🐦 The IBIS Challenge
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Nikita Gryzunov
nikgr
AI & ML interests
Interested in developing classification models (CNNs, etc) for transcription factor (TF) binding sites (TFBS). The IBIS Challenge (https://ibis.autosome.org) developer and GRECO-BIT consortium (https://thegreco.org) member.
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Post
1558
🐦 Do you remember IBIS? Not a fancy bird but the open challenge in Inferring Binding Specificities of unexplored human transcription factors. Check our site (https://ibis.autosome.org/) and have a sip of fresh news below.
👥 More than 100 teams registered for the challenge yet only two dozen are using the opportunity to explore their models on the Leaderboard. Don't miss the chance to participate in the Leaderboard stage, although independently of that you can submit the final solution.
🌐 Remember, the training data for Leaderboard and Final are available online, and you are free to mix-and-match it in any combination.
🌌 For Leaderboard, we have received 650 total submissions of AAA (advanced ML) and 296 PWM models (a whopping set of 6682 PWMs in total).
🚀 For PWMs, the baseline is left far behind, but some TFs remain tough nuts to be cracked (see the attached figure 1).
📈 For AAAs, there is a solid improvement over the best-submitted PWMs in A2G, but the G2A discipline remains unpopular (see the attached figure 2). Free hint: this is your chance!
💡 Another free hint: If your model tends to overfit given a limited set of data for some TFs don't forget to use reverse-complement and shift augmentations. Also, don't hesitate to use multitarget models i.e. predicting the binding of multiple TFs at the same time.
💡 Last but not least, try to combine knowledge from all accessible experiment types, especially for G2A discipline (ChIP-Seq & genomic HT-SELEX) in a single model!
📣 Finally and importantly, following the requests from the community, we decided to EXTEND the Leaderboard until the final submission deadline.
🗓️ The final submission deadline is also EXTENDED until Aug 15. The final submission form and details will be posted on the IBIS website in the first half of July, follow our Telegram group and mailing list (see the links at https://ibis.autosome.org).
👥 More than 100 teams registered for the challenge yet only two dozen are using the opportunity to explore their models on the Leaderboard. Don't miss the chance to participate in the Leaderboard stage, although independently of that you can submit the final solution.
🌐 Remember, the training data for Leaderboard and Final are available online, and you are free to mix-and-match it in any combination.
🌌 For Leaderboard, we have received 650 total submissions of AAA (advanced ML) and 296 PWM models (a whopping set of 6682 PWMs in total).
🚀 For PWMs, the baseline is left far behind, but some TFs remain tough nuts to be cracked (see the attached figure 1).
📈 For AAAs, there is a solid improvement over the best-submitted PWMs in A2G, but the G2A discipline remains unpopular (see the attached figure 2). Free hint: this is your chance!
💡 Another free hint: If your model tends to overfit given a limited set of data for some TFs don't forget to use reverse-complement and shift augmentations. Also, don't hesitate to use multitarget models i.e. predicting the binding of multiple TFs at the same time.
💡 Last but not least, try to combine knowledge from all accessible experiment types, especially for G2A discipline (ChIP-Seq & genomic HT-SELEX) in a single model!
📣 Finally and importantly, following the requests from the community, we decided to EXTEND the Leaderboard until the final submission deadline.
🗓️ The final submission deadline is also EXTENDED until Aug 15. The final submission form and details will be posted on the IBIS website in the first half of July, follow our Telegram group and mailing list (see the links at https://ibis.autosome.org).
Post
1910
🐦 The IBIS Challenge: an open competition in Inferring and predicting transcription factor Binding Specificities: modeling DNA patterns recognized by human regulatory proteins.
🧬 Deciphering human gene regulation is a cornerstone of modern molecular biology and biomedicine. Gene activity is controlled by special regulatory proteins, the transcription factors, which recognize DNA sequence patterns. We invite you to join IBIS in our search for the best method to model binding specificities of yet unexplored human regulatory proteins.
In the challenge, you may use classic methods to represent sequence patterns or any modern approaches
🚀 including decision trees, CNNs, RNNs, LSTMs, and transformers.
💡IBIS allows using arbitrary genome or random sequences to pre-train an artificial neural network or to extract features, and use a few existing datasets, see the IBIS documentation (https://ibis.autosome.org/docs/technical_details).
📊 Yet, the main power and opportunity come with a diverse array of experimental data on 40 human regulatory proteins, many of which remained unexplored until now.
🏆 The best methods will be highlighted in the post-challenge high-impact scientific paper 📝, while the winners 🥇of the Primary track of the Final round will be invited to contribute as co-authors.
🌐 Learn more at https://ibis.autosome.org/
🤗 Our article at HF: https://huggingface.co/blog/nikgr/the-ibis-challenge
👥 Organizers - GRECO-BIT & Codebook consortia: https://ibis.autosome.org/docs/about_us
🧬 Deciphering human gene regulation is a cornerstone of modern molecular biology and biomedicine. Gene activity is controlled by special regulatory proteins, the transcription factors, which recognize DNA sequence patterns. We invite you to join IBIS in our search for the best method to model binding specificities of yet unexplored human regulatory proteins.
In the challenge, you may use classic methods to represent sequence patterns or any modern approaches
🚀 including decision trees, CNNs, RNNs, LSTMs, and transformers.
💡IBIS allows using arbitrary genome or random sequences to pre-train an artificial neural network or to extract features, and use a few existing datasets, see the IBIS documentation (https://ibis.autosome.org/docs/technical_details).
📊 Yet, the main power and opportunity come with a diverse array of experimental data on 40 human regulatory proteins, many of which remained unexplored until now.
🏆 The best methods will be highlighted in the post-challenge high-impact scientific paper 📝, while the winners 🥇of the Primary track of the Final round will be invited to contribute as co-authors.
🌐 Learn more at https://ibis.autosome.org/
🤗 Our article at HF: https://huggingface.co/blog/nikgr/the-ibis-challenge
👥 Organizers - GRECO-BIT & Codebook consortia: https://ibis.autosome.org/docs/about_us
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