allowing it to learn to express uncertainty (dim borders in the figure) for these empty patches (e.g. predict equal probability in/out-of-focus).

What's Next?
Deep learning-based approaches for scientific image analysis will improve accuracy, reduce manual parameter tuning and may reveal new insights. Clearly, the sharing and availability of datasets and models, and implementation into tools that are proven to be useful within respective communities, will be important for widespread adoption.

Acknowledgements
We thank Claire McQuin, Allen Goodman, Anne Carpenter of the Broad Institute and Kevin Eliceiri of the University of Wisconsin at Madison for assistance with CellProfiler and Fiji integration, respectively.

Using Evolutionary AutoML to Discover Neural Network Architectures



The brain has evolved over a long time, from very simple worm brains 500 million years ago to a diversity of modern structures today. The human brain, for example, can accomplish a wide variety of activities, many of them effortlessly — telling whether a visual scene contains animals or buildings feels trivial to us, for example. To perform activities like these, artificial neural networks require careful design by experts over years of difficult research, and typically address one specific task, such as to find what's in a photograph, to call a genetic variant, or to help diagnose a disease. Ideally, one would want to have an automated method to generate the right architecture for any given task.

One approach to generate these architectures is through the use of evolutionary algorithms. Traditional research into neuro-evolution of topologies (e.g. Stanley and Miikkulainen 2002) has laid the foundations that allow us to apply these algorithms at scale today, and many groups are working on the subject, including OpenAI, Uber Labs, Sentient Labs and DeepMind. Of course, the Google Brain team has been thinking about AutoML too. In addition to learning-based approaches (eg. reinforcement learning), we wondered if we could use our computational resources to programmatically evolve image classifiers at unprecedented scale. Can we achieve solutions with minimal expert participation? How good can today's artificially-evolved neural networks be? We address these questions through two papers.

In “Large-Scale Evolution of Image Classifiers,” presented at ICML 2017, we set up an evolutionary process with simple building blocks and trivial initial conditions. The idea was to "sit back" and let evolution at scale do the work of constructing the architecture. Starting from very simple networks, the process found classifiers comparable to hand-designed models at the time. This was encouraging because many applications may require little user participation. For example, some users may need a better model but may not have the time to become machine learning experts. A natural question to consider next was whether a combination of hand-design and evolution could do better than either approach alone. Thus, in our more recent paper, “Regularized Evolution for Image Classifier Architecture Search” (2018), we participated in the process by providing sophisticated building blocks and good initial conditions (discussed below). Moreover, we scaled up computation using Google's new TPUv2 chips. This combination of modern hardware, expert knowledge, and evolution worked together to produce state-of-the-art models on CIFAR-10 and ImageNet, two popular benchmarks for image classification.

A Simple Approach
The following is an example of an experiment from our first paper. In the figure below, each dot is a neural network trained on the CIFAR-10 dataset, which is commonly used to train image classifiers. Initially, the population consists of one thousand identical simple seed models (no hidden layers). Starting from simple seed models is important — if we had started from a high-quality model with initial conditions containing expert knowledge, it would have been easier to get a high-quality model in the end. Once seeded with the simple models, the process advances in steps. At each step, a pair of neural networks is chosen at random. The network with higher accuracy is selected as a parent and is copied and mutated to generate a child that is then added to the population, while the other neural network dies out. All other networks remain unchanged during the step. With the application of many such steps in succession, the population evolves.
Progress of an evolution experiment. Each dot represents an individual in the population. The four diagrams show examples of discovered architectures. These correspond to the best individual (rightmost; selected by validation accuracy) and three of its ancestors.
The mutations in our first paper are purposefully simple: remove a convolution at random, add a skip connection between arbitrary layers, or change the learning rate, to name a few. This way, the results show the potential of the evolutionary algorithm, as opposed to the quality of the search space. For example, if we had used a single mutation that transforms one of the seed networks into an Inception-ResNet classifier in one step, we would be incorrectly concluding that the algorithm found a good answer. Yet, in that case, all we would have done is hard-coded the final answer into a complex mutation, rigging the outcome. If instead we stick with simple mutations, this cannot happen and evolution is truly doing the job. In the experiment in the figure, simple mutations and the selection process cause the networks to improve over time and reach high test accuracies, even though the test set had never been seen during the process. In this paper, the networks can also inherit their parent's weights. Thus, in addition to evolving the architecture, the population trains its networks while exploring the search space of initial conditions and learning-rate schedules. As a result, the process yields fully trained models with optimized hyperparameters. No expert input is needed after the experiment starts.

In all the above, even though we were minimizing the researcher's participation by having simple initial architectures and intuitive mutations, a good amount of expert knowledge went into the building blocks those architectures were made of. These included important inventions such as convolutions, ReLUs and batch-normalization layers. We were evolving an architecture made up of these components. The term "architecture" is not accidental: this is analogous to constructing a house with high-quality bricks.

Combining Evolution and Hand Design
After our first paper, we wanted to reduce the search space to something more manageable by giving the algorithm fewer choices to explore. Using our architectural analogy, we removed all the possible ways of making large-scale errors, such as putting the wall above the roof, from the search space. Similarly with neural network architecture searches, by fixing the large-scale structure of the network, we can help the algorithm out. So how to do this? The inception-like modules introduced in Zoph et al. (2017) for the purpose of architecture search proved very powerful. Their idea is to have a deep stack of repeated modules called cells. The stack is fixed but the architecture of the individual modules can change.
The building blocks introduced in Zoph et al. (2017). The diagram on the left is the outer structure of the full neural network, which parses the input data from bottom to top through a stack of repeated cells. The diagram on the right is the inside structure of a cell. The goal is to find a cell that yields an accurate network.
In our second paper, “Regularized Evolution for Image Classifier Architecture Search” (2018), we presented the results of applying evolutionary algorithms to the search space described above. The mutations modify the cell by randomly reconnecting the inputs (the arrows on the right diagram in the figure) or randomly replacing the operations (for example, they can replace the "max 3x3" in the figure, a max-pool operation, with an arbitrary alternative). These mutations are still relatively simple, but the initial conditions are not: the population is now initialized with models that must conform to the outer stack of cells, which was designed by an expert. Even though the cells in these seed models are random, we are no longer starting from simple models, which makes it easier to get to high-quality models in the end. If the evolutionary algorithm is contributing meaningfully, the final networks should be significantly better than the networks we already know can be constructed within this search space. Our paper shows that evolution can indeed find state-of-the-art models that either match or outperform hand-designs.

A Controlled Comparison
Even though the mutation/selection evolutionary process is not complicated, maybe an even more straightforward approach (like random search) could have done the same. Other alternatives, though not simpler, also exist in the literature (like reinforcement learning). Because of this, the main purpose of our second paper was to provide a controlled comparison between techniques.
Comparison between evolution, reinforcement learning, and random search for the purposes of architecture search. These experiments were done on the CIFAR-10 dataset, under the same conditions as Zoph et al. (2017), where the search space was originally used with reinforcement learning.
The figure above compares evolution, reinforcement learning, and random search. On the left, each curve represents the progress of an experiment, showing that evolution is faster than reinforcement learning in the earlier stages of the search. This is significant because with less compute power available, the experiments may have to stop early. Moreover evolution is quite robust to changes in the dataset or search space. Overall, the goal of this controlled comparison is to provide the research community with the results of a computationally expensive experiment. In doing so, it is our hope to facilitate architecture searches for everyone by providing a case study of the relationship between the different search algorithms. Note, for example, that the figure above shows that the final models obtained with evolution can reach very high accuracy while using fewer floating-point operations.

One important feature of the evolutionary algorithm we used in our second paper is a form of regularization: instead of letting the worst neural networks die, we remove the oldest ones — regardless of how good they are. This improves robustness to changes in the task being optimized and tends to produce more accurate networks in the end. One reason for this may be that since we didn't allow weight inheritance, all networks must train from scratch. Therefore, this form of regularization selects for networks that remain good when they are re-trained. In other words, because a model can be more accurate just by chance — noise in the training process means even identical architectures may get different accuracy values — only architectures that remain accurate through the generations will survive in the long run, leading to the selection of networks that retrain well. More details of this conjecture can be found in the paper.

The state-of-the-art models we evolved are nicknamed AmoebaNets, and are one of the latest results from our AutoML efforts. All these experiments took a lot of computation — we used hundreds of GPUs/TPUs for days. Much like a single modern computer can outperform thousands of decades-old machines, we hope that in the future these experiments will become household. Here we aimed to provide a glimpse into that future.

Acknowledgements
We would like to thank Alok Aggarwal, Yanping Huang, Andrew Selle, Sherry Moore, Saurabh Saxena, Yutaka Leon Suematsu, Jie Tan, Alex Kurakin, Quoc Le, Barret Zoph, Jon Shlens, Vijay Vasudevan, Vincent Vanhoucke, Megan Kacholia, Jeff Dean, and the rest of the Google Brain team for the collaborations that made this work possible.

Semantic Image Segmentation with DeepLab in Tensorflow



Semantic image segmentation, the task of assigning a semantic label, such as “road”, “sky”, “person”, “dog”, to every pixel in an image enables numerous new applications, such as the synthetic shallow depth-of-field effect shipped in the portrait mode of the Pixel 2 and Pixel 2 XL smartphones and mobile real-time video segmentation. Assigning these semantic labels requires pinpointing the outline of objects, and thus imposes much stricter localization accuracy requirements than other visual entity recognition tasks such as image-level classification or bounding box-level detection.
Today, we are excited to announce the open source release of our latest and best performing semantic image segmentation model, DeepLab-v3+ [1], implemented in Tensorflow. This release includes DeepLab-v3+ models built on top of a powerful convolutional neural network (CNN) backbone architecture [2, 3] for the most accurate results, intended for server-side deployment. As part of this release, we are additionally sharing our Tensorflow model training and evaluation code, as well as models already pre-trained on the Pascal VOC 2012 and Cityscapes benchmark semantic segmentation tasks.

Since the first incarnation of our DeepLab model [4] three years ago, improved CNN feature extractors, better object scale modeling, careful assimilation of contextual information, improved training procedures, and increasingly powerful hardware and software have led to improvements with DeepLab-v2 [5] and DeepLab-v3 [6]. With DeepLab-v3+, we extend DeepLab-v3 by adding a simple yet effective decoder module to refine the segmentation results especially along object boundaries. We further apply the depthwise separable convolution to both atrous spatial pyramid pooling [5, 6] and decoder modules, resulting in a faster and stronger encoder-decoder network for semantic segmentation.
Modern semantic image segmentation systems built on top of convolutional neural networks (CNNs) have reached accuracy levels that were hard to imagine even five years ago, thanks to advances in methods, hardware, and datasets. We hope that publicly sharing our system with the community will make it easier for other groups in academia and industry to reproduce and further improve upon state-of-art systems, train models on new datasets, and envision new applications for this technology.

Acknowledgements
We would like to thank the support and valuable discussions with Iasonas Kokkinos, Kevin Murphy, Alan L. Yuille (co-authors of DeepLab-v1 and -v2), as well as Mark Sandler, Andrew Howard, Menglong Zhu, Chen Sun, Derek Chow, Andre Araujo, Haozhi Qi, Jifeng Dai, and the Google Mobile Vision team.

References
  1. Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation, Liang-Chieh Chen, Yukun Zhu, George Papandreou, Florian Schroff, and Hartwig Adam, arXiv: 1802.02611, 2018.
  2. Xception: Deep Learning with Depthwise Separable Convolutions, François Chollet, Proc. of CVPR, 2017.
  3. Deformable Convolutional Networks — COCO Detection and Segmentation Challenge 2017 Entry, Haozhi Qi, Zheng Zhang, Bin Xiao, Han Hu, Bowen Cheng, Yichen Wei, and Jifeng Dai, ICCV COCO Challenge Workshop, 2017.
  4. Semantic Image Segmentation with Deep Convolutional Nets and Fully Connected CRFs, Liang-Chieh Chen, George Papandreou, Iasonas Kokkinos, Kevin Murphy, and Alan L. Yuille, Proc. of ICLR, 2015.
  5. Deeplab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs, Liang-Chieh Chen, George Papandreou, Iasonas Kokkinos, Kevin Murphy, and Alan L. Yuille, TPAMI, 2017.
  6. Rethinking Atrous Convolution for Semantic Image Segmentation, Liang-Chieh Chen, George Papandreou, Florian Schroff, and Hartwig Adam, arXiv:1706.05587, 2017.