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How Fake Viruses Can Help Us Make the Best Possible Vaccines

Roughly 15 years ago, in a seeming prank, a pair of smiley faces graced the cover of Nature, one of the world’s preeminent science journals. Flash forward to today, and those smiley faces may be key to saving us from the Covid-19 pandemic—or other viral foes lurking in our future. The smiley faces were an […]

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Roughly 15 years ago, in a seeming prank, a pair of smiley faces graced the cover of Nature, one of the world’s preeminent science journals. Flash forward to today, and those smiley faces may be key to saving us from the Covid-19 pandemic—or other viral foes lurking in our future.

The smiley faces were an early example of DNA origami, a method of folding DNA—the biological hardware on which life’s code is written—into biomolecular machines. These nanostructures can do more than just create famous images under the microscope. When folded into 3D shapes resembling natural viruses, they become the perfect Trojan horses to safely train our immune system to make antibodies that can attack the real thing.

That is, DNA origami may help us make a new generation of highly efficient designer vaccines.

This month, in a paper published in Nature Nanotechnology, a team led by MIT’s Dr. Darrell Irvine and Dr. Mark Bathe described how they systematically built virus-like DNA structures to probe the laws of vaccine design. By coating DNA origami nanoparticles with proteins that normally dot the surface of HIV viruses, the team teased out how viral proteins—dubbed “antigens”—should be arranged to better stimulate an immune response, and thus, make a stronger vaccine.

It’s like working out where to place blueberries on a muffin to get the best taste. But in this case the “muffin” is a 3D, 20-face die made of synthetic DNA, and the blueberries are protruding strands tipped with viral antigens (the things that trigger the immune system).

Although their initial focus was on HIV, the team is rapidly pivoting to SARS-CoV-2, the virus that causes Covid-19.

“DNA origami has offered crucial insight,” the team said. “The rough design rules that are starting to come out of this work should be generically applicable across disease antigens and diseases,” added Irvine.

DN-Ori-What?

DNA’s weirdly bipolar in the biomedical world.

On one hand, it’s massively important as the blueprint of life. On the other, it’s a sturdy, boring molecule that isn’t electrically, chemically, or optically active. Sure, it’s great for long-term, compact data storage. But everything else? Seemingly inept.

At least, that was the general consensus, until Dr. Nadrian Seeman came along. A chemistry professor at New York University, Seeman realized in the 1980s that he could tap DNA’s ability to self-assemble into precise and repeatable nanostructures. All he needed was a long, two-dimensional chain—natural or synthetic—and the chain should fold itself automatically, similar to how it folds into the double helix inside our bodies.

That spark of insight ignited the field of DNA origami. Named after the traditional Japanese art of folding paper, origami “invokes the idea of starting with a simple object—a square of paper pregnant with possibilities—that we can fold into any shape we want,” said Dr. Paul Rothemund at Caltech, who uses the technology for nanoscale electronics and photonics.

Since Seeman’s revolutionary idea, scientists have learned to build DNA nanomachines of a dazzling variety. Rather than manually folding DNA into complex shapes, scientists can put together planned sequences of molecules that trigger self-assembly into desired structures (like a smiley face or 20-sided die). These “living” structures can hunt down and capture proteins, so we understand how they work. They can also deliver drugs or act as a biological “circuit board” on which biomolecules perform traditional computations.

Yet of all these possibilities, one has gained special prominence: Folded DNA nanoparticles that mimic viral cores in size and shape. These cores can then be dotted with any antigen to trigger an immune response.

That is, the code of life can now be disguised as a full-fledged viral enemy to train the protein descendants of that code. Whoa.

DNA Trojan Horses

Viruses are deadly, but biologically simple. Generally, they have just two main components: one, their genetic code—strands of either DNA or RNA—and two, a layer of outer proteins that help the virus invade cells to replicate. Picture a pin cushion, only replace the pins with antigen proteins, and you’re pretty much there.

How viruses interact with our immune system, however, is far more complicated. Generally, the antigen “pins” catch the attention of a type of immune cell called a B cell, which triggers the production of antibodies. Released throughout the body, these antibodies neutralize the virus and protect the rest of us from infection. So, optimizing the interaction between the antigen “pins” and B cells is critical to making vaccines that actually work.

Here’s where DNA origami comes in.

Rather than using live viruses or ones that are less deadly, we can simulate viruses using DNA nanoparticles. Back in 2016, Bathe’s lab developed an algorithm to consistently build viral-like 3D shapes out of DNA. Even better, it’s possible to engineer attachment anchors onto these basic shapes, which makes it easy to play with different viral structures and see how those structural changes, in turn, alter our B cell response.

“The DNA structure is like a pegboard where the antigens can be attached at any position,” said Bathe. Other researchers have tried using proteins or polymers to mimic the viral core before, the team explained, but are limited in the variety of viral protein placements because of the material’s properties.

DNA origami, then, is a great way to understand what triggers a strong antibody attack.

New Rules to Vaccines

As a proof-of-concept, the team first engineered DNA strands that self-folded into the shape of a 20-sided die, also called an icosahedron. D&D jokes aside, the shape and size of the nanoparticles perfectly mimicked the size of most viruses. Short floating attachment anchors sprouted from the dice, like an octopus’s arms, each chemically fused to an antigen protein.

By changing the location and density of the anchors on the DNA nanoparticle, the team could systematically test which antigen patterns best triggered B cells into antibody-spewing action.

The team first tagged gp120—a protein normally scattered across an HIV particle—to the nanoparticles’ anchors at various densities and distances. Thus, they made a variety of pseudo-HIV particles—some less potent, others a hell of a lot more. According to the authors, the traditional vaccine-making strategy is to pile as many of these gp120 proteins as possible onto a fake virus. After all, the more protein targets for the immune system, the better the antibody response, right?

Surprisingly, no. A few experiments showed that more isn’t always better. Packing antigens all over the DNA nanoparticle surface didn’t trigger the best response. Instead, when they widened the distance between the anchors the immune response actually went up.

This is likely because our immune B cells need some space to grab onto each viral antigen, the authors explained. If too tightly packed, the B cells simply can’t squeeze in.

Path Towards Rational Vaccine Design

Aggregating their results, the authors put forth a new model for optimal B cell activation—that is, the best types of fake viruses to stimulate an antibody response against HIV.

For example, a DNA origami particle needs at least five or more antigen proteins on its surface, but the antigens also need a bit of separation. And it’s beneficial to use rigid anchors, rather than floppy ones, to attach antigens to the nanoparticle.

The study used HIV as an example, but the system is ready to examine another foe—SARS-CoV-2.

“Our platform technology allows you to easily swap out different subunit antigens and peptides from different types of viruses to test whether they may potentially be functional as vaccines,” said Bathe.

As positive cases are again spiking in the south and southwest United States, the team is rapidly pivoting their DNA nanomachines to mimic the new coronavirus, in hopes of informing better vaccine design. DNA origami, like its namesake, is now living out one of its endless possibilities.

Image credit: Colin BehrensPixabay 

Source: https://singularityhub.com/2020/07/07/how-fake-viruses-can-help-us-make-powerful-new-vaccines/

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Bringing real-time machine learning-powered insights to rugby using Amazon SageMaker

The Guinness Six Nations Championship began in 1883 as the Home Nations Championship among England, Ireland, Scotland, and Wales, with the inclusion of France in 1910 and Italy in 2000. It is among the oldest surviving rugby traditions and one of the best-attended sporting events in the world. The COVID-19 outbreak disrupted the end of […]

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The Guinness Six Nations Championship began in 1883 as the Home Nations Championship among England, Ireland, Scotland, and Wales, with the inclusion of France in 1910 and Italy in 2000. It is among the oldest surviving rugby traditions and one of the best-attended sporting events in the world. The COVID-19 outbreak disrupted the end of the 2020 Championship and four games were postponed. The remaining rounds resumed on October 24. With the increasing application of artificial intelligence and machine learning (ML) in sports analytics, AWS and Stats Perform partnered to bring ML-powered, real-time stats to the game of rugby, to enhance fan engagement and provide valuable insights into the game.

This post summarizes the collaborative effort between the Guinness Six Nations Rugby Championship, Stats Perform, and AWS to develop an ML-driven approach with Amazon SageMaker and other AWS services that predicts the probability of a successful penalty kick, computed in real time and broadcast live during the game. AWS infrastructure enables single-digit millisecond latency for kick predictions during inference. The Kick Predictor stat is one of the many new AWS-powered, on-screen dynamic Matchstats that provide fans with a greater understanding of key in-game events, including scrum analysis, play patterns, rucks and tackles, and power game analysis. For more information about other stats developed for rugby using AWS services, see the Six Nations Rugby website.

Rugby is a form of football with a 23-player match day squad. 15 players on each team are on the field, with additional substitutions waiting to get involved in the full-contact sport. The objective of the game is to outscore the opposing team, and one way of scoring is to kick a goal. The ability to kick accurately is one of the most critical elements of rugby, and there are two ways to score with a kick: through a conversion (worth two points) and a penalty (worth three points).

Predicting the likelihood of a successful kick is important because it enhances fan engagement during the game by showing the success probability before the player kicks the ball. There are usually 40–60 seconds of stoppage time while the player sets up for the kick, during which the Kick Predictor stat can appear on-screen to fans. Commentators also have time to predict the outcome, quantify the difficulty of each kick, and compare kickers in similar situations. Moreover, teams may start to use kicking probability models in the future to determine which player should kick given the position of the penalty on the pitch.

Developing an ML solution

To calculate the penalty success probability, the Amazon Machine Learning Solutions Lab used Amazon SageMaker to train, test, and deploy an ML model from historical in-game events data, which calculates the kick predictions from anywhere in the field. The following sections explain the dataset and preprocessing steps, the model training, and model deployment procedures.

Dataset and preprocessing

Stats Perform provided the dataset for training the goal kick model. It contained millions of events from historical rugby matches from 46 leagues from 2007–2019. The raw JSON events data that was collected during live rugby matches was ingested and stored on Amazon Simple Storage Service (Amazon S3). It was then parsed and preprocessed in an Amazon SageMaker notebook instance. After selecting the kick-related events, the training data comprised approximately 67,000 kicks, with approximately 50,000 (75%) successful kicks and 17,000 misses (25%).

The following graph shows a summary of kicks taken during a sample game. The athletes kicked from different angles and various distances.

Rugby experts contributed valuable insights to the data preprocessing, which included detecting and removing anomalies, such as unreasonable kicks. The clean CSV data went back to an S3 bucket for ML training.

The following graph depicts the heatmap of the kicks after preprocessing. The left-side kicks are mirrored. The brighter colors indicated a higher chance of scoring, standardized between 0 to 1.

Feature engineering

To better capture the real-world event, the ML Solutions Lab engineered several features using exploratory data analysis and insights from rugby experts. The features that went into the modeling fell into three main categories:

  • Location-based features – The zone in which the athlete takes the kick and the distance and angle of the kick to the goal. The x-coordinates of the kicks are mirrored along the center of the rugby pitch to eliminate the left or right bias in the model.
  • Player performance features – The mean success rates of the kicker in a given field zone, in the Championship, and in the kicker’s entire career.
  • In-game situational features – The kicker’s team (home or away), the scoring situation before they take the kick, and the period of the game in which they take the kick.

The location-based and player performance features are the most important features in the model.

After feature engineering, the categorical variables were one-hot encoded, and to avoid the bias of the model towards large-value variables, the numerical predictors were standardized. During the model training phase, a player’s historical performance features were pushed to Amazon DynamoDB tables. DynamoDB helped provide single-digit millisecond latency for kick predictions during inference.

Training and deploying models

To explore a wide range of classification algorithms (such as logistic regression, random forests, XGBoost, and neural networks), a 10-fold stratified cross-validation approach was used for model training. After exploring different algorithms, the built-in XGBoost in Amazon SageMaker was used due to its better prediction performance and inference speed. Additionally, its implementation has a smaller memory footprint, better logging, and improved hyperparameter optimization (HPO) compared to the original code base.

HPO, or tuning, is the process of choosing a set of optimal hyperparameters for a learning algorithm, and is a challenging element in any ML problem. HPO in Amazon SageMaker uses an implementation of Bayesian optimization to choose the best hyperparameters for the next training job. Amazon SageMaker HPO automatically launches multiple training jobs with different hyperparameter settings, evaluates the results of those training jobs based on a predefined objective metric, and selects improved hyperparameter settings for future attempts based on previous results.

The following diagram illustrates the model training workflow.

Optimizing hyperparameters in Amazon SageMaker

You can configure training jobs and when the hyperparameter tuning job launches by initializing an estimator, which includes the container image for the algorithm (for this use case, XGBoost), configuration for the output of the training jobs, the values of static algorithm hyperparameters, and the type and number of instances to use for the training jobs. For more information, see Train a Model.

To create the XGBoost estimator for this use case, enter the following code:

import boto3
import sagemaker
from sagemaker.tuner import IntegerParameter, CategoricalParameter, ContinuousParameter, HyperparameterTuner
from sagemaker.amazon.amazon_estimator import get_image_uri
BUCKET = <bucket name>
PREFIX = 'kicker/xgboost/'
region = boto3.Session().region_name
role = sagemaker.get_execution_role()
smclient = boto3.Session().client('sagemaker')
sess = sagemaker.Session()
s3_output_path = ‘s3://{}/{}/output’.format(BUCKET, PREFIX) container = get_image_uri(region, 'xgboost', repo_version='0.90-1') xgb = sagemaker.estimator.Estimator(container, role, train_instance_count=4, train_instance_type= 'ml.m4.xlarge', output_path=s3_output_path, sagemaker_session=sess)

After you create the XGBoost estimator object, set its initial hyperparameter values as shown in the following code:

xgb.set_hyperparameters(eval_metric='auc', objective= 'binary:logistic', num_round=200, rate_drop=0.3, max_depth=5, subsample=0.8, gamma=2, eta=0.2, scale_pos_weight=2.85) #For class imbalance weights # Specifying the objective metric (auc on validation set)
OBJECTIVE_METRIC_NAME = ‘validation:auc’ # specifying the hyper parameters and their ranges
HYPERPARAMETER_RANGES = {'eta': ContinuousParameter(0, 1), 'alpha': ContinuousParameter(0, 2), 'max_depth': IntegerParameter(1, 10)}

For this post, AUC (area under the ROC curve) is the evaluation metric. This enables the tuning job to measure the performance of the different training jobs. The kick prediction is also a binary classification problem, which is specified in the objective argument as a binary:logistic. There is also a set of XGBoost-specific hyperparameters that you can tune. For more information, see Tune an XGBoost model.

Next, create a HyperparameterTuner object by indicating the XGBoost estimator, the hyperparameter ranges, passing the parameters, the objective metric name and definition, and tuning resource configurations, such as the number of training jobs to run in total and how many training jobs can run in parallel. Amazon SageMaker extracts the metric from Amazon CloudWatch Logs with a regular expression. See the following code:

tuner = HyperparameterTuner(xgb, OBJECTIVE_METRIC_NAME, HYPERPARAMETER_RANGES, max_jobs=20, max_parallel_jobs=4)
s3_input_train = sagemaker.s3_input(s3_data='s3://{}/{}/train'.format(BUCKET, PREFIX), content_type='csv')
s3_input_validation = sagemaker.s3_input(s3_data='s3://{}/{}/validation/'.format(BUCKET, PREFIX), content_type='csv')
tuner.fit({'train': s3_input_train, 'validation':

Finally, launch a hyperparameter tuning job by calling the fit() function. This function takes the paths of the training and validation datasets in the S3 bucket. After you create the hyperparameter tuning job, you can track its progress via the Amazon SageMaker console. The training time depends on the instance type and number of instances you selected during tuning setup.

Deploying the model on Amazon SageMaker

When the training jobs are complete, you can deploy the best performing model. If you’d like to compare models for A/B testing, Amazon SageMaker supports hosting representational state transfer (REST) endpoints for multiple models. To set this up, create an endpoint configuration that describes the distribution of traffic across the models. In addition, the endpoint configuration describes the instance type required for model deployment. The first step is to get the name of the best performing training job and create the model name.

After you create the endpoint configuration, you’re ready to deploy the actual endpoint for serving inference requests. The result is an endpoint that can you can validate and incorporate into production applications. For more information about deploying models, see Deploy the Model to Amazon SageMaker Hosting Services. To create the endpoint configuration and deploy it, enter the following code:

endpoint_name = 'Kicker-XGBoostEndpoint'
xgb_predictor = tuner.deploy(initial_instance_count=1, instance_type='ml.t2.medium', endpoint_name=endpoint_name)

After you create the endpoint, you can request a prediction in real time.

Building a RESTful API for real-time model inference

You can create a secure and scalable RESTful API that enables you to request the model prediction based on the input values. It’s easy and convenient to develop different APIs using AWS services.

The following diagram illustrates the model inference workflow.

First, you request the probability of the kick conversion by passing parameters through Amazon API Gateway, such as the location and zone of the kick, kicker ID, league and Championship ID, the game’s period, if the kicker’s team is playing home or away, and the team score status.

The API Gateway passes the values to the AWS Lambda function, which parses the values and requests additional features related to the player’s performance from DynamoDB lookup tables. These include the mean success rates of the kicking player in a given field zone, in the Championship, and in the kicker’s entire career. If the player doesn’t exist in the database, the model uses the average performance in the database in the given kicking location. After the function combines all the values, it standardizes the data and sends it to the Amazon SageMaker model endpoint for prediction.

The model performs the prediction and returns the predicted probability to the Lambda function. The function parses the returned value and sends it back to API Gateway. API Gateway responds with the output prediction. The end-to-end process latency is less than a second.

The following screenshot shows example input and output of the API. The RESTful API also outputs the average success rate of all the players in the given location and zone to get the comparison of the player’s performance with the overall average.

For instructions on creating a RESTful API, see Call an Amazon SageMaker model endpoint using Amazon API Gateway and AWS Lambda.

Bringing design principles into sports analytics

To create the first real-time prediction model for the tournament with a millisecond latency requirement, the ML Solutions Lab team worked backwards to identify areas in which design thinking could save time and resources. The team worked on an end-to-end notebook within an Amazon SageMaker environment, which enabled data access, raw data parsing, data preprocessing and visualization, feature engineering, model training and evaluation, and model deployment in one place. This helped in automating the modeling process.

Moreover, the ML Solutions Lab team implemented a model update iteration for when the model was updated with newly generated data, in which the model parses and processes only the additional data. This brings computational and time efficiencies to the modeling.

In terms of next steps, the Stats Perform AI team has been looking at the next stage of rugby analysis by breaking down the other strategic facets as line-outs, scrums and teams, and continuous phases of play using the fine-grain spatio-temporal data captured. The state-of-the-art feature representations and latent factor modelling (which have been utilized so effectively in Stats Perform’s “Edge” match-analysis and recruitment products in soccer) means that there is plenty of fertile space for innovation that can be explored in rugby.

Conclusion

Six Nations Rugby, Stats Perform, and AWS came together to bring the first real-time prediction model to the 2020 Guinness Six Nations Rugby Championship. The model determined a penalty or conversion kick success probability from anywhere in the field. They used Amazon SageMaker to build, train, and deploy the ML model with variables grouped into three main categories: location-based features, player performance features, and in-game situational features. The Amazon SageMaker endpoint provided prediction results with subsecond latency. The model was used by broadcasters during the live games in the Six Nations 2020 Championship, bringing a new metric to millions of rugby fans.

You can find full, end-to-end examples of creating custom training jobs, training state-of-the-art object detection models, and model deployment on Amazon SageMaker on the AWS Labs GitHub repo. To learn more about the ML Solutions Lab, see Amazon Machine Learning Solutions Lab.


About the Authors

Mehdi Noori is a Data Scientist at the Amazon ML Solutions Lab, where he works with customers across various verticals, and helps them to accelerate their cloud migration journey, and to solve their ML problems using state-of-the-art solutions and technologies.

Tesfagabir Meharizghi is a Data Scientist at the Amazon ML Solutions Lab where he works with customers across different verticals accelerate their use of artificial intelligence and AWS cloud services to solve their business challenges. Outside of work, he enjoys spending time with his family and reading books.

Patrick Lucey is the Chief Scientist at Stats Perform. Patrick started the Artificial Intelligence group at Stats Perform in 2015, with thegroup focusing on both computer vision and predictive modelling capabilities in sport. Previously, he was at Disney Research for 5 years, where he conducted research into automatic sports broadcasting using large amounts of spatiotemporal tracking data. He received his BEng(EE) from USQ and PhD from QUT, Australia in 2003 and 2008 respectively. He was also co-author of the best paper at the 2016 MIT Sloan Sports Analytics Conference and in 2017 & 2018 was co-author of best-paper runner-up at the same conference.

Xavier Ragot is Data Scientist with the Amazon ML Solution Lab team where he helps design creative ML solution to address customers’ business problems in various industries.

Source: https://aws.amazon.com/blogs/machine-learning/bringing-real-time-machine-learning-powered-insights-to-rugby-using-amazon-sagemaker/

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Bringing real-time machine learning-powered insights to rugby using Amazon SageMaker

The Guinness Six Nations Championship began in 1883 as the Home Nations Championship among England, Ireland, Scotland, and Wales, with the inclusion of France in 1910 and Italy in 2000. It is among the oldest surviving rugby traditions and one of the best-attended sporting events in the world. The COVID-19 outbreak disrupted the end of […]

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The Guinness Six Nations Championship began in 1883 as the Home Nations Championship among England, Ireland, Scotland, and Wales, with the inclusion of France in 1910 and Italy in 2000. It is among the oldest surviving rugby traditions and one of the best-attended sporting events in the world. The COVID-19 outbreak disrupted the end of the 2020 Championship and four games were postponed. The remaining rounds resumed on October 24. With the increasing application of artificial intelligence and machine learning (ML) in sports analytics, AWS and Stats Perform partnered to bring ML-powered, real-time stats to the game of rugby, to enhance fan engagement and provide valuable insights into the game.

This post summarizes the collaborative effort between the Guinness Six Nations Rugby Championship, Stats Perform, and AWS to develop an ML-driven approach with Amazon SageMaker and other AWS services that predicts the probability of a successful penalty kick, computed in real time and broadcast live during the game. AWS infrastructure enables single-digit millisecond latency for kick predictions during inference. The Kick Predictor stat is one of the many new AWS-powered, on-screen dynamic Matchstats that provide fans with a greater understanding of key in-game events, including scrum analysis, play patterns, rucks and tackles, and power game analysis. For more information about other stats developed for rugby using AWS services, see the Six Nations Rugby website.

Rugby is a form of football with a 23-player match day squad. 15 players on each team are on the field, with additional substitutions waiting to get involved in the full-contact sport. The objective of the game is to outscore the opposing team, and one way of scoring is to kick a goal. The ability to kick accurately is one of the most critical elements of rugby, and there are two ways to score with a kick: through a conversion (worth two points) and a penalty (worth three points).

Predicting the likelihood of a successful kick is important because it enhances fan engagement during the game by showing the success probability before the player kicks the ball. There are usually 40–60 seconds of stoppage time while the player sets up for the kick, during which the Kick Predictor stat can appear on-screen to fans. Commentators also have time to predict the outcome, quantify the difficulty of each kick, and compare kickers in similar situations. Moreover, teams may start to use kicking probability models in the future to determine which player should kick given the position of the penalty on the pitch.

Developing an ML solution

To calculate the penalty success probability, the Amazon Machine Learning Solutions Lab used Amazon SageMaker to train, test, and deploy an ML model from historical in-game events data, which calculates the kick predictions from anywhere in the field. The following sections explain the dataset and preprocessing steps, the model training, and model deployment procedures.

Dataset and preprocessing

Stats Perform provided the dataset for training the goal kick model. It contained millions of events from historical rugby matches from 46 leagues from 2007–2019. The raw JSON events data that was collected during live rugby matches was ingested and stored on Amazon Simple Storage Service (Amazon S3). It was then parsed and preprocessed in an Amazon SageMaker notebook instance. After selecting the kick-related events, the training data comprised approximately 67,000 kicks, with approximately 50,000 (75%) successful kicks and 17,000 misses (25%).

The following graph shows a summary of kicks taken during a sample game. The athletes kicked from different angles and various distances.

Rugby experts contributed valuable insights to the data preprocessing, which included detecting and removing anomalies, such as unreasonable kicks. The clean CSV data went back to an S3 bucket for ML training.

The following graph depicts the heatmap of the kicks after preprocessing. The left-side kicks are mirrored. The brighter colors indicated a higher chance of scoring, standardized between 0 to 1.

Feature engineering

To better capture the real-world event, the ML Solutions Lab engineered several features using exploratory data analysis and insights from rugby experts. The features that went into the modeling fell into three main categories:

  • Location-based features – The zone in which the athlete takes the kick and the distance and angle of the kick to the goal. The x-coordinates of the kicks are mirrored along the center of the rugby pitch to eliminate the left or right bias in the model.
  • Player performance features – The mean success rates of the kicker in a given field zone, in the Championship, and in the kicker’s entire career.
  • In-game situational features – The kicker’s team (home or away), the scoring situation before they take the kick, and the period of the game in which they take the kick.

The location-based and player performance features are the most important features in the model.

After feature engineering, the categorical variables were one-hot encoded, and to avoid the bias of the model towards large-value variables, the numerical predictors were standardized. During the model training phase, a player’s historical performance features were pushed to Amazon DynamoDB tables. DynamoDB helped provide single-digit millisecond latency for kick predictions during inference.

Training and deploying models

To explore a wide range of classification algorithms (such as logistic regression, random forests, XGBoost, and neural networks), a 10-fold stratified cross-validation approach was used for model training. After exploring different algorithms, the built-in XGBoost in Amazon SageMaker was used due to its better prediction performance and inference speed. Additionally, its implementation has a smaller memory footprint, better logging, and improved hyperparameter optimization (HPO) compared to the original code base.

HPO, or tuning, is the process of choosing a set of optimal hyperparameters for a learning algorithm, and is a challenging element in any ML problem. HPO in Amazon SageMaker uses an implementation of Bayesian optimization to choose the best hyperparameters for the next training job. Amazon SageMaker HPO automatically launches multiple training jobs with different hyperparameter settings, evaluates the results of those training jobs based on a predefined objective metric, and selects improved hyperparameter settings for future attempts based on previous results.

The following diagram illustrates the model training workflow.

Optimizing hyperparameters in Amazon SageMaker

You can configure training jobs and when the hyperparameter tuning job launches by initializing an estimator, which includes the container image for the algorithm (for this use case, XGBoost), configuration for the output of the training jobs, the values of static algorithm hyperparameters, and the type and number of instances to use for the training jobs. For more information, see Train a Model.

To create the XGBoost estimator for this use case, enter the following code:

import boto3
import sagemaker
from sagemaker.tuner import IntegerParameter, CategoricalParameter, ContinuousParameter, HyperparameterTuner
from sagemaker.amazon.amazon_estimator import get_image_uri
BUCKET = <bucket name>
PREFIX = 'kicker/xgboost/'
region = boto3.Session().region_name
role = sagemaker.get_execution_role()
smclient = boto3.Session().client('sagemaker')
sess = sagemaker.Session()
s3_output_path = ‘s3://{}/{}/output’.format(BUCKET, PREFIX) container = get_image_uri(region, 'xgboost', repo_version='0.90-1') xgb = sagemaker.estimator.Estimator(container, role, train_instance_count=4, train_instance_type= 'ml.m4.xlarge', output_path=s3_output_path, sagemaker_session=sess)

After you create the XGBoost estimator object, set its initial hyperparameter values as shown in the following code:

xgb.set_hyperparameters(eval_metric='auc', objective= 'binary:logistic', num_round=200, rate_drop=0.3, max_depth=5, subsample=0.8, gamma=2, eta=0.2, scale_pos_weight=2.85) #For class imbalance weights # Specifying the objective metric (auc on validation set)
OBJECTIVE_METRIC_NAME = ‘validation:auc’ # specifying the hyper parameters and their ranges
HYPERPARAMETER_RANGES = {'eta': ContinuousParameter(0, 1), 'alpha': ContinuousParameter(0, 2), 'max_depth': IntegerParameter(1, 10)}

For this post, AUC (area under the ROC curve) is the evaluation metric. This enables the tuning job to measure the performance of the different training jobs. The kick prediction is also a binary classification problem, which is specified in the objective argument as a binary:logistic. There is also a set of XGBoost-specific hyperparameters that you can tune. For more information, see Tune an XGBoost model.

Next, create a HyperparameterTuner object by indicating the XGBoost estimator, the hyperparameter ranges, passing the parameters, the objective metric name and definition, and tuning resource configurations, such as the number of training jobs to run in total and how many training jobs can run in parallel. Amazon SageMaker extracts the metric from Amazon CloudWatch Logs with a regular expression. See the following code:

tuner = HyperparameterTuner(xgb, OBJECTIVE_METRIC_NAME, HYPERPARAMETER_RANGES, max_jobs=20, max_parallel_jobs=4)
s3_input_train = sagemaker.s3_input(s3_data='s3://{}/{}/train'.format(BUCKET, PREFIX), content_type='csv')
s3_input_validation = sagemaker.s3_input(s3_data='s3://{}/{}/validation/'.format(BUCKET, PREFIX), content_type='csv')
tuner.fit({'train': s3_input_train, 'validation':

Finally, launch a hyperparameter tuning job by calling the fit() function. This function takes the paths of the training and validation datasets in the S3 bucket. After you create the hyperparameter tuning job, you can track its progress via the Amazon SageMaker console. The training time depends on the instance type and number of instances you selected during tuning setup.

Deploying the model on Amazon SageMaker

When the training jobs are complete, you can deploy the best performing model. If you’d like to compare models for A/B testing, Amazon SageMaker supports hosting representational state transfer (REST) endpoints for multiple models. To set this up, create an endpoint configuration that describes the distribution of traffic across the models. In addition, the endpoint configuration describes the instance type required for model deployment. The first step is to get the name of the best performing training job and create the model name.

After you create the endpoint configuration, you’re ready to deploy the actual endpoint for serving inference requests. The result is an endpoint that can you can validate and incorporate into production applications. For more information about deploying models, see Deploy the Model to Amazon SageMaker Hosting Services. To create the endpoint configuration and deploy it, enter the following code:

endpoint_name = 'Kicker-XGBoostEndpoint'
xgb_predictor = tuner.deploy(initial_instance_count=1, instance_type='ml.t2.medium', endpoint_name=endpoint_name)

After you create the endpoint, you can request a prediction in real time.

Building a RESTful API for real-time model inference

You can create a secure and scalable RESTful API that enables you to request the model prediction based on the input values. It’s easy and convenient to develop different APIs using AWS services.

The following diagram illustrates the model inference workflow.

First, you request the probability of the kick conversion by passing parameters through Amazon API Gateway, such as the location and zone of the kick, kicker ID, league and Championship ID, the game’s period, if the kicker’s team is playing home or away, and the team score status.

The API Gateway passes the values to the AWS Lambda function, which parses the values and requests additional features related to the player’s performance from DynamoDB lookup tables. These include the mean success rates of the kicking player in a given field zone, in the Championship, and in the kicker’s entire career. If the player doesn’t exist in the database, the model uses the average performance in the database in the given kicking location. After the function combines all the values, it standardizes the data and sends it to the Amazon SageMaker model endpoint for prediction.

The model performs the prediction and returns the predicted probability to the Lambda function. The function parses the returned value and sends it back to API Gateway. API Gateway responds with the output prediction. The end-to-end process latency is less than a second.

The following screenshot shows example input and output of the API. The RESTful API also outputs the average success rate of all the players in the given location and zone to get the comparison of the player’s performance with the overall average.

For instructions on creating a RESTful API, see Call an Amazon SageMaker model endpoint using Amazon API Gateway and AWS Lambda.

Bringing design principles into sports analytics

To create the first real-time prediction model for the tournament with a millisecond latency requirement, the ML Solutions Lab team worked backwards to identify areas in which design thinking could save time and resources. The team worked on an end-to-end notebook within an Amazon SageMaker environment, which enabled data access, raw data parsing, data preprocessing and visualization, feature engineering, model training and evaluation, and model deployment in one place. This helped in automating the modeling process.

Moreover, the ML Solutions Lab team implemented a model update iteration for when the model was updated with newly generated data, in which the model parses and processes only the additional data. This brings computational and time efficiencies to the modeling.

In terms of next steps, the Stats Perform AI team has been looking at the next stage of rugby analysis by breaking down the other strategic facets as line-outs, scrums and teams, and continuous phases of play using the fine-grain spatio-temporal data captured. The state-of-the-art feature representations and latent factor modelling (which have been utilized so effectively in Stats Perform’s “Edge” match-analysis and recruitment products in soccer) means that there is plenty of fertile space for innovation that can be explored in rugby.

Conclusion

Six Nations Rugby, Stats Perform, and AWS came together to bring the first real-time prediction model to the 2020 Guinness Six Nations Rugby Championship. The model determined a penalty or conversion kick success probability from anywhere in the field. They used Amazon SageMaker to build, train, and deploy the ML model with variables grouped into three main categories: location-based features, player performance features, and in-game situational features. The Amazon SageMaker endpoint provided prediction results with subsecond latency. The model was used by broadcasters during the live games in the Six Nations 2020 Championship, bringing a new metric to millions of rugby fans.

You can find full, end-to-end examples of creating custom training jobs, training state-of-the-art object detection models, and model deployment on Amazon SageMaker on the AWS Labs GitHub repo. To learn more about the ML Solutions Lab, see Amazon Machine Learning Solutions Lab.


About the Authors

Mehdi Noori is a Data Scientist at the Amazon ML Solutions Lab, where he works with customers across various verticals, and helps them to accelerate their cloud migration journey, and to solve their ML problems using state-of-the-art solutions and technologies.

Tesfagabir Meharizghi is a Data Scientist at the Amazon ML Solutions Lab where he works with customers across different verticals accelerate their use of artificial intelligence and AWS cloud services to solve their business challenges. Outside of work, he enjoys spending time with his family and reading books.

Patrick Lucey is the Chief Scientist at Stats Perform. Patrick started the Artificial Intelligence group at Stats Perform in 2015, with thegroup focusing on both computer vision and predictive modelling capabilities in sport. Previously, he was at Disney Research for 5 years, where he conducted research into automatic sports broadcasting using large amounts of spatiotemporal tracking data. He received his BEng(EE) from USQ and PhD from QUT, Australia in 2003 and 2008 respectively. He was also co-author of the best paper at the 2016 MIT Sloan Sports Analytics Conference and in 2017 & 2018 was co-author of best-paper runner-up at the same conference.

Xavier Ragot is Data Scientist with the Amazon ML Solution Lab team where he helps design creative ML solution to address customers’ business problems in various industries.

Source: https://aws.amazon.com/blogs/machine-learning/bringing-real-time-machine-learning-powered-insights-to-rugby-using-amazon-sagemaker/

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Bringing real-time machine learning-powered insights to rugby using Amazon SageMaker

The Guinness Six Nations Championship began in 1883 as the Home Nations Championship among England, Ireland, Scotland, and Wales, with the inclusion of France in 1910 and Italy in 2000. It is among the oldest surviving rugby traditions and one of the best-attended sporting events in the world. The COVID-19 outbreak disrupted the end of […]

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The Guinness Six Nations Championship began in 1883 as the Home Nations Championship among England, Ireland, Scotland, and Wales, with the inclusion of France in 1910 and Italy in 2000. It is among the oldest surviving rugby traditions and one of the best-attended sporting events in the world. The COVID-19 outbreak disrupted the end of the 2020 Championship and four games were postponed. The remaining rounds resumed on October 24. With the increasing application of artificial intelligence and machine learning (ML) in sports analytics, AWS and Stats Perform partnered to bring ML-powered, real-time stats to the game of rugby, to enhance fan engagement and provide valuable insights into the game.

This post summarizes the collaborative effort between the Guinness Six Nations Rugby Championship, Stats Perform, and AWS to develop an ML-driven approach with Amazon SageMaker and other AWS services that predicts the probability of a successful penalty kick, computed in real time and broadcast live during the game. AWS infrastructure enables single-digit millisecond latency for kick predictions during inference. The Kick Predictor stat is one of the many new AWS-powered, on-screen dynamic Matchstats that provide fans with a greater understanding of key in-game events, including scrum analysis, play patterns, rucks and tackles, and power game analysis. For more information about other stats developed for rugby using AWS services, see the Six Nations Rugby website.

Rugby is a form of football with a 23-player match day squad. 15 players on each team are on the field, with additional substitutions waiting to get involved in the full-contact sport. The objective of the game is to outscore the opposing team, and one way of scoring is to kick a goal. The ability to kick accurately is one of the most critical elements of rugby, and there are two ways to score with a kick: through a conversion (worth two points) and a penalty (worth three points).

Predicting the likelihood of a successful kick is important because it enhances fan engagement during the game by showing the success probability before the player kicks the ball. There are usually 40–60 seconds of stoppage time while the player sets up for the kick, during which the Kick Predictor stat can appear on-screen to fans. Commentators also have time to predict the outcome, quantify the difficulty of each kick, and compare kickers in similar situations. Moreover, teams may start to use kicking probability models in the future to determine which player should kick given the position of the penalty on the pitch.

Developing an ML solution

To calculate the penalty success probability, the Amazon Machine Learning Solutions Lab used Amazon SageMaker to train, test, and deploy an ML model from historical in-game events data, which calculates the kick predictions from anywhere in the field. The following sections explain the dataset and preprocessing steps, the model training, and model deployment procedures.

Dataset and preprocessing

Stats Perform provided the dataset for training the goal kick model. It contained millions of events from historical rugby matches from 46 leagues from 2007–2019. The raw JSON events data that was collected during live rugby matches was ingested and stored on Amazon Simple Storage Service (Amazon S3). It was then parsed and preprocessed in an Amazon SageMaker notebook instance. After selecting the kick-related events, the training data comprised approximately 67,000 kicks, with approximately 50,000 (75%) successful kicks and 17,000 misses (25%).

The following graph shows a summary of kicks taken during a sample game. The athletes kicked from different angles and various distances.

Rugby experts contributed valuable insights to the data preprocessing, which included detecting and removing anomalies, such as unreasonable kicks. The clean CSV data went back to an S3 bucket for ML training.

The following graph depicts the heatmap of the kicks after preprocessing. The left-side kicks are mirrored. The brighter colors indicated a higher chance of scoring, standardized between 0 to 1.

Feature engineering

To better capture the real-world event, the ML Solutions Lab engineered several features using exploratory data analysis and insights from rugby experts. The features that went into the modeling fell into three main categories:

  • Location-based features – The zone in which the athlete takes the kick and the distance and angle of the kick to the goal. The x-coordinates of the kicks are mirrored along the center of the rugby pitch to eliminate the left or right bias in the model.
  • Player performance features – The mean success rates of the kicker in a given field zone, in the Championship, and in the kicker’s entire career.
  • In-game situational features – The kicker’s team (home or away), the scoring situation before they take the kick, and the period of the game in which they take the kick.

The location-based and player performance features are the most important features in the model.

After feature engineering, the categorical variables were one-hot encoded, and to avoid the bias of the model towards large-value variables, the numerical predictors were standardized. During the model training phase, a player’s historical performance features were pushed to Amazon DynamoDB tables. DynamoDB helped provide single-digit millisecond latency for kick predictions during inference.

Training and deploying models

To explore a wide range of classification algorithms (such as logistic regression, random forests, XGBoost, and neural networks), a 10-fold stratified cross-validation approach was used for model training. After exploring different algorithms, the built-in XGBoost in Amazon SageMaker was used due to its better prediction performance and inference speed. Additionally, its implementation has a smaller memory footprint, better logging, and improved hyperparameter optimization (HPO) compared to the original code base.

HPO, or tuning, is the process of choosing a set of optimal hyperparameters for a learning algorithm, and is a challenging element in any ML problem. HPO in Amazon SageMaker uses an implementation of Bayesian optimization to choose the best hyperparameters for the next training job. Amazon SageMaker HPO automatically launches multiple training jobs with different hyperparameter settings, evaluates the results of those training jobs based on a predefined objective metric, and selects improved hyperparameter settings for future attempts based on previous results.

The following diagram illustrates the model training workflow.

Optimizing hyperparameters in Amazon SageMaker

You can configure training jobs and when the hyperparameter tuning job launches by initializing an estimator, which includes the container image for the algorithm (for this use case, XGBoost), configuration for the output of the training jobs, the values of static algorithm hyperparameters, and the type and number of instances to use for the training jobs. For more information, see Train a Model.

To create the XGBoost estimator for this use case, enter the following code:

import boto3
import sagemaker
from sagemaker.tuner import IntegerParameter, CategoricalParameter, ContinuousParameter, HyperparameterTuner
from sagemaker.amazon.amazon_estimator import get_image_uri
BUCKET = <bucket name>
PREFIX = 'kicker/xgboost/'
region = boto3.Session().region_name
role = sagemaker.get_execution_role()
smclient = boto3.Session().client('sagemaker')
sess = sagemaker.Session()
s3_output_path = ‘s3://{}/{}/output’.format(BUCKET, PREFIX) container = get_image_uri(region, 'xgboost', repo_version='0.90-1') xgb = sagemaker.estimator.Estimator(container, role, train_instance_count=4, train_instance_type= 'ml.m4.xlarge', output_path=s3_output_path, sagemaker_session=sess)

After you create the XGBoost estimator object, set its initial hyperparameter values as shown in the following code:

xgb.set_hyperparameters(eval_metric='auc', objective= 'binary:logistic', num_round=200, rate_drop=0.3, max_depth=5, subsample=0.8, gamma=2, eta=0.2, scale_pos_weight=2.85) #For class imbalance weights # Specifying the objective metric (auc on validation set)
OBJECTIVE_METRIC_NAME = ‘validation:auc’ # specifying the hyper parameters and their ranges
HYPERPARAMETER_RANGES = {'eta': ContinuousParameter(0, 1), 'alpha': ContinuousParameter(0, 2), 'max_depth': IntegerParameter(1, 10)}

For this post, AUC (area under the ROC curve) is the evaluation metric. This enables the tuning job to measure the performance of the different training jobs. The kick prediction is also a binary classification problem, which is specified in the objective argument as a binary:logistic. There is also a set of XGBoost-specific hyperparameters that you can tune. For more information, see Tune an XGBoost model.

Next, create a HyperparameterTuner object by indicating the XGBoost estimator, the hyperparameter ranges, passing the parameters, the objective metric name and definition, and tuning resource configurations, such as the number of training jobs to run in total and how many training jobs can run in parallel. Amazon SageMaker extracts the metric from Amazon CloudWatch Logs with a regular expression. See the following code:

tuner = HyperparameterTuner(xgb, OBJECTIVE_METRIC_NAME, HYPERPARAMETER_RANGES, max_jobs=20, max_parallel_jobs=4)
s3_input_train = sagemaker.s3_input(s3_data='s3://{}/{}/train'.format(BUCKET, PREFIX), content_type='csv')
s3_input_validation = sagemaker.s3_input(s3_data='s3://{}/{}/validation/'.format(BUCKET, PREFIX), content_type='csv')
tuner.fit({'train': s3_input_train, 'validation':

Finally, launch a hyperparameter tuning job by calling the fit() function. This function takes the paths of the training and validation datasets in the S3 bucket. After you create the hyperparameter tuning job, you can track its progress via the Amazon SageMaker console. The training time depends on the instance type and number of instances you selected during tuning setup.

Deploying the model on Amazon SageMaker

When the training jobs are complete, you can deploy the best performing model. If you’d like to compare models for A/B testing, Amazon SageMaker supports hosting representational state transfer (REST) endpoints for multiple models. To set this up, create an endpoint configuration that describes the distribution of traffic across the models. In addition, the endpoint configuration describes the instance type required for model deployment. The first step is to get the name of the best performing training job and create the model name.

After you create the endpoint configuration, you’re ready to deploy the actual endpoint for serving inference requests. The result is an endpoint that can you can validate and incorporate into production applications. For more information about deploying models, see Deploy the Model to Amazon SageMaker Hosting Services. To create the endpoint configuration and deploy it, enter the following code:

endpoint_name = 'Kicker-XGBoostEndpoint'
xgb_predictor = tuner.deploy(initial_instance_count=1, instance_type='ml.t2.medium', endpoint_name=endpoint_name)

After you create the endpoint, you can request a prediction in real time.

Building a RESTful API for real-time model inference

You can create a secure and scalable RESTful API that enables you to request the model prediction based on the input values. It’s easy and convenient to develop different APIs using AWS services.

The following diagram illustrates the model inference workflow.

First, you request the probability of the kick conversion by passing parameters through Amazon API Gateway, such as the location and zone of the kick, kicker ID, league and Championship ID, the game’s period, if the kicker’s team is playing home or away, and the team score status.

The API Gateway passes the values to the AWS Lambda function, which parses the values and requests additional features related to the player’s performance from DynamoDB lookup tables. These include the mean success rates of the kicking player in a given field zone, in the Championship, and in the kicker’s entire career. If the player doesn’t exist in the database, the model uses the average performance in the database in the given kicking location. After the function combines all the values, it standardizes the data and sends it to the Amazon SageMaker model endpoint for prediction.

The model performs the prediction and returns the predicted probability to the Lambda function. The function parses the returned value and sends it back to API Gateway. API Gateway responds with the output prediction. The end-to-end process latency is less than a second.

The following screenshot shows example input and output of the API. The RESTful API also outputs the average success rate of all the players in the given location and zone to get the comparison of the player’s performance with the overall average.

For instructions on creating a RESTful API, see Call an Amazon SageMaker model endpoint using Amazon API Gateway and AWS Lambda.

Bringing design principles into sports analytics

To create the first real-time prediction model for the tournament with a millisecond latency requirement, the ML Solutions Lab team worked backwards to identify areas in which design thinking could save time and resources. The team worked on an end-to-end notebook within an Amazon SageMaker environment, which enabled data access, raw data parsing, data preprocessing and visualization, feature engineering, model training and evaluation, and model deployment in one place. This helped in automating the modeling process.

Moreover, the ML Solutions Lab team implemented a model update iteration for when the model was updated with newly generated data, in which the model parses and processes only the additional data. This brings computational and time efficiencies to the modeling.

In terms of next steps, the Stats Perform AI team has been looking at the next stage of rugby analysis by breaking down the other strategic facets as line-outs, scrums and teams, and continuous phases of play using the fine-grain spatio-temporal data captured. The state-of-the-art feature representations and latent factor modelling (which have been utilized so effectively in Stats Perform’s “Edge” match-analysis and recruitment products in soccer) means that there is plenty of fertile space for innovation that can be explored in rugby.

Conclusion

Six Nations Rugby, Stats Perform, and AWS came together to bring the first real-time prediction model to the 2020 Guinness Six Nations Rugby Championship. The model determined a penalty or conversion kick success probability from anywhere in the field. They used Amazon SageMaker to build, train, and deploy the ML model with variables grouped into three main categories: location-based features, player performance features, and in-game situational features. The Amazon SageMaker endpoint provided prediction results with subsecond latency. The model was used by broadcasters during the live games in the Six Nations 2020 Championship, bringing a new metric to millions of rugby fans.

You can find full, end-to-end examples of creating custom training jobs, training state-of-the-art object detection models, and model deployment on Amazon SageMaker on the AWS Labs GitHub repo. To learn more about the ML Solutions Lab, see Amazon Machine Learning Solutions Lab.


About the Authors

Mehdi Noori is a Data Scientist at the Amazon ML Solutions Lab, where he works with customers across various verticals, and helps them to accelerate their cloud migration journey, and to solve their ML problems using state-of-the-art solutions and technologies.

Tesfagabir Meharizghi is a Data Scientist at the Amazon ML Solutions Lab where he works with customers across different verticals accelerate their use of artificial intelligence and AWS cloud services to solve their business challenges. Outside of work, he enjoys spending time with his family and reading books.

Patrick Lucey is the Chief Scientist at Stats Perform. Patrick started the Artificial Intelligence group at Stats Perform in 2015, with thegroup focusing on both computer vision and predictive modelling capabilities in sport. Previously, he was at Disney Research for 5 years, where he conducted research into automatic sports broadcasting using large amounts of spatiotemporal tracking data. He received his BEng(EE) from USQ and PhD from QUT, Australia in 2003 and 2008 respectively. He was also co-author of the best paper at the 2016 MIT Sloan Sports Analytics Conference and in 2017 & 2018 was co-author of best-paper runner-up at the same conference.

Xavier Ragot is Data Scientist with the Amazon ML Solution Lab team where he helps design creative ML solution to address customers’ business problems in various industries.

Source: https://aws.amazon.com/blogs/machine-learning/bringing-real-time-machine-learning-powered-insights-to-rugby-using-amazon-sagemaker/

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