Tag Archives: deep learning

Improving Connectomics by an Order of Magnitude



The field of connectomics aims to comprehensively map the structure of the neuronal networks that are found in the nervous system, in order to better understand how the brain works. This process requires imaging brain tissue in 3D at nanometer resolution (typically using electron microscopy), and then analyzing the resulting image data to trace the brain’s neurites and identify individual synaptic connections. Due to the high resolution of the imaging, even a cubic millimeter of brain tissue can generate over 1,000 terabytes of data! When combined with the fact that the structures in these images can be extraordinarily subtle and complex, the primary bottleneck in brain mapping has been automating the interpretation of these data, rather than acquisition of the data itself.

Today, in collaboration with colleagues at the Max Planck Institute of Neurobiology, we published “High-Precision Automated Reconstruction of Neurons with Flood-Filling Networks” in Nature Methods, which shows how a new type of recurrent neural network can improve the accuracy of automated interpretation of connectomics data by an order of magnitude over previous deep learning techniques. An open-access version of this work is also available from biorXiv (2017).

3D Image Segmentation with Flood-Filling Networks
Tracing neurites in large-scale electron microscopy data is an example of an image segmentation problem. Traditional algorithms have divided the process into at least two steps: finding boundaries between neurites using an edge detector or a machine-learning classifier, and then grouping together image pixels that are not separated by a boundary using an algorithm like watershed or graph cut. In 2015, we began experimenting with an alternative approach based on recurrent neural networks that unifies these two steps. The algorithm is seeded at a specific pixel location and then iteratively “fills” a region using a recurrent convolutional neural network that predicts which pixels are part of the same object as the seed. Since 2015, we have been working to apply this new approach to large-scale connectomics datasets and rigorously quantify its accuracy.
A flood-filling network segmenting an object in 2d. The yellow dot is the center of the current area of focus; the algorithm expands the segmented region (blue) as it iteratively examines more of the overall image.
Measuring Accuracy via Expected Run Length
Working with our partners at the Max Planck Institute, we devised a metric we call “expected run length” (ERL) that measures the following: given a random point within a random neuron in a 3d image of a brain, how far can we trace the neuron before making some kind of mistake? This is an example of a mean-time-between-failure metric, except that in this case we measure the amount of space between failures rather than the amount of time. For engineers, the appeal of ERL is that it relates a linear, physical path length to the frequency of individual mistakes that are made by an algorithm, and that it can be computed in a straightforward way. For biologists, the appeal is that a particular numerical value of ERL can be related to biologically relevant quantities, such as the average path length of neurons in different parts of the nervous system.
Progress in expected run length (blue line) leading up to the results shared today in Nature Methods. The red line shows progress in the “merge rate,” which measures the frequency with which two separate neurites were erroneously traced as a single object; achieving a very low merge rate is important for enabling efficient strategies for manual identification and correction of the remaining errors in the reconstruction.
Songbird Connectomics
We used ERL to measure our progress on a ground-truth set of neurons within a 1-million cubic micron zebra finch song-bird brain imaged by our collaborators using serial block-face scanning electron microscopy and found that our approach performed much better than previous deep learning pipelines applied to the same dataset.
Our algorithm in action as it traces a single neurite in 3d in a songbird brain.
We segmented every neuron in a small portion of a zebra finch song-bird brain using the new flood-filling network approach, as depicted here:
Reconstruction of a portion of zebra finch brain. Colors denote distinct objects in the segmentation that was automatically generated using a flood-filling network. Gold spheres represent synaptic locations automatically identified using a previously published approach.
By combining these automated results with a small amount of additional human effort required to fix the remaining errors, our collaborators at the Max Planck Institute are now able to study the songbird connectome to derive new insights into how zebra finch birds sing their song and test theories related to how they learn their song.

Next Steps
We will continue to improve connectomics reconstruction technology, with the aim of fully automating synapse-resolution connectomics and contributing to ongoing connectomics projects at the Max Planck Institute and elsewhere. In order to help support the larger research community in developing connectomics techniques, we have also open-sourced the TensorFlow code for the flood-filling network approach, along with WebGL visualization software for 3d datasets that we developed to help us understand and improve our reconstruction results.

Acknowledgements
We would like to acknowledge core contributions from Tim Blakely, Peter Li, Larry Lindsey, Jeremy Maitin-Shepard, Art Pope and Mike Tyka (Google), as well as Joergen Kornfeld and Winfried Denk (Max Planck Institute).

Source: Google AI Blog


Automating Drug Discoveries Using Computer Vision



“Every time you miss a protein crystal, because they are so rare, you risk missing on an important biomedical discovery.”
- Patrick Charbonneau, Duke University Dept. of Chemistry and Lead Researcher, MARCO initiative.

Protein crystallization is a key step to biomedical research concerned with discovering the structure of complex biomolecules. Because that structure determines the molecule’s function, it helps scientists design new drugs that are specifically targeted to that function. However, protein crystals are rare and difficult to find. Hundreds of experiments are typically run for each protein, and while the setup and imaging are mostly automated, finding individual protein crystals remains largely performed through visual inspection and thus prone to human error. Critically, missing these structures can result in lost opportunity for important biomedical discoveries for advancing the state of medicine.

In collaboration with researchers from the MAchine Recognition of Crystallization Outcomes (MARCO) initiative, we have published “Classification of Crystallization Outcomes using Deep Convolutional Neural Networks” in PLOS One (ArXiv preprint), in which we discuss how we used some of the most recent architectures of deep convolutional networks and customized them to achieve an accuracy of more than 94% on the visual recognition task of identifying protein crystals. In order to spur further research in this area, we have made the data freely accessible, and open-sourced our model as part of the TensorFlow research model repository, and available to researchers as a Cloud ML Engine endpoint.
Image of protein crystal, courtesy of the MARCO repository (CC-BY-4.0 license)
The MARCO initiative is a joint project between several pharmaceutical companies and academic research centers to pool and host a large repository of curated crystallography images, and make them available to the community to help develop better image analysis tools. When a member of the initiative reached out to Google with a well-defined problem, and half a million labelled images, we embraced the challenge of trying to apply the recent advances in deep learning to the problem.

Due to the large variability between imaging technologies and data acquisition approaches, coming up with a single approach to the visual recognition problem may appear daunting. Crystals can be very small, which makes them rare structures in a large image containing otherwise undifferentiated visual clutter.
Samples from the MARCO repository, illustrating the degree of variability between data sources.
Fortunately, given sufficient training data, modern deep convolutional networks are well suited to handle extreme variability in visual appearance. We modified the basic Inception V3 model to handle larger images while still being able to be trained quickly. The model achieves a level of precision and recall that makes its use practical in automated assessment pipelines.

This work is a great example of the effectiveness of multi-institutional collaborations aimed at solving problems that require data in amounts and level of diversity that no single collaborator has access to. We invite researchers to take advantage of these resources that are the result of this work and share what they learn. This research was conducted as a personal 20% project by the author. To learn more about this work, please see our paper here and read the recent Duke Research Blog post.

Source: Google AI Blog


Scalable Deep Reinforcement Learning for Robotic Manipulation



How can robots acquire skills that generalize effectively to diverse, real-world objects and situations? While designing robotic systems that effectively perform repetitive tasks in controlled environments, like building products on an assembly line, is fairly routine, designing robots that can observe their surroundings and decide the best course of action while reacting to unexpected outcomes is exceptionally difficult. However, there are two tools that can help robots acquire such skills from experience: deep learning, which is excellent at handling unstructured real-world scenarios, and reinforcement learning, which enables longer-term reasoning while exhibiting more complex and robust sequential decision making. Combining these two techniques has the potential to enable robots to learn continuously from their experience, allowing them to master basic sensorimotor skills using data rather than manual engineering.

Designing reinforcement learning algorithms for robot learning introduces its own set of challenges: real-world objects span a wide variety of visual and physical properties, subtle differences in contact forces can make predicting object motion difficult and objects of interest can be obstructed from view. Furthermore, robotic sensors are inherently noisy, adding to the complexity. All of these factors makes it incredibly difficult to learn a general solution, unless there is enough variety in the training data, which takes time to collect. This motivates exploring learning algorithms that can effectively reuse past experience, similar to our previous work on grasping which benefited from large datasets. However, this previous work could not reason about the long-term consequences of its actions, which is important for learning how to grasp. For example, if multiple objects are clumped together, pushing one of them apart (called “singulation”) will make the grasp easier, even if doing so does not directly result in a successful grasp.
Examples of singulation.

To be more efficient, we need to use off-policy reinforcement learning, which can learn from data that was collected hours, days, or weeks ago. To design such an off-policy reinforcement learning algorithm that can benefit from large amounts of diverse experience from past interactions, we combined large-scale distributed optimization with a new fitted deep Q-learning algorithm that we call QT-Opt. A preprint is available on arXiv.

QT-Opt is a distributed Q-learning algorithm that supports continuous action spaces, making it well-suited to robotics problems. To use QT-Opt, we first train a model entirely offline, using whatever data we’ve already collected. This doesn’t require running the real robot, making it easier to scale. We then deploy and finetune that model on the real robot, further training it on newly collected data. As we run QT-Opt, we accumulate more offline data, letting us train better models, which lets us collect better data, and so on.

To apply this approach to robotic grasping, we used 7 real-world robots, which ran for 800 total robot hours over the course of 4 months. To bootstrap collection, we started with a hand-designed policy that succeeded 15-30% of the time. Data collection switched to the learned model when it started performing better. The policy takes a camera image and returns how the arm and gripper should move. The offline data contained grasps on over 1000 different objects.
Some of the training objects used.
In the past, we’ve seen that sharing experience across robots can accelerate learning. We scaled this training and data gathering process to ten GPUs, seven robots, and many CPUs, allowing us to collect and process a large dataset of over 580,000 grasp attempts. At the end of this process, we successfully trained a grasping policy that runs on a real world robot and generalizes to a diverse set of challenging objects that were not seen at training time.
Seven robots collecting grasp data.
Quantitatively, the QT-Opt approach succeeded in 96% of the grasp attempts across 700 trial grasps on previously unseen objects. Compared to our previous supervised-learning based grasping approach, which had a 78% success rate, our method reduced the error rate by more than a factor of five.
The objects used at evaluation time. To make the task challenging, we aimed for a large variety of object sizes, textures, and shapes.

Notably, the policy exhibits a variety of closed-loop, reactive behaviors that are often not found in standard robotic grasping systems:
  • When presented with a set of interlocking blocks that cannot be picked up together, the policy separates one of the blocks from the rest before picking it up.
  • When presented with a difficult-to-grasp object, the policy figures out it should reposition the gripper and regrasp it until it has a firm hold.
  • When grasping in clutter, the policy probes different objects until the fingers hold one of them firmly, before lifting.
  • When we perturbed the robot by intentionally swatting the object out of the gripper -- something it had not seen during training -- it automatically repositioned the gripper for another attempt.
Crucially, none of these behaviors were engineered manually. They emerged automatically from self-supervised training with QT-Opt, because they improve the model’s long-term grasp success.
Examples of the learned behaviors. In the left GIF, the policy corrects for the moved ball. In the right GIF, the policy tries several grasps until it succeeds at picking up the tricky object.

Additionally, we’ve found that QT-Opt reaches this higher success rate using less training data, albeit with taking longer to converge. This is especially exciting for robotics, where the bottleneck is usually collecting real robot data, rather than training time. Combining this with other data efficiency techniques (such as our prior work on domain adaptation for grasping) could open several interesting avenues in robotics. We’re also interested in combining QT-Opt with recent work on learning how to self-calibrate, which could further improve the generality.

Overall, the QT-Opt algorithm is a general reinforcement learning approach that’s giving us good results on real world robots. Besides the reward definition, nothing about QT-Opt is specific to robot grasping. We see this as a strong step towards more general robot learning algorithms, and are excited to see what other robotics tasks we can apply it to. You can learn more about this work in the short video below.
Acknowledgements
This research was conducted by Dmitry Kalashnikov, Alex Irpan, Peter Pastor, Julian Ibarz, Alexander Herzog, Eric Jang, Deirdre Quillen, Ethan Holly, Mrinal Kalakrishnan, Vincent Vanhoucke, and Sergey Levine. We’d also like to give special thanks to Iñaki Gonzalo and John-Michael Burke for overseeing the robot operations, Chelsea Finn, Timothy Lillicrap, and Arun Nair for valuable discussions, and other people at Google and X who’ve contributed their expertise and time towards this research. A preprint is available on arXiv.

Source: Google AI Blog


Teaching Uncalibrated Robots to Visually Self-Adapt



People are remarkably proficient at manipulating objects without needing to adjust their viewpoint to a fixed or specific pose. This capability (referred to as visual motor integration) is learned during childhood from manipulating objects in various situations, and governed by a self-adaptation and mistake correction mechanism that uses rich sensory cues and vision as feedback. However, this capability is quite difficult for vision-based controllers in robotics, which until now have been built on a rigid setup for reading visual input data from a fixed mounted camera which should not be moved or repositioned at train and test time. The ability to quickly acquire visual motor control skills under large viewpoint variation would have substantial implications for autonomous robotic systems — for example, this capability would be particularly desirable for robots that can help rescue efforts in emergency or disaster zones.

In “Sim2Real Viewpoint Invariant Visual Servoing by Recurrent Control” presented at CVPR 2018 this week, we study a novel deep network architecture (consisting of two fully convolutional networks and a long short-term memory unit) that learns from a past history of actions and observations to self-calibrate. Using diverse simulated data consisting of demonstrated trajectories and reinforcement learning objectives, our visually-adaptive network is able to control a robotic arm to reach a diverse set of visually-indicated goals, from various viewpoints and independent of camera calibration.
Viewpoint invariant manipulation for visually indicated goal reaching with a physical robotic arm. We learn a single policy that can reach diverse goals from sensory input captured from drastically different camera viewpoints. First row shows the visually indicated goals.

The Challenge
Discovering how the controllable degrees of freedom (DoF) affect visual motion can be ambiguous and underspecified from a single image captured from an unknown viewpoint. Identifying the effect of actions on image-space motion and successfully performing the desired task requires a robust perception system augmented with the ability to maintain a memory of past actions. To be able to tackle this challenging problem, we had to address the following essential questions:
  • How can we make it feasible to provide the right amount of experience for the robot to learn the self-adaptation behavior based on pure visual observations that simulate a lifelong learning paradigm?
  • How can we design a model that integrates robust perception and self-adaptive control such that it can quickly transfer to unseen environments?
To do so, we devised a new manipulation task where a seven-DoF robot arm is provided with an image of an object and is directed to reach that particular goal amongst a set of distractor objects, while viewpoints change drastically from one trial to another. In doing so, we were able to simulate both the learning of complex behaviors and the transfer to unseen environments.
Visually indicated goal reaching task with a physical robotic arm and diverse camera viewpoints.
Harnessing Simulation to Learn Complex Behaviors
Collecting robot experience data is difficult and time-consuming. In a previous post, we showed how to scale up learning skills by distributing the data collection and trials to multiple robots. Although this approach expedited learning, it is still not feasibly extendable to learning complex behaviors such as visual self-calibration, where we need to expose robots to a huge space of various viewpoints. Instead, we opt to learn such complex behavior in simulation where we can collect unlimited robot trials and easily move the camera to various random viewpoints. In addition to fast data collection in simulation, we can also surpass hardware limitations requiring the installation of multiple cameras around a robot.
We use domain randomization technique to learn generalizable policies in simulation.
To learn visually robust features to transfer to unseen environments, we used a technique known as domain randomization (a.k.a. simulation randomization) introduced by Sadeghi & Levine (2017), that enables robots to learn vision-based policies entirely in simulation such that they can generalize to the real world. This technique was shown to work well for various robotic tasks such as indoor navigation, object localization, pick and placing, etc. In addition, to learn complex behaviors like self-calibration, we harnessed the simulation capabilities to generate synthetic demonstrations and combined reinforcement learning objectives to learn a robust controller for the robotic arm.
Viewpoint invariant manipulation for visually indicated goal reaching with a simulated seven-DoF robotic arm. We learn a single policy that can reach diverse goals from sensory input captured from dramatically different camera viewpoints.

Disentangling Perception from Control
To enable fast transfer to unseen environments, we devised a deep neural network that combines perception and control trained end-to-end simultaneously, while also allowing each to be learned independently if needed. This disentanglement between perception and control eases transfer to unseen environments, and makes the model both flexible and efficient in that each of its parts (i.e. 'perception' or 'control') can be independently adapted to new environments with small amounts of data. Additionally, while the control portion of the network was entirely trained by the simulated data, the perception part of our network was complemented by collecting a small amount of static images with object bounding boxes without needing to collect the whole action sequence trajectory with a physical robot. In practice, we fine-tuned the perception part of our network with only 76 object bounding boxes coming from 22 images.
Real-world robot and moving camera setup. First row shows the scene arrangements and the second row shows the visual sensory input to the robot.
Early Results
We tested the visually-adapted version of our network on a physical robot and on real objects with drastically different appearances than the ones used in simulation. Experiments were performed with both one or two objects on a table — “seen objects” (as labeled in the figure below) were used for visual adaptation using small collection of real static images, while “unseen objects” had not been seen during visual adaptation. During the test, the robot arm was directed to reach a visually indicated object from various viewpoints. For the two object experiments the second object was to "fool" the robotic arm. While the simulation-only network has good generalization capability (due to being trained with domain randomization technique), the very small amount of static visual data to visually adapt the controller boosted the performance, due to the flexible architecture of our network.
After adapting the visual features with the small amount of real images, performance was boosted by more than 10%. All used real objects are drastically different from the objects seen in simulation.
We believe that learning online visual self-adaptation is an important and yet challenging problem with the goal of learning generalizable policies for robots that can act in diverse and unstructured real world setup. Our approach can be extended to any sort of automatic self-calibration. See the video below for more information on this work.
Acknowledgements
This research was conducted by Fereshteh Sadeghi, Alexander Toshev, Eric Jang and Sergey Levine. We would also like to thank Erwin Coumans and Yunfei Bai for providing pybullet, and Vincent Vanhoucke for insightful discussions.




Source: Google AI Blog


Advances in Semantic Textual Similarity



The recent rapid progress of neural network-based natural language understanding research, especially on learning semantic text representations, can enable truly novel products such as Smart Compose and Talk to Books. It can also help improve performance on a variety of natural language tasks which have limited amounts of training data, such as building strong text classifiers from as few as 100 labeled examples.

Below, we discuss two papers reporting recent progress on semantic representation research at Google, as well as two new models available for download on TensorFlow Hub that we hope developers will use to build new and exciting applications.

Semantic Textual Similarity
In “Learning Semantic Textual Similarity from Conversations”, we introduce a new way to learn sentence representations for semantic textual similarity. The intuition is that sentences are semantically similar if they have a similar distribution of responses. For example, “How old are you?” and “What is your age?” are both questions about age, which can be answered by similar responses such as “I am 20 years old”. In contrast, while “How are you?” and “How old are you?” contain almost identical words, they have very different meanings and lead to different responses.
Sentences are semantically similar if they can be answered by the same responses. Otherwise, they are semantically different.
In this work, we aim to learn semantic similarity by way of a response classification task: given a conversational input, we wish to classify the correct response from a batch of randomly selected responses. But, the ultimate goal is to learn a model that can return encodings representing a variety of natural language relationships, including similarity and relatedness. By adding another prediction task (In this case, the SNLI entailment dataset) and forcing both through shared encoding layers, we get even better performance on similarity measures such as the STSBenchmark (a sentence similarity benchmark) and CQA task B (a question/question similarity task). This is because logical entailment is quite different from simple equivalence and provides more signal for learning complex semantic representations.
For a given input, classification is considered a ranking problem against potential candidates.
Universal Sentence Encoder
In “Universal Sentence Encoder”, we introduce a model that extends the multitask training described above by adding more tasks, jointly training them with a skip-thought-like model that predicts sentences surrounding a given selection of text. However, instead of the encoder-decoder architecture in the original skip-thought model, we make use of an encode-only architecture by way of a shared encoder to drive the prediction tasks. In this way, training time is greatly reduced while preserving the performance on a variety of transfer tasks including sentiment and semantic similarity classification. The aim is to provide a single encoder that can support as wide a variety of applications as possible, including paraphrase detection, relatedness, clustering and custom text classification.
Pairwise semantic similarity comparison via outputs from TensorFlow Hub Universal Sentence Encoder.
As described in our paper, one version of the Universal Sentence Encoder model uses a deep average network (DAN) encoder, while a second version uses a more complicated self attended network architecture, Transformer.
Multi-task training as described in “Universal Sentence Encoder”. A variety of tasks and task structures are joined by shared encoder layers/parameters (grey boxes).
With the more complicated architecture, the model performs better than the simpler DAN model on a variety of sentiment and similarity classification tasks, and for short sentences is only moderately slower. However, compute time for the model using Transformer increases noticeably as sentence length increases, whereas the compute time for the DAN model stays nearly constant as sentence length is increased.

New Models
In addition to the Universal Sentence Encoder model described above, we are also sharing two new models on TensorFlow Hub: the Universal Sentence Encoder - Large and Universal Sentence Encoder - Lite. These are pretrained Tensorflow models that return a semantic encoding for variable-length text inputs. The encodings can be used for semantic similarity measurement, relatedness, classification, or clustering of natural language text.
  • The Large model is trained with the Transformer encoder described in our second paper. It targets scenarios requiring high precision semantic representations and the best model performance at the cost of speed & size.
  • The Lite model is trained on a Sentence Piece vocabulary instead of words in order to significantly reduce the vocabulary size, which is a major contributor of model size. It targets scenarios where resources like memory and CPU are limited, such as on-device or browser based implementations.
We're excited to share this research, and these models, with the community. We believe that what we're showing here is just the beginning, and that there remain important research problems to be addressed, such as extending the techniques to more languages (the models discussed above currently support English). We also hope to further develop this technology so it can understand text at the paragraph or even document level. In achieving these tasks, it may be possible to make an encoder that is truly “universal”.

Acknowledgements
Daniel Cer, Mario Guajardo-Cespedes, Sheng-Yi Kong, Noah Constant for training the models, Nan Hua, Nicole Limtiaco, Rhomni St. John for transferring tasks, Steve Yuan, Yunhsuan Sung, Brian Strope, Ray Kurzweil for discussion of the model architecture. Special thanks to Sheng-Yi Kong and Noah Constant for training the Lite model.

Source: Google AI Blog


Custom On-Device ML Models with Learn2Compress



Successful deep learning models often require significant amounts of computational resources, memory and power to train and run, which presents an obstacle if you want them to perform well on mobile and IoT devices. On-device machine learning allows you to run inference directly on the devices, with the benefits of data privacy and access everywhere, regardless of connectivity. On-device ML systems, such as MobileNets and ProjectionNets, address the resource bottlenecks on mobile devices by optimizing for model efficiency. But what if you wanted to train your own customized, on-device models for your personal mobile application?

Yesterday at Google I/O, we announced ML Kit to make machine learning accessible for all mobile developers. One of the core ML Kit capabilities that will be available soon is an automatic model compression service powered by “Learn2Compress” technology developed by our research team. Learn2Compress enables custom on-device deep learning models in TensorFlow Lite that run efficiently on mobile devices, without developers having to worry about optimizing for memory and speed. We are pleased to make Learn2Compress for image classification available soon through ML Kit. Learn2Compress will be initially available to a small number of developers, and will be offered more broadly in the coming months. You can sign up here if you are interested in using this feature for building your own models.

How it Works
Learn2Compress generalizes the learning framework introduced in previous works like ProjectionNet and incorporates several state-of-the-art techniques for compressing neural network models. It takes as input a large pre-trained TensorFlow model provided by the user, performs training and optimization and automatically generates ready-to-use on-device models that are smaller in size, more memory-efficient, more power-efficient and faster at inference with minimal loss in accuracy.
Learn2Compress for automatically generating on-device ML models.
To do this, Learn2Compress uses multiple neural network optimization and compression techniques including:
  • Pruning reduces model size by removing weights or operations that are least useful for predictions (e.g.low-scoring weights). This can be very effective especially for on-device models involving sparse inputs or outputs, which can be reduced up to 2x in size while retaining 97% of the original prediction quality.
  • Quantization techniques are particularly effective when applied during training and can improve inference speed by reducing the number of bits used for model weights and activations. For example, using 8-bit fixed point representation instead of floats can speed up the model inference, reduce power and further reduce size by 4x.
  • Joint training and distillation approaches follow a teacher-student learning strategy — we use a larger teacher network (in this case, user-provided TensorFlow model) to train a compact student network (on-device model) with minimal loss in accuracy.
    Joint training and distillation approach to learn compact student models.
    The teacher network can be fixed (as in distillation) or jointly optimized, and even train multiple student models of different sizes simultaneously. So instead of a single model, Learn2Compress generates multiple on-device models in a single shot, at different sizes and inference speeds, and lets the developer pick one best suited for their application needs.
These and other techniques like transfer learning also make the compression process more efficient and scalable to large-scale datasets.

How well does it work?
To demonstrate the effectiveness of Learn2Compress, we used it to build compact on-device models of several state-of-the-art deep networks used in image and natural language tasks such as MobileNets, NASNet, Inception, ProjectionNet, among others. For a given task and dataset, we can generate multiple on-device models at different inference speeds and model sizes.
Accuracy at various sizes for Learn2Compress models and full-sized baseline networks on CIFAR-10 (left) and ImageNet (right) image classification tasks. Student networks used to produce the compressed variants for CIFAR-10 and ImageNet are modeled using NASNet and MobileNet-inspired architectures, respectively.
For image classification, Learn2Compress can generate small and fast models with good prediction accuracy suited for mobile applications. For example, on ImageNet task, Learn2Compress achieves a model 22x smaller than Inception v3 baseline and 4x smaller than MobileNet v1 baseline with just 4.6-7% drop in accuracy. On CIFAR-10, jointly training multiple Learn2Compress models with shared parameters, takes only 10% more time than training a single Learn2Compress large model, but yields 3 compressed models that are upto 94x smaller in size and upto 27x faster with up to 36x lower cost and good prediction quality (90-95% top-1 accuracy).
Computation cost and average prediction latency (on Pixel phone) for baseline and Learn2Compress models on CIFAR-10 image classification task. Learn2Compress-optimized models use NASNet-style network architecture.
We are also excited to see how well this performs on developer use-cases. For example, Fishbrain, a social platform for fishing enthusiasts, used Learn2Compress to compress their existing image classification cloud model (80MB+ in size and 91.8% top-3 accuracy) to a much smaller on-device model, less than 5MB in size, with similar accuracy. In some cases, we observe that it is possible for the compressed models to even slightly outperform the original large model’s accuracy due to better regularization effects.

We will continue to improve Learn2Compress with future advances in ML and deep learning, and extend to more use-cases beyond image classification. We are excited and looking forward to make this available soon through ML Kit’s compression service on the Cloud. We hope this will make it easy for developers to automatically build and optimize their own on-device ML models so that they can focus on building great apps and cool user experiences involving computer vision, natural language and other machine learning applications.

Acknowledgments
I would like to acknowledge our core contributors Gaurav Menghani, Prabhu Kaliamoorthi and Yicheng Fan along with Wei Chai, Kang Lee, Sheng Xu and Pannag Sanketi. Special thanks to Dave Burke, Brahim Elbouchikhi, Hrishikesh Aradhye, Hugues Vincent, and Arun Venkatesan from the Android team; Sachin Kotwani, Wesley Tarle, Pavel Jbanov and from the Firebase team; Andrei Broder, Andrew Tomkins, Robin Dua, Patrick McGregor, Gaurav Nemade, the Google Expander team and TensorFlow team.


Source: Google AI Blog


Deep Learning for Electronic Health Records



When patients get admitted to a hospital, they have many questions about what will happen next. When will I be able to go home? Will I get better? Will I have to come back to the hospital? Having precise answers to those questions helps doctors and nurses make care better, safer, and faster — if a patient’s health is deteriorating, doctors could be sent proactively to act before things get worse.

Predicting what will happen next is a natural application of machine learning. We wondered if the same types of machine learning that predict traffic during your commute or the next word in a translation from English to Spanish could be used for clinical predictions. For predictions to be useful in practice they should be, at least:
  1. Scalable: Predictions should be straightforward to create for any important outcome and for different hospital systems. Since healthcare data is very complicated and requires much data wrangling, this requirement is not straightforward to satisfy.
  2. Accurate: Predictions should alert clinicians to problems but not distract them with false alarms. With the widespread adoption of electronic health records, we set out to use that data to create more accurate prediction models.
Together with colleagues at UC San Francisco, Stanford Medicine, and The University of Chicago Medicine, we published “Scalable and Accurate Deep Learning with Electronic Health Records” in Nature Partner Journals: Digital Medicine, which contributes to these two aims.
We used deep learning models to make a broad set of predictions relevant to hospitalized patients using de-identified electronic health records. Importantly, we were able to use the data as-is, without the laborious manual effort typically required to extract, clean, harmonize, and transform relevant variables in those records. Our partners had removed sensitive individual information before we received it, and on our side, we protected the data using state-of-the-art security including logical separation, strict access controls, and encryption of data at rest and in transit.

Scalability
Electronic health records (EHRs) are tremendously complicated. Even a temperature measurement has a different meaning depending on if it’s taken under the tongue, through your eardrum, or on your forehead. And that's just a simple vital sign. Moreover, each health system customizes their EHR system, making the data collected at one hospital look different than data on a similar patient receiving similar care at another hospital. Before we could even apply machine learning, we needed a consistent way to represent patient records, which we built on top of the open Fast Healthcare Interoperability Resources (FHIR) standard as described in an earlier blog post.

Once in a consistent format, we did not have to manually select or harmonize the variables to use. Instead, for each prediction, a deep learning model reads all the data-points from earliest to most recent and then learns which data helps predict the outcome. Since there are thousands of data points involved, we had to develop some new types of deep learning modeling approaches based on recurrent neural networks (RNNs) and feedforward networks.
Data in a patient's record is represented as a timeline. For illustrative purposes, we display various types of clinical data (e.g. encounters, lab tests) by row. Each piece of data, indicated as a little grey dot, is stored in FHIR, an open data standard that can be used by any healthcare institution. A deep learning model analyzed a patient's chart by reading the timeline from left to right, from the beginning of a chart to the current hospitalization, and used this data to make different types of predictions.
Thus we engineered a computer system to render predictions without hand-crafting a new dataset for each task, in a scalable manner. But setting up the data is only one part of the work; the predictions also need to be accurate.

Prediction Accuracy
The most common way to assess accuracy is by a measure called the area-under-the-receiver-operator curve, which measures how well a model distinguishes between a patient who will have a particular future outcome compared to one who will not. In this metric, 1.00 is perfect, and 0.50 is no better than random chance, so higher numbers mean the model is more accurate. By this measure, the models we reported in the paper scored 0.86 in predicting if patients will stay long in the hospital (traditional logistic regression scored 0.76); they scored 0.95 in predicting inpatient mortality (traditional methods were 0.86), and they scored 0.77 in predicting unexpected readmissions after patients are discharged (traditional methods were 0.70). These gains were statistically significant.

We also used these models to identify the conditions for which the patients were being treated. For example, if a doctor prescribed ceftriaxone and doxycycline for a patient with an elevated temperature, fever and cough, the model could identify these as signals that the patient was being treated for pneumonia. We emphasize that the model is not diagnosing patients — it picks up signals about the patient, their treatments and notes written by their clinicians, so the model is more like a good listener than a master diagnostician.

An important focus of our work includes the interpretability of the deep learning models used. An “attention map” of each prediction shows the important data points considered by the models as they make that prediction. We show an example as a proof-of-concept and see this as an important part of what makes predictions useful for clinicians.
A deep learning model was used to render a prediction 24 hours after a patient was admitted to the hospital. The timeline (top of figure) contains months of historical data and the most recent data is shown enlarged in the middle. The model "attended" to information highlighted in red that was in the patient's chart to "explain" its prediction. In this case-study, the model highlighted pieces of information that make sense clinically. Figure from our paper.
What does this mean for patients and clinicians?
The results of this work are early and on retrospective data only. Indeed, this paper represents just the beginning of the work that is needed to test the hypothesis that machine learning can be used to make healthcare better. Doctors are already inundated with alerts and demands on their attention — could models help physicians with tedious, administrative tasks so they can better focus on the patient in front of them or ones that need extra attention? Can we help patients get high-quality care no matter where they seek it? We look forward to collaborating with doctors and patients to figure out the answers to these questions and more.

Source: Google AI Blog


Google at ICLR 2018



This week, Vancouver, Canada hosts the 6th International Conference on Learning Representations (ICLR 2018), a conference focused on how one can learn meaningful and useful representations of data for machine learning. ICLR includes conference and workshop tracks, with invited talks along with oral and poster presentations of some of the latest research on deep learning, metric learning, kernel learning, compositional models, non-linear structured prediction, and issues regarding non-convex optimization.

At the forefront of innovation in cutting-edge technology in neural networks and deep learning, Google focuses on both theory and application, developing learning approaches to understand and generalize. As Platinum Sponsor of ICLR 2018, Google will have a strong presence with over 130 researchers attending, contributing to and learning from the broader academic research community by presenting papers and posters, in addition to participating on organizing committees and in workshops.

If you are attending ICLR 2018, we hope you'll stop by our booth and chat with our researchers about the projects and opportunities at Google that go into solving interesting problems for billions of people. You can also learn more about our research being presented at ICLR 2018 in the list below (Googlers highlighted in blue)

Senior Program Chairs include:
Tara Sainath

Steering Committee includes:
Hugo Larochelle

Oral Contributions
Wasserstein Auto-Encoders
Ilya Tolstikhin, Olivier Bousquet, Sylvain Gelly, Bernhard Scholkopf

On the Convergence of Adam and Beyond (Best Paper Award)
Sashank J. Reddi, Satyen Kale, Sanjiv Kumar

Ask the Right Questions: Active Question Reformulation with Reinforcement Learning
Christian Buck, Jannis Bulian, Massimiliano Ciaramita, Wojciech Gajewski, Andrea Gesmundo, Neil Houlsby, Wei Wang

Beyond Word Importance: Contextual Decompositions to Extract Interactions from LSTMs
W. James Murdoch, Peter J. Liu, Bin Yu

Conference Posters
Boosting the Actor with Dual Critic
Bo Dai, Albert Shaw, Niao He, Lihong Li, Le Song

MaskGAN: Better Text Generation via Filling in the _______
William Fedus, Ian Goodfellow, Andrew M. Dai

Scalable Private Learning with PATE
Nicolas Papernot, Shuang Song, Ilya Mironov, Ananth Raghunathan, Kunal Talwar, Ulfar Erlingsson

Deep Gradient Compression: Reducing the Communication Bandwidth for Distributed Training
Yujun Lin, Song Han, Huizi Mao, Yu Wang, William J. Dally

Flipout: Efficient Pseudo-Independent Weight Perturbations on Mini-Batches
Yeming Wen, Paul Vicol, Jimmy Ba, Dustin Tran, Roger Grosse

Latent Constraints: Learning to Generate Conditionally from Unconditional Generative Models
Adam Roberts, Jesse Engel, Matt Hoffman

Multi-Mention Learning for Reading Comprehension with Neural Cascades
Swabha Swayamdipta, Ankur P. Parikh, Tom Kwiatkowski

QANet: Combining Local Convolution with Global Self-Attention for Reading Comprehension
Adams Wei Yu, David Dohan, Thang Luong, Rui Zhao, Kai Chen, Mohammad Norouzi, Quoc V. Le

Sensitivity and Generalization in Neural Networks: An Empirical Study
Roman Novak, Yasaman Bahri, Daniel A. Abolafia, Jeffrey Pennington, Jascha Sohl-Dickstein

Action-dependent Control Variates for Policy Optimization via Stein Identity
Hao Liu, Yihao Feng, Yi Mao, Dengyong Zhou, Jian Peng, Qiang Liu

An Efficient Framework for Learning Sentence Representations
Lajanugen Logeswaran, Honglak Lee

Fidelity-Weighted Learning
Mostafa Dehghani, Arash Mehrjou, Stephan Gouws, Jaap Kamps, Bernhard Schölkopf

Generating Wikipedia by Summarizing Long Sequences
Peter J. Liu, Mohammad Saleh, Etienne Pot, Ben Goodrich, Ryan Sepassi, Lukasz Kaiser, Noam Shazeer

Matrix Capsules with EM Routing
Geoffrey Hinton, Sara Sabour, Nicholas Frosst

Temporal Difference Models: Model-Free Deep RL for Model-Based Control
Sergey Levine, Shixiang Gu, Murtaza Dalal, Vitchyr Pong

Deep Neural Networks as Gaussian Processes
Jaehoon Lee, Yasaman Bahri, Roman Novak, Samuel L. Schoenholz, Jeffrey Pennington, Jascha Sohl-Dickstein

Many Paths to Equilibrium: GANs Do Not Need to Decrease a Divergence at Every Step
William Fedus, Mihaela Rosca, Balaji Lakshminarayanan, Andrew M. Dai, Shakir Mohamed, Ian Goodfellow

Initialization Matters: Orthogonal Predictive State Recurrent Neural Networks
Krzysztof Choromanski, Carlton Downey, Byron Boots

Learning Differentially Private Recurrent Language Models
H. Brendan McMahan, Daniel Ramage, Kunal Talwar, Li Zhang

Learning Latent Permutations with Gumbel-Sinkhorn Networks
Gonzalo Mena, David Belanger, Scott Linderman, Jasper Snoek

Leave no Trace: Learning to Reset for Safe and Autonomous Reinforcement Learning
Benjamin Eysenbach, Shixiang Gu, Julian IbarzSergey Levine

Meta-Learning for Semi-Supervised Few-Shot Classification
Mengye Ren, Eleni Triantafillou, Sachin Ravi, Jake Snell, Kevin Swersky, Josh Tenenbaum, Hugo Larochelle, Richard Zemel

Thermometer Encoding: One Hot Way to Resist Adversarial Examples
Jacob Buckman, Aurko Roy, Colin Raffel, Ian Goodfellow

A Hierarchical Model for Device Placement
Azalia Mirhoseini, Anna Goldie, Hieu Pham, Benoit Steiner, Quoc V. LeJeff Dean

Monotonic Chunkwise Attention
Chung-Cheng Chiu, Colin Raffel

Training Confidence-calibrated Classifiers for Detecting Out-of-Distribution Samples
Kimin Lee, Honglak Lee, Kibok Lee, Jinwoo Shin

Trust-PCL: An Off-Policy Trust Region Method for Continuous Control
Ofir Nachum, Mohammad Norouzi, Kelvin Xu, Dale Schuurmans

Ensemble Adversarial Training: Attacks and Defenses
Florian Tramèr, Alexey Kurakin, Nicolas Papernot, Ian Goodfellow, Dan Boneh, Patrick McDaniel

Stochastic Variational Video Prediction
Mohammad Babaeizadeh, Chelsea Finn, Dumitru Erhan, Roy Campbell, Sergey Levine

Depthwise Separable Convolutions for Neural Machine Translation
Lukasz Kaiser, Aidan N. Gomez, Francois Chollet

Don’t Decay the Learning Rate, Increase the Batch Size
Samuel L. Smith, Pieter-Jan Kindermans, Chris Ying, Quoc V. Le

Generative Models of Visually Grounded Imagination
Ramakrishna Vedantam, Ian Fischer, Jonathan Huang, Kevin Murphy

Large Scale Distributed Neural Network Training through Online Distillation
Rohan Anil, Gabriel Pereyra, Alexandre Passos, Robert Ormandi, George E. Dahl, Geoffrey E. Hinton

Learning a Neural Response Metric for Retinal Prosthesis
Nishal P. Shah, Sasidhar Madugula, Alan Litke, Alexander Sher, EJ Chichilnisky, Yoram Singer, Jonathon Shlens

Neumann Optimizer: A Practical Optimization Algorithm for Deep Neural Networks
Shankar Krishnan, Ying Xiao, Rif A. Saurous

A Neural Representation of Sketch Drawings
David HaDouglas Eck

Deep Bayesian Bandits Showdown: An Empirical Comparison of Bayesian Deep Networks for Thompson Sampling
Carlos Riquelme, George Tucker, Jasper Snoek

Generalizing Hamiltonian Monte Carlo with Neural Networks
Daniel Levy, Matthew D. HoffmanJascha Sohl-Dickstein

Leveraging Grammar and Reinforcement Learning for Neural Program Synthesis
Rudy Bunel, Matthew Hausknecht, Jacob Devlin, Rishabh Singh, Pushmeet Kohli

On the Discrimination-Generalization Tradeoff in GANs
Pengchuan Zhang, Qiang Liu, Dengyong Zhou, Tao Xu, Xiaodong He

A Bayesian Perspective on Generalization and Stochastic Gradient Descent
Samuel L. Smith, Quoc V. Le

Learning how to Explain Neural Networks: PatternNet and PatternAttribution
Pieter-Jan Kindermans, Kristof T. Schütt, Maximilian Alber, Klaus-Robert Müller, Dumitru Erhan, Been Kim, Sven Dähne

Skip RNN: Learning to Skip State Updates in Recurrent Neural Networks
Víctor Campos, Brendan Jou, Xavier Giró-i-Nieto, Jordi Torres, Shih-Fu Chang

Towards Neural Phrase-based Machine Translation
Po-Sen Huang, Chong Wang, Sitao Huang, Dengyong Zhou, Li Deng

Unsupervised Cipher Cracking Using Discrete GANs
Aidan N. Gomez, Sicong Huang, Ivan Zhang, Bryan M. Li, Muhammad Osama, Lukasz Kaiser

Variational Image Compression With A Scale Hyperprior
Johannes Ballé, David Minnen, Saurabh Singh, Sung Jin Hwang, Nick Johnston

Workshop Posters
Local Explanation Methods for Deep Neural Networks Lack Sensitivity to Parameter Values
Julius Adebayo, Justin Gilmer, Ian Goodfellow, Been Kim

Stoachastic Gradient Langevin Dynamics that Exploit Neural Network Structure
Zachary Nado, Jasper Snoek, Bowen Xu, Roger Grosse, David Duvenaud, James Martens

Towards Mixed-initiative generation of multi-channel sequential structure
Anna Huang, Sherol Chen, Mark J. Nelson, Douglas Eck

Can Deep Reinforcement Learning Solve Erdos-Selfridge-Spencer Games?
Maithra Raghu, Alex Irpan, Jacob Andreas, Robert Kleinberg, Quoc V. Le, Jon Kleinberg

GILBO: One Metric to Measure Them All
Alexander Alemi, Ian Fischer

HoME: a Household Multimodal Environment
Simon Brodeur, Ethan Perez, Ankesh Anand, Florian Golemo, Luca Celotti, Florian Strub, Jean Rouat, Hugo Larochelle, Aaron Courville

Learning to Learn without Labels
Luke Metz, Niru Maheswaranathan, Brian Cheung, Jascha Sohl-Dickstein

Learning via Social Awareness: Improving Sketch Representations with Facial Feedback
Natasha Jaques, Jesse Engel, David Ha, Fred Bertsch, Rosalind Picard, Douglas Eck

Negative Eigenvalues of the Hessian in Deep Neural Networks
Guillaume Alain, Nicolas Le Roux, Pierre-Antoine Manzagol

Realistic Evaluation of Semi-Supervised Learning Algorithms
Avital Oliver, Augustus Odena, Colin Raffel, Ekin Cubuk, lan Goodfellow

Winner's Curse? On Pace, Progress, and Empirical Rigor
D. Sculley, Jasper Snoek, Alex Wiltschko, Ali Rahimi

Meta-Learning for Batch Mode Active Learning
Sachin Ravi, Hugo Larochelle

To Prune, or Not to Prune: Exploring the Efficacy of Pruning for Model Compression
Michael Zhu, Suyog Gupta

Adversarial Spheres
Justin Gilmer, Luke Metz, Fartash Faghri, Sam Schoenholz, Maithra Raghu,,Martin Wattenberg, Ian Goodfellow

Clustering Meets Implicit Generative Models
Francesco Locatello, Damien Vincent, Ilya Tolstikhin, Gunnar Ratsch, Sylvain Gelly, Bernhard Scholkopf

Decoding Decoders: Finding Optimal Representation Spaces for Unsupervised Similarity Tasks
Vitalii Zhelezniak, Dan Busbridge, April Shen, Samuel L. Smith, Nils Y. Hammerla

Learning Longer-term Dependencies in RNNs with Auxiliary Losses
Trieu Trinh, Quoc Le, Andrew Dai, Thang Luong

Graph Partition Neural Networks for Semi-Supervised Classification
Alexander Gaunt, Danny Tarlow, Marc Brockschmidt, Raquel Urtasun, Renjie Liao, Richard Zemel

Searching for Activation Functions
Prajit Ramachandran, Barret Zoph, Quoc Le

Time-Dependent Representation for Neural Event Sequence Prediction
Yang Li, Nan Du, Samy Bengio

Faster Discovery of Neural Architectures by Searching for Paths in a Large Model
Hieu Pham, Melody Guan, Barret Zoph, Quoc V. Le, Jeff Dean

Intriguing Properties of Adversarial Examples
Ekin Dogus Cubuk, Barret Zoph, Sam Schoenholz, Quoc Le

PPP-Net: Platform-aware Progressive Search for Pareto-optimal Neural Architectures
Jin-Dong Dong, An-Chieh Cheng, Da-Cheng Juan, Wei Wei, Min Sun

The Mirage of Action-Dependent Baselines in Reinforcement Learning
George Tucker, Surya Bhupatiraju, Shixiang Gu, Richard E. Turner, Zoubin Ghahramani, Sergey Levine

Learning to Organize Knowledge with N-Gram Machines
Fan Yang, Jiazhong Nie, William W. Cohen, Ni Lao

Online variance-reducing optimization
Nicolas Le Roux, Reza Babanezhad, Pierre-Antoine Manzagol

Google at ICLR 2018



This week, Vancouver, Canada hosts the 6th International Conference on Learning Representations (ICLR 2018), a conference focused on how one can learn meaningful and useful representations of data for machine learning. ICLR includes conference and workshop tracks, with invited talks along with oral and poster presentations of some of the latest research on deep learning, metric learning, kernel learning, compositional models, non-linear structured prediction, and issues regarding non-convex optimization.

At the forefront of innovation in cutting-edge technology in neural networks and deep learning, Google focuses on both theory and application, developing learning approaches to understand and generalize. As Platinum Sponsor of ICLR 2018, Google will have a strong presence with over 130 researchers attending, contributing to and learning from the broader academic research community by presenting papers and posters, in addition to participating on organizing committees and in workshops.

If you are attending ICLR 2018, we hope you'll stop by our booth and chat with our researchers about the projects and opportunities at Google that go into solving interesting problems for billions of people. You can also learn more about our research being presented at ICLR 2018 in the list below (Googlers highlighted in blue)

Senior Program Chair:
Tara Sainath

Steering Committee includes:
Hugo Larochelle

Oral Contributions
Wasserstein Auto-Encoders
Ilya Tolstikhin, Olivier Bousquet, Sylvain Gelly, Bernhard Scholkopf

On the Convergence of Adam and Beyond (Best Paper Award)
Sashank J. Reddi, Satyen Kale, Sanjiv Kumar

Ask the Right Questions: Active Question Reformulation with Reinforcement Learning
Christian Buck, Jannis Bulian, Massimiliano Ciaramita, Wojciech Gajewski, Andrea Gesmundo, Neil Houlsby, Wei Wang

Beyond Word Importance: Contextual Decompositions to Extract Interactions from LSTMs
W. James Murdoch, Peter J. Liu, Bin Yu

Conference Posters
Boosting the Actor with Dual Critic
Bo Dai, Albert Shaw, Niao He, Lihong Li, Le Song

MaskGAN: Better Text Generation via Filling in the _______
William Fedus, Ian Goodfellow, Andrew M. Dai

Scalable Private Learning with PATE
Nicolas Papernot, Shuang Song, Ilya Mironov, Ananth Raghunathan, Kunal Talwar, Ulfar Erlingsson

Deep Gradient Compression: Reducing the Communication Bandwidth for Distributed Training
Yujun Lin, Song Han, Huizi Mao, Yu Wang, William J. Dally

Flipout: Efficient Pseudo-Independent Weight Perturbations on Mini-Batches
Yeming Wen, Paul Vicol, Jimmy Ba, Dustin Tran, Roger Grosse

Latent Constraints: Learning to Generate Conditionally from Unconditional Generative Models
Adam Roberts, Jesse Engel, Matt Hoffman

Multi-Mention Learning for Reading Comprehension with Neural Cascades
Swabha Swayamdipta, Ankur P. Parikh, Tom Kwiatkowski

QANet: Combining Local Convolution with Global Self-Attention for Reading Comprehension
Adams Wei Yu, David Dohan, Thang Luong, Rui Zhao, Kai Chen, Mohammad Norouzi, Quoc V. Le

Sensitivity and Generalization in Neural Networks: An Empirical Study
Roman Novak, Yasaman Bahri, Daniel A. Abolafia, Jeffrey Pennington, Jascha Sohl-Dickstein

Action-dependent Control Variates for Policy Optimization via Stein Identity
Hao Liu, Yihao Feng, Yi Mao, Dengyong Zhou, Jian Peng, Qiang Liu

An Efficient Framework for Learning Sentence Representations
Lajanugen Logeswaran, Honglak Lee

Fidelity-Weighted Learning
Mostafa Dehghani, Arash Mehrjou, Stephan Gouws, Jaap Kamps, Bernhard Schölkopf

Generating Wikipedia by Summarizing Long Sequences
Peter J. Liu, Mohammad Saleh, Etienne Pot, Ben Goodrich, Ryan Sepassi, Lukasz Kaiser, Noam Shazeer

Matrix Capsules with EM Routing
Geoffrey Hinton, Sara Sabour, Nicholas Frosst

Temporal Difference Models: Model-Free Deep RL for Model-Based Control
Sergey Levine, Shixiang Gu, Murtaza Dalal, Vitchyr Pong

Deep Neural Networks as Gaussian Processes
Jaehoon Lee, Yasaman Bahri, Roman Novak, Samuel L. Schoenholz, Jeffrey Pennington, Jascha Sohl-Dickstein

Many Paths to Equilibrium: GANs Do Not Need to Decrease a Divergence at Every Step
William Fedus, Mihaela Rosca, Balaji Lakshminarayanan, Andrew M. Dai, Shakir Mohamed, Ian Goodfellow

Initialization Matters: Orthogonal Predictive State Recurrent Neural Networks
Krzysztof Choromanski, Carlton Downey, Byron Boots

Learning Differentially Private Recurrent Language Models
H. Brendan McMahan, Daniel Ramage, Kunal Talwar, Li Zhang

Learning Latent Permutations with Gumbel-Sinkhorn Networks
Gonzalo Mena, David Belanger, Scott Linderman, Jasper Snoek

Leave no Trace: Learning to Reset for Safe and Autonomous Reinforcement Learning
Benjamin Eysenbach, Shixiang Gu, Julian IbarzSergey Levine

Meta-Learning for Semi-Supervised Few-Shot Classification
Mengye Ren, Eleni Triantafillou, Sachin Ravi, Jake Snell, Kevin Swersky, Josh Tenenbaum, Hugo Larochelle, Richard Zemel

Thermometer Encoding: One Hot Way to Resist Adversarial Examples
Jacob Buckman, Aurko Roy, Colin Raffel, Ian Goodfellow

A Hierarchical Model for Device Placement
Azalia Mirhoseini, Anna Goldie, Hieu Pham, Benoit Steiner, Quoc V. LeJeff Dean

Monotonic Chunkwise Attention
Chung-Cheng Chiu, Colin Raffel

Training Confidence-calibrated Classifiers for Detecting Out-of-Distribution Samples
Kimin Lee, Honglak Lee, Kibok Lee, Jinwoo Shin

Trust-PCL: An Off-Policy Trust Region Method for Continuous Control
Ofir Nachum, Mohammad Norouzi, Kelvin Xu, Dale Schuurmans

Ensemble Adversarial Training: Attacks and Defenses
Florian Tramèr, Alexey Kurakin, Nicolas Papernot, Ian Goodfellow, Dan Boneh, Patrick McDaniel

Stochastic Variational Video Prediction
Mohammad Babaeizadeh, Chelsea Finn, Dumitru Erhan, Roy Campbell, Sergey Levine

Depthwise Separable Convolutions for Neural Machine Translation
Lukasz Kaiser, Aidan N. Gomez, Francois Chollet

Don’t Decay the Learning Rate, Increase the Batch Size
Samuel L. Smith, Pieter-Jan Kindermans, Chris Ying, Quoc V. Le

Generative Models of Visually Grounded Imagination
Ramakrishna Vedantam, Ian Fischer, Jonathan Huang, Kevin Murphy

Large Scale Distributed Neural Network Training through Online Distillation
Rohan Anil, Gabriel Pereyra, Alexandre Passos, Robert Ormandi, George E. Dahl, Geoffrey E. Hinton

Learning a Neural Response Metric for Retinal Prosthesis
Nishal P. Shah, Sasidhar Madugula, Alan Litke, Alexander Sher, EJ Chichilnisky, Yoram Singer, Jonathon Shlens

Neumann Optimizer: A Practical Optimization Algorithm for Deep Neural Networks
Shankar Krishnan, Ying Xiao, Rif A. Saurous

A Neural Representation of Sketch Drawings
David HaDouglas Eck

Deep Bayesian Bandits Showdown: An Empirical Comparison of Bayesian Deep Networks for Thompson Sampling
Carlos Riquelme, George Tucker, Jasper Snoek

Generalizing Hamiltonian Monte Carlo with Neural Networks
Daniel Levy, Matthew D. HoffmanJascha Sohl-Dickstein

Leveraging Grammar and Reinforcement Learning for Neural Program Synthesis
Rudy Bunel, Matthew Hausknecht, Jacob Devlin, Rishabh Singh, Pushmeet Kohli

On the Discrimination-Generalization Tradeoff in GANs
Pengchuan Zhang, Qiang Liu, Dengyong Zhou, Tao Xu, Xiaodong He

A Bayesian Perspective on Generalization and Stochastic Gradient Descent
Samuel L. Smith, Quoc V. Le

Learning how to Explain Neural Networks: PatternNet and PatternAttribution
Pieter-Jan Kindermans, Kristof T. Schütt, Maximilian Alber, Klaus-Robert Müller, Dumitru Erhan, Been Kim, Sven Dähne

Skip RNN: Learning to Skip State Updates in Recurrent Neural Networks
Víctor Campos, Brendan Jou, Xavier Giró-i-Nieto, Jordi Torres, Shih-Fu Chang

Towards Neural Phrase-based Machine Translation
Po-Sen Huang, Chong Wang, Sitao Huang, Dengyong Zhou, Li Deng

Unsupervised Cipher Cracking Using Discrete GANs
Aidan N. Gomez, Sicong Huang, Ivan Zhang, Bryan M. Li, Muhammad Osama, Lukasz Kaiser

Variational Image Compression With A Scale Hyperprior
Johannes Ballé, David Minnen, Saurabh Singh, Sung Jin Hwang, Nick Johnston

Workshop Posters
Local Explanation Methods for Deep Neural Networks Lack Sensitivity to Parameter Values
Julius Adebayo, Justin Gilmer, Ian Goodfellow, Been Kim

Stoachastic Gradient Langevin Dynamics that Exploit Neural Network Structure
Zachary Nado, Jasper Snoek, Bowen Xu, Roger Grosse, David Duvenaud, James Martens

Towards Mixed-initiative generation of multi-channel sequential structure
Anna Huang, Sherol Chen, Mark J. Nelson, Douglas Eck

Can Deep Reinforcement Learning Solve Erdos-Selfridge-Spencer Games?
Maithra Raghu, Alex Irpan, Jacob Andreas, Robert Kleinberg, Quoc V. Le, Jon Kleinberg

GILBO: One Metric to Measure Them All
Alexander Alemi, Ian Fischer

HoME: a Household Multimodal Environment
Simon Brodeur, Ethan Perez, Ankesh Anand, Florian Golemo, Luca Celotti, Florian Strub, Jean Rouat, Hugo Larochelle, Aaron Courville

Learning to Learn without Labels
Luke Metz, Niru Maheswaranathan, Brian Cheung, Jascha Sohl-Dickstein

Learning via Social Awareness: Improving Sketch Representations with Facial Feedback
Natasha Jaques, Jesse Engel, David Ha, Fred Bertsch, Rosalind Picard, Douglas Eck

Negative Eigenvalues of the Hessian in Deep Neural Networks
Guillaume Alain, Nicolas Le Roux, Pierre-Antoine Manzagol

Realistic Evaluation of Semi-Supervised Learning Algorithms
Avital Oliver, Augustus Odena, Colin Raffel, Ekin Cubuk, lan Goodfellow

Winner's Curse? On Pace, Progress, and Empirical Rigor
D. Sculley, Jasper Snoek, Alex Wiltschko, Ali Rahimi

Meta-Learning for Batch Mode Active Learning
Sachin Ravi, Hugo Larochelle

To Prune, or Not to Prune: Exploring the Efficacy of Pruning for Model Compression
Michael Zhu, Suyog Gupta

Adversarial Spheres
Justin Gilmer, Luke Metz, Fartash Faghri, Sam Schoenholz, Maithra Raghu,,Martin Wattenberg, Ian Goodfellow

Clustering Meets Implicit Generative Models
Francesco Locatello, Damien Vincent, Ilya Tolstikhin, Gunnar Ratsch, Sylvain Gelly, Bernhard Scholkopf

Decoding Decoders: Finding Optimal Representation Spaces for Unsupervised Similarity Tasks
Vitalii Zhelezniak, Dan Busbridge, April Shen, Samuel L. Smith, Nils Y. Hammerla

Learning Longer-term Dependencies in RNNs with Auxiliary Losses
Trieu Trinh, Quoc Le, Andrew Dai, Thang Luong

Graph Partition Neural Networks for Semi-Supervised Classification
Alexander Gaunt, Danny Tarlow, Marc Brockschmidt, Raquel Urtasun, Renjie Liao, Richard Zemel

Searching for Activation Functions
Prajit Ramachandran, Barret Zoph, Quoc Le

Time-Dependent Representation for Neural Event Sequence Prediction
Yang Li, Nan Du, Samy Bengio

Faster Discovery of Neural Architectures by Searching for Paths in a Large Model
Hieu Pham, Melody Guan, Barret Zoph, Quoc V. Le, Jeff Dean

Intriguing Properties of Adversarial Examples
Ekin Dogus Cubuk, Barret Zoph, Sam Schoenholz, Quoc Le

PPP-Net: Platform-aware Progressive Search for Pareto-optimal Neural Architectures
Jin-Dong Dong, An-Chieh Cheng, Da-Cheng Juan, Wei Wei, Min Sun

The Mirage of Action-Dependent Baselines in Reinforcement Learning
George Tucker, Surya Bhupatiraju, Shixiang Gu, Richard E. Turner, Zoubin Ghahramani, Sergey Levine

Learning to Organize Knowledge with N-Gram Machines
Fan Yang, Jiazhong Nie, William W. Cohen, Ni Lao

Online variance-reducing optimization
Nicolas Le Roux, Reza Babanezhad, Pierre-Antoine Manzagol

Source: Google AI Blog


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.

Source: Google AI Blog