Tag Archives: Visualization

Distill: Supporting Clarity in Machine Learning



Science isn't just about discovering new results. It’s also about human understanding. Scientists need to develop notations, analogies, visualizations, and explanations of ideas. This human dimension of science isn't a minor side project. It's deeply tied to the heart of science.

That’s why, in collaboration with OpenAI, DeepMind, YC Research, and others, we’re excited to announce the launch of Distill, a new open science journal and ecosystem supporting human understanding of machine learning. Distill is an independent organization, dedicated to fostering a new segment of the research community.

Modern web technology gives us powerful new tools for expressing this human dimension of science. We can create interactive diagrams and user interfaces the enable intuitive exploration of research ideas. Over the last few years we've seen many incredible demonstrations of this kind of work.
An interactive diagram explaining the Neural Turing Machine from Olah & Carter, 2016.
Unfortunately, while there are a plethora of conferences and journals in machine learning, there aren’t any research venues that are dedicated to publishing this kind of work. This is partly an issue of focus, and partly because traditional publication venues can't, by virtue of their medium, support interactive visualizations. Without a venue to publish in, many significant contributions don’t count as “real academic contributions” and their authors can’t access the academic support structure.

That’s why Distill aims to build an ecosystem to support this kind of work, starting with three pieces: a research journal, prizes recognizing outstanding work, and tools to facilitate the creation of interactive articles.
Distill is an ecosystem to support clarity in Machine Learning.
Led by a diverse steering committee of leaders from the machine learning and user interface communities, we are very excited to see where Distill will go. To learn more about Distill, see the overview page or read the latest articles.

Open sourcing the Embedding Projector: a tool for visualizing high dimensional data

Originally posted on the Google Research Blog

Recent advances in machine learning (ML) have shown impressive results, with applications ranging from image recognition, language translation, medical diagnosis and more. With the widespread adoption of ML systems, it is increasingly important for research scientists to be able to explore how the data is being interpreted by the models. However, one of the main challenges in exploring this data is that it often has hundreds or even thousands of dimensions, requiring special tools to investigate the space.

To enable a more intuitive exploration process, we are open-sourcing the Embedding Projector, a web application for interactive visualization and analysis of high-dimensional data recently shown as an A.I. Experiment, as part of TensorFlow. We are also releasing a standalone version at projector.tensorflow.org, where users can visualize their high-dimensional data without the need to install and run TensorFlow.


Exploring Embeddings

The data needed to train machine learning systems comes in a form that computers don't immediately understand. To translate the things we understand naturally (e.g. words, sounds, or videos) to a form that the algorithms can process, we use embeddings, a mathematical vector representation that captures different facets (dimensions) of the data. For example, in this language embedding, similar words are mapped to points that are close to each other.

With the Embedding Projector, you can navigate through views of data in either a 2D or a 3D mode, zooming, rotating, and panning using natural click-and-drag gestures. Below is a figure showing the nearest points to the embedding for the word “important” after training a TensorFlow model using the word2vec tutorial. Clicking on any point (which represents the learned embedding for a given word) in this visualization, brings up a list of nearest points and distances, which shows which words the algorithm has learned to be semantically related. This type of interaction represents an important way in which one can explore how an algorithm is performing.


Methods of Dimensionality Reduction

The Embedding Projector offers three commonly used methods of data dimensionality reduction, which allow easier visualization of complex data: PCA, t-SNE and custom linear projections. PCA is often effective at exploring the internal structure of the embeddings, revealing the most influential dimensions in the data. t-SNE, on the other hand, is useful for exploring local neighborhoods and finding clusters, allowing developers to make sure that an embedding preserves the meaning in the data (e.g. in the MNIST dataset, seeing that the same digits are clustered together). Finally, custom linear projections can help discover meaningful "directions" in data sets - such as the distinction between a formal and casual tone in a language generation model - which would allow the design of more adaptable ML systems.

A custom linear projection of the 100 nearest points of "See attachments." onto the "yes" - "yeah" vector (“yes” is right, “yeah” is left) of a corpus of 35k frequently used phrases in emails
The Embedding Projector website includes a few datasets to play with. We’ve also made it easy for users to publish and share their embeddings with others (just click on the “Publish” button on the left pane). It is our hope that the Embedding Projector will be a useful tool to help the research community explore and refine their ML applications, as well as enable anyone to better understand how ML algorithms interpret data. If you'd like to get the full details on the Embedding Projector, you can read the paper here. Have fun exploring the world of embeddings!

By Daniel Smilkov and the Big Picture group

Open sourcing the Embedding Projector: a tool for visualizing high dimensional data



Recent advances in Machine Learning (ML) have shown impressive results, with applications ranging from image recognition, language translation, medical diagnosis and more. With the widespread adoption of ML systems, it is increasingly important for research scientists to be able to explore how the data is being interpreted by the models. However, one of the main challenges in exploring this data is that it often has hundreds or even thousands of dimensions, requiring special tools to investigate the space.

To enable a more intuitive exploration process, we are open-sourcing the Embedding Projector, a web application for interactive visualization and analysis of high-dimensional data recently shown as an A.I. Experiment, as part of TensorFlow. We are also releasing a standalone version at projector.tensorflow.org, where users can visualize their high-dimensional data without the need to install and run TensorFlow.


Exploring Embeddings

The data needed to train machine learning systems comes in a form that computers don't immediately understand. To translate the things we understand naturally (e.g. words, sounds, or videos) to a form that the algorithms can process, we use embeddings, a mathematical vector representation that captures different facets (dimensions) of the data. For example, in this language embedding, similar words are mapped to points that are close to each other.

With the Embedding Projector, you can navigate through views of data in either a 2D or a 3D mode, zooming, rotating, and panning using natural click-and-drag gestures. Below is a figure showing the nearest points to the embedding for the word “important” after training a TensorFlow model using the word2vec tutorial. Clicking on any point (which represents the learned embedding for a given word) in this visualization, brings up a list of nearest points and distances, which shows which words the algorithm has learned to be semantically related. This type of interaction represents an important way in which one can explore how an algorithm is performing.


Methods of Dimensionality Reduction

The Embedding Projector offers three commonly used methods of data dimensionality reduction, which allow easier visualization of complex data: PCA, t-SNE and custom linear projections. PCA is often effective at exploring the internal structure of the embeddings, revealing the most influential dimensions in the data. t-SNE, on the other hand, is useful for exploring local neighborhoods and finding clusters, allowing developers to make sure that an embedding preserves the meaning in the data (e.g. in the MNIST dataset, seeing that the same digits are clustered together). Finally, custom linear projections can help discover meaningful "directions" in data sets - such as the distinction between a formal and casual tone in a language generation model - which would allow the design of more adaptable ML systems.
A custom linear projection of the 100 nearest points of "See attachments." onto the "yes" - "yeah" vector (“yes” is right, “yeah” is left) of a corpus of 35k frequently used phrases in emails
The Embedding Projector website includes a few datasets to play with. We’ve also made it easy for users to publish and share their embeddings with others (just click on the “Publish” button on the left pane). It is our hope that the Embedding Projector will be a useful tool to help the research community explore and refine their ML applications, as well as enable anyone to better understand how ML algorithms interpret data. Have fun exploring the world of embeddings!


Open Source Visualization of GPS Displacements for Earthquake Cycle Physics



The Earth’s surface is moving, ever so slightly, all the time. This slow, small, but persistent movement of the Earth's crust is responsible for the formation of mountain ranges, sudden earthquakes, and even the positions of the continents. Scientists around the world measure these almost imperceptible movements using arrays of Global Navigation Satellite System (GNSS) receivers to better understand all phases of an earthquake cycle—both how the surface responds after an earthquake, and the storage of strain energy between earthquakes.

To help researchers explore this data and better understand the Earthquake cycle, we are releasing a new, interactive data visualization which draws geodetic velocity lines on top of a relief map by amplifying position estimates relative to their true positions. Unlike existing approaches, which focus on small time slices or individual stations, our visualization can show all the data for a whole array of stations at once. Open sourced under an Apache 2 license, and available on GitHub, this visualization technique is a collaboration between Harvard’s Department of Earth and Planetary Sciences and Google's Machine Perception and Big Picture teams.

Our approach helps scientists quickly assess deformations across all phases of the earthquake cycle—both during earthquakes (coseismic) and the time between (interseismic). For example, we can see azimuth (direction) reversals of stations as they relate to topographic structures and active faults. Digging into these movements will help scientists vet their models and their data, both of which are crucial for developing accurate computer representations that may help predict future earthquakes.

Classical approaches to visualizing these data have fallen into two general categories: 1) a map view of velocity/displacement vectors over a fixed time interval and 2) time versus position plots of each GNSS component (longitude, latitude and altitude).

Examples of classical approaches. On the left is a map view showing average velocity vectors over the period from 1997 to 2001[1]. On the right you can see a time versus eastward (longitudinal) position plot for a single station.

Each of these approaches have proved to be informative ways to understand the spatial distribution of crustal movements and the time evolution of solid earth deformation. However, because geodetic shifts happen in almost imperceptible distances (mm) and over long timescales, both approaches can only show a small subset of the data at any time—a condensed average velocity per station, or a detailed view of a single station, respectively. Our visualization enables a scientist to see all the data at once, then interactively drill down to a specific subset of interest.

Our visualization approach is straightforward; by magnifying the daily longitude and latitude position changes, we show tracks of the evolution of the position of each station. These magnified position tracks are shown as trails on top of a shaded relief topography to provide a sense of position evolution in geographic context.

To see how it works in practice, let’s step through an an example. Consider this tiny set of longitude/latitude pairs for a single GNSS station, with the differing digits shown in bold:

Day Index
Longitude
Latitude
0
139.06990407
34.949757897
1
139.06990400
34.949757882
2
139.06990413
34.949757941
3
139.06990409
34.949757921
4
139.06990413
34.949757904

If we were to draw line segments between these points directly on a map, they’d be much too small to see at any reasonable scale. So we take these minute differences and multiply them by a user-controlled scaling factor. By default this factor is 105.5 (about 316,000x).

To help the user identify which end is the start of the line, we give the start and end points different colors and interpolate between them. Blue and red are the default colors, but they’re user-configurable. Although day-to-day movement of stations may seem erratic, by using this method, one can make out a general trend in the relative motion of a station.
Close-up of a single station’s movement during the three year period from 2003 to 2006.

However, static renderings of this sort suffer from the same problem that velocity vector images do; in regions with a high density of GNSS stations, tracks overlap significantly with one another, obscuring details. To solve this problem, our visualization lets the user interactively control the time range of interest, the amount of amplification and other settings. In addition, by animating the lines from start to finish, the user gets a real sense of motion that’s difficult to achieve in a static image.

We’ve applied our new visualization to the ~20 years of data from the GEONET array in Japan. Through it, we can see small but coherent changes in direction before and after the great 2011 Tohoku earthquake.
GPS data sets (in .json format) for both the GEONET data in Japan and the Plate Boundary Observatory (PBO) data in the western US are available at earthquake.rc.fas.harvard.edu.

This short animation shows many of the visualization’s interactive features. In order:
  1. Modifying the multiplier adjusts how significantly the movements are magnified.
  2. We can adjust the time slider nubs to select a particular time range of interest.
  3. Using the map controls provided by the Google Maps JavaScript API, we can zoom into a tiny region of the map.
  4. By enabling map markers, we can see information about individual GNSS stations.
By focusing on a stations of interest, we can even see curvature changes in the time periods before and after the event.
Station designated 960601 of Japan’s GEONET array is located on the island of Mikura-jima. Here we see the period from 2006 to 2012, with movement magnified 105.1 times (126,000x).

To achieve fast rendering of the line segments, we created a custom overlay using THREE.js to render the lines in WebGL. Data for the GNSS stations is passed to the GPU in a data texture, which allows our vertex shader to position each point on-screen dynamically based on user settings and animation.

We’re excited to continue this productive collaboration between Harvard and Google as we explore opportunities for groundbreaking, new earthquake visualizations. If you’d like to try out the visualization yourself, follow the instructions at earthquake.rc.fas.harvard.edu. It will walk you through the setup steps, including how to download the available data sets. If you’d like to report issues, great! Please submit them through the GitHub project page.

Acknowledgments

We wish to thank Bill Freeman, a researcher on Machine Perception, who hatched the idea and developed the initial prototypes, and Fernanda Viégas and Martin Wattenberg of the Big Picture Team for their visualization design guidance.

References

[1] Loveless, J. P., and Meade, B. J. (2010). Geodetic imaging of plate motions, slip rates, and partitioning of deformation in Japan, Journal of Geophysical Research.


Open source visualization of GPS displacements for earthquake cycle physics

The Earth’s surface is moving, ever so slightly, all the time. This slow, small, but persistent movement of the Earth's crust is responsible for the formation of mountain ranges, sudden earthquakes, and even the positions of the continents. Scientists around the world measure these almost imperceptible movements using arrays of Global Navigation Satellite System (GNSS) receivers to better understand all phases of an earthquake cycle—both how the surface responds after an earthquake, and the storage of strain energy between earthquakes.

To help researchers explore this data and better understand the Earthquake cycle, we are releasing a new, interactive data visualization which draws geodetic velocity lines on top of a relief map by amplifying position estimates relative to their true positions. Unlike existing approaches, which focus on small time slices or individual stations, our visualization can show all the data for a whole array of stations at once. Open sourced under an Apache 2 license, and available on GitHub, this visualization technique is a collaboration between Harvard’s Department of Earth and Planetary Sciences and Google's Machine Perception and Big Picture teams.

Our approach helps scientists quickly assess deformations across all phases of the earthquake cycle—both during earthquakes (coseismic) and the time between (interseismic). For example, we can see azimuth (direction) reversals of stations as they relate to topographic structures and active faults. Digging into these movements will help scientists vet their models and their data, both of which are crucial for developing accurate computer representations that may help predict future earthquakes.

Classical approaches to visualizing these data have fallen into two general categories: 1) a map view of velocity/displacement vectors over a fixed time interval and 2) time versus position plots of each GNSS component (longitude, latitude and altitude).

Examples of classical approaches. On the left is a map view showing average velocity vectors over the period from 1997 to 2001[1]. On the right you can see a time versus eastward (longitudinal) position plot for a single station.

Each of these approaches have proved to be informative ways to understand the spatial distribution of crustal movements and the time evolution of solid earth deformation. However, because geodetic shifts happen in almost imperceptible distances (mm) and over long timescales, both approaches can only show a small subset of the data at any time—a condensed average velocity per station, or a detailed view of a single station, respectively. Our visualization enables a scientist to see all the data at once, then interactively drill down to a specific subset of interest.

Our visualization approach is straightforward; by magnifying the daily longitude and latitude position changes, we show tracks of the evolution of the position of each station. These magnified position tracks are shown as trails on top of a shaded relief topography to provide a sense of position evolution in geographic context.

To see how it works in practice, let’s step through an an example. Consider this tiny set of longitude/latitude pairs for a single GNSS station, with the differing digits shown in bold:


Day IndexLongitudeLatitude
0139.0699040734.949757897
1139.0699040034.949757882
2139.0699041334.949757941
3139.0699040934.949757921
4139.0699041334.949757904

If we were to draw line segments between these points directly on a map, they’d be much too small to see at any reasonable scale. So we take these minute differences and multiply them by a user-controlled scaling factor. By default this factor is 105.5 (about 316,000x).


To help the user identify which end is the start of the line, we give the start and end points different colors and interpolate between them. Blue and red are the default colors, but they’re user-configurable. Although day-to-day movement of stations may seem erratic, by using this method, one can make out a general trend in the relative motion of a station.
Close-up of a single station’s movement during the three year period from 2003 to 2006.
However, static renderings of this sort suffer from the same problem that velocity vector images do; in regions with a high density of GNSS stations, tracks overlap significantly with one another, obscuring details. To solve this problem, our visualization lets the user interactively control the time range of interest, the amount of amplification and other settings. In addition, by animating the lines from start to finish, the user gets a real sense of motion that’s difficult to achieve in a static image.

We’ve applied our new visualization to the ~20 years of data from the GEONET array in Japan. Through it, we can see small but coherent changes in direction before and after the great 2011 Tohoku earthquake.
GPS data sets (in .json format) for both the GEONET data in Japan and the Plate Boundary Observatory (PBO) data in the western US are available at earthquake.rc.fas.harvard.edu.
This short animation shows many of the visualization’s interactive features. In order:
  1. Modifying the multiplier adjusts how significantly the movements are magnified.
  2. We can adjust the time slider nubs to select a particular time range of interest.
  3. Using the map controls provided by the Google Maps JavaScript API, we can zoom into a tiny region of the map.
  4. By enabling map markers, we can see information about individual GNSS stations.
By focusing on a stations of interest, we can even see curvature changes in the time periods before and after the event.
Station designate 960601 of Japan’s GEONET array during the period from 2006 to 2012. Movement magnified 105.1 times (126,000x).
To achieve fast rendering of the line segments, we created a custom overlay using THREE.js to render the lines in WebGL. Data for the GNSS stations is passed to the GPU in a data texture, which allows our vertex shader to position each point on-screen dynamically based on user settings and animation.

We’re excited to continue this productive collaboration between Harvard and Google as we explore opportunities for groundbreaking, new earthquake visualizations. If you’d like to try out the visualization yourself, follow the instructions at earthquake.rc.fas.harvard.edu. It will walk you through the setup steps, including how to download the available data sets. If you’d like to report issues, great! Please submit them through the GitHub project page.

Acknowledgments

We wish to thank Bill Freeman, a researcher on Machine Perception, who hatched the idea and developed the initial prototypes, and Fernanda Viégas and Martin Wattenberg of the Big Picture team for their visualization design guidance.

References

[1] Loveless, J. P., and Meade, B. J. (2010). Geodetic imaging of plate motions, slip rates, and partitioning of deformation in Japan, Journal of Geophysical Research.

By Jimbo Wilson, Software Engineer, Big Picture Team and Brendan Meade, Professor, Harvard Department of Earth and Planetary Sciences