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Binding-and-folding recognition of an intrinsically disordered protein using online learning molecular dynamics

arXiv.org Artificial Intelligence

Intrinsically disordered proteins participate in many biological processes by folding upon binding with other proteins. However, coupled folding and binding processes are not well understood from an atomistic point of view. One of the main questions is whether folding occurs prior to or after binding. Here we use a novel unbiased high-throughput adaptive sampling approach to reconstruct the binding and folding between the disordered transactivation domain of \mbox{c-Myb} and the KIX domain of the CREB-binding protein. The reconstructed long-term dynamical process highlights the binding of a short stretch of amino acids on \mbox{c-Myb} as a folded $\alpha$-helix. Leucine residues, specially Leu298 to Leu302, establish initial native contacts that prime the binding and folding of the rest of the peptide, with a mixture of conformational selection on the N-terminal region with an induced fit of the C-terminal.



AI Decoded: New online course seeks to demystify Artificial Intelligence for all

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Article AI Decoded: New online course seeks to demystify Artificial Intelligence for all Artificial Intelligence is fast becoming an essential part of how we work, live and interact with one another, yet many people lack basic knowledge of what AI is, and the impact it might have. Destination AI, a new open online course produced by Institut Montaigne in collaboration with UNESCO, OpenClassrooms and Fondation Abeona, seeks to close this knowledge gap, offering an inventive and informative approach to learning about what makes AI tick. Institut Montaigne 2 November 2022 Today, over 50% of organizations worldwide report using some form of AI in their operations, but many people still lack foundational knowledge concerning what AI is, or its potential risks, benefits, and impacts. Moreover, women and girls are 25% less likely than men to know how to leverage digital technology for basic purposes, pointing to a further critical gender divide in the future of AI skill development. If left unchecked, these knowledge gaps may prove detrimental not only to the future of mental health and work in the digital age but may also prevent the next generation from adequately leveraging the opportunities AI presents.


HOPE: Human-Centric Off-Policy Evaluation for E-Learning and Healthcare

arXiv.org Artificial Intelligence

Reinforcement learning (RL) has been extensively researched for enhancing human-environment interactions in various human-centric tasks, including e-learning and healthcare. Since deploying and evaluating policies online are high-stakes in such tasks, off-policy evaluation (OPE) is crucial for inducing effective policies. In human-centric environments, however, OPE is challenging because the underlying state is often unobservable, while only aggregate rewards can be observed (students' test scores or whether a patient is released from the hospital eventually). In this work, we propose a human-centric OPE (HOPE) to handle partial observability and aggregated rewards in such environments. Specifically, we reconstruct immediate rewards from the aggregated rewards considering partial observability to estimate expected total returns. We provide a theoretical bound for the proposed method, and we have conducted extensive experiments in real-world human-centric tasks, including sepsis treatments and an intelligent tutoring system. Our approach reliably predicts the returns of different policies and outperforms state-of-the-art benchmarks using both standard validation methods and human-centric significance tests.


The 2023 Machine Learning Engineer RoadMap

#artificialintelligence

Learning this fabulous programming language is not just mandatory to start your journey in machine learning. Still, it is an investment in yourself that you may need all your life because you can even shift your career to another one and still use python in that new industry. This is almost the most popular course among python developers which will help you learn the basics of this language and use the Python built-in data structure, accessing the web, which will be very useful when you are trying to get the data from the web, and using python with the database. The course has more than a million students with a 4.8 rating score which is an excellent resource. Alternatively, you can start your Machine Learning Career with R programming language.


Improved Online Conformal Prediction via Strongly Adaptive Online Learning

arXiv.org Artificial Intelligence

We study the problem of uncertainty quantification via prediction sets, in an online setting where the data distribution may vary arbitrarily over time. Recent work develops online conformal prediction techniques that leverage regret minimization algorithms from the online learning literature to learn prediction sets with approximately valid coverage and small regret. However, standard regret minimization could be insufficient for handling changing environments, where performance guarantees may be desired not only over the full time horizon but also in all (sub-)intervals of time. We develop new online conformal prediction methods that minimize the strongly adaptive regret, which measures the worst-case regret over all intervals of a fixed length. We prove that our methods achieve near-optimal strongly adaptive regret for all interval lengths simultaneously, and approximately valid coverage. Experiments show that our methods consistently obtain better coverage and smaller prediction sets than existing methods on real-world tasks, such as time series forecasting and image classification under distribution shift.


DKT-STDRL: Spatial and Temporal Representation Learning Enhanced Deep Knowledge Tracing for Learning Performance Prediction

arXiv.org Artificial Intelligence

Knowledge tracing (KT) serves as a primary part of intelligent education systems. Most current KTs either rely on expert judgments or only exploit a single network structure, which affects the full expression of learning features. To adequately mine features of students' learning process, Deep Knowledge Tracing Based on Spatial and Temporal Deep Representation Learning for Learning Performance Prediction (DKT-STDRL) is proposed in this paper. DKT-STDRL extracts spatial features from students' learning history sequence, and then further extracts temporal features to extract deeper hidden information. Specifically, firstly, the DKT-STDRL model uses CNN to extract the spatial feature information of students' exercise sequences. Then, the spatial features are connected with the original students' exercise features as joint learning features. Then, the joint features are input into the BiLSTM part. Finally, the BiLSTM part extracts the temporal features from the joint learning features to obtain the prediction information of whether the students answer correctly at the next time step. Experiments on the public education datasets ASSISTment2009, ASSISTment2015, Synthetic-5, ASSISTchall, and Statics2011 prove that DKT-STDRL can achieve better prediction effects than DKT and CKT.


Building a Career in Data Science

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I currently work at Rebaie Analytics Group to develop algorithms in computer vision, natural language processing, and other deep learning fields. In college, I started reading about the impact of data science in transforming business and even in the way humans interact with machines in our daily lives. Further inspired by the AI influencer and keynote speaker Ali Rebaie, I wanted to apply an anthropological perspective to solve current AI challenges. Like I do with any subject I'm interested in, I jumped right into learning everything I could, starting with taking machine learning courses online. I was glad to find Coursera -- it's really the most effective and interactive e-learning platform out there.


A Human-Centered Review of Algorithms in Decision-Making in Higher Education

arXiv.org Artificial Intelligence

The use of algorithms for decision-making in higher education is steadily growing, promising cost-savings to institutions and personalized service for students but also raising ethical challenges around surveillance, fairness, and interpretation of data. To address the lack of systematic understanding of how these algorithms are currently designed, we reviewed an extensive corpus of papers proposing algorithms for decision-making in higher education. We categorized them based on input data, computational method, and target outcome, and then investigated the interrelations of these factors with the application of human-centered lenses: theoretical, participatory, or speculative design. We found that the models are trending towards deep learning, and increased use of student personal data and protected attributes, with the target scope expanding towards automated decisions. However, despite the associated decrease in interpretability and explainability, current development predominantly fails to incorporate human-centered lenses. We discuss the challenges with these trends and advocate for a human-centered approach.


Optimal Stochastic Non-smooth Non-convex Optimization through Online-to-Non-convex Conversion

arXiv.org Artificial Intelligence

We present new algorithms for optimizing non-smooth, non-convex stochastic objectives based on a novel analysis technique. This improves the current best-known complexity for finding a $(\delta,\epsilon)$-stationary point from $O(\epsilon^{-4}\delta^{-1})$ stochastic gradient queries to $O(\epsilon^{-3}\delta^{-1})$, which we also show to be optimal. Our primary technique is a reduction from non-smooth non-convex optimization to online learning, after which our results follow from standard regret bounds in online learning. For deterministic and second-order smooth objectives, applying more advanced optimistic online learning techniques enables a new complexity of $O(\epsilon^{-1.5}\delta^{-0.5})$. Our techniques also recover all optimal or best-known results for finding $\epsilon$ stationary points of smooth or second-order smooth objectives in both stochastic and deterministic settings.