Genetic Engineering Attribution Challenge
Genetic engineering is a powerful tool that demands responsible use. Your goal is to create an algorithm that identifies the lab-of-origin for genetically engineered DNA with the highest accuracy level possible. Competition hosted by altLabs. #science
Genetic engineering is a powerful tool that demands responsible use. Your goal is to create an algorithm that identifies the lab-of-origin for genetically engineered DNA with the highest accuracy level possible.
We were blown away by the results of this competition, and are really excited to see how the attribution field continues to develop from here.
— Will Bradshaw, Competition Director at altLabs
Synthetic biology offers fantastic benefits for society, but its anonymity opens the door for reckless or malicious actors to cause serious harm. Currently, there is no easy way of tracing genetically engineered DNA back to its lab-of-origin. This task is known as attribution, and it's a pivotal part of ensuring that genetic engineering progresses responsibly.
When manipulating DNA, a designer has many decisions she must make, such as promoter choice and cloning method. These choices leave clues in the genetic material, and together, compose a "genetic fingerprint" that can be traced back to the designer.
The goal of the Genetic Engineering Attribution Challenge was to develop tools that help human decision makers identify the lab-of-origin from genetically engineered DNA. This competition was composed of two tracks. In the Prediction Track, participants competed to attribute DNA samples to its lab-of-origin with the highest possible accuracy. In the Innovation Track, competitors that beat the BLAST benchmark were invited to submit reports demonstrating how their lab-of-origin prediction models excel in domains beyond raw accuracy.
When attributing DNA to its source, simply narrowing the field of possible labs would be a boon to human decision makers. This is why top-10 accuracy was chosen as the competition metric. The top model was able to achieve over 95% top-10 accuracy with 1,314 possible labs present in the dataset, compared with the pre-existing BLAST baseline of 76.9%. Moreover, three of the top four submissions were able to to achieve more than 80% top-1 accuracy.
Solutions were also tested against an out-of-sample verification set from data that was collected after the competition concluded. The verification data included both "previously seen" labs included in the competition dataset and "unseen" labs (predictions for "unseen" labs are considered correct if labeled "unknown"). On the previously seen dataset, top models were able to score an impressive top-10 accuracy of 78 - 85%, substantially exceeding the baseline performance of 59.5%.
To further promote the development and use of attribution technology in the future, all code from winning submissions will be made open-source, and altLabs has reached out to winning teams to discuss their plans for publication of their results.
Genetic Engineering Attribution Challenge: Rules and Terms of Data Use
DrivenData Competition Rules
One account per participant
You cannot sign up to DrivenData from multiple accounts and therefore you cannot submit from multiple accounts.
Private sharing of code
Privately sharing code or data outside of teams is not permitted.
Winner license/assignment type: Assignment to Competition Sponsor
Winning solutions must be assigned to the Competition Sponsor in order to be eligible for recognition and prize money if offered. Public sharing of code or IP is prohibited in order to be eligible for a prize.
Documentation for winning solutions
Winning solutions must be documented using the provided Winning Model Documentation Template in order to be eligible for recognition and prize money if offered.
The number of submissions per day is restricted to a fixed value on a per-competition basis. Any attempt to circumvent this limit will result in disqualification.
External data is not allowed unless otherwise noted explicitly on these competition pages. Participants agree to make no attempt to use additional data or data sources not provided on these competition pages.
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Selection of winners
This Competition is a challenge of skill and the final results are determined by evaluating a combination of quantitative and qualitative factors, as more fully described on the Competition Website. For that portion of the Competition evaluated quantitatively, the results will be determined solely by leaderboard ranking on the private leaderboard based on an objective statistical evaluation metric published on the Competition Website prior to commencement of the Competition (subject to compliance with these Competition Rules). Participants' scores and ranks on the Competition Website at any given stage of the Competition will be based on the objective statistical evaluation metric described on the Competition Website, as determined by applying the predictions in the Submission to the ground truth of a validation dataset whose instances were a fixed set sampled from the Data. For that portion of the Competition evaluated qualitatively, the results will be determined by a panel of judges, as more fully described on the Competition Website. As more fully described on the Competition Website, the Competition may have a quantitative winner, a qualitative winner, a combined quantitative and qualitative winner, or all three.
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- disqualify your Submission(s); or
- require that you remediate within one week all issues identified in your Submission(s) (including, without limitation, the resolution of license conflicts, the fulfillment of all obligations required by software licenses, and the removal of any software that violates the software restrictions).
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Prizes and conditions
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Data use and code sharing
DATA. "Data" means the Data or Datasets linked from the Competition Website for the purpose of use by Participants in the Competition. For the avoidance of doubt, Data is deemed for the purpose of these Competition Rules to include any prototype or executable code provided to Participants by DrivenData or via the Competition Website. Participants must use the Data only as permitted by these Competition Rules and any associated data use rules specified on the Competition Website.
Unless otherwise permitted by the terms of the Competition Website, Participants must use the Data solely for the purpose and duration of the Competition, including but not limited to reading and learning from the Data, analyzing the Data, modifying the Data and generally preparing your Submission and any underlying models and participating in forum discussions on the Competition Website. Participants agree to use suitable measures to prevent persons who have not formally agreed to these Competition Rules from gaining access to the Data and agree not to transmit, duplicate, publish, redistribute or otherwise provide or make available the Data to any party not participating in the Competition. Participants agree to notify DrivenData immediately upon learning of any possible unauthorized transmission or unauthorized access of the Data and agree to work with DrivenData to rectify any unauthorized transmission. Participants agree that participation in the Competition shall not be construed as having or being granted a license (expressly, by implication, estoppel, or otherwise) under, or any right of ownership in, any of the Data.
EXTERNAL DATA. Unless otherwise expressly stated on the Competition Website, Participants must not use data other than the Data to develop and test their models and Submissions. Competition Sponsor reserves the right in its sole discretion to disqualify any Participant who Competition Sponsor discovers has undertaken or attempted to undertake the use of data other than the Data, or who uses the Data other than as permitted according to the Competition Website and in these Competition Rules, in the course of the Competition.
CODE SHARING. Participants are prohibited from privately sharing source or executable code developed in connection with or based upon the Data, and any such sharing is a breach of these Competition Rules and may result in disqualification. Participants are permitted to publicly share source or executable code developed in connection with or based upon the Data, or otherwise relevant to the Competition, provided that such sharing does not violate the intellectual property rights of any third party. By so sharing, the sharing Participant is thereby deemed to have licensed the shared code under the MIT License (an open source software license commonly described at http://opensource.org/licenses/MIT), and therefore is not eligible to receive a prize for this Competition.
OPEN-SOURCE CODE. A Submission will be ineligible to win a prize if it was developed using code containing or depending on software licensed under an open source license:
- other than an Open Source Initiative-approved license (see http://opensource.org/licenses); or
- an open source license that prohibits commercial use.
Participant warranties and obligations
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