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Enzyme Function Prediction from Amino Acid Sequence: How AI is Leading the Way - CBIRT

#artificialintelligence

An innovative artificial intelligence program called CLEAN (contrastive learningโ€“enabled enzyme annotation) has the ability to predict enzyme activities based on their amino acid sequences, even if the enzymes are unfamiliar or inadequately understood. The researchers have reported that CLEAN has surpassed the most advanced tools in terms of precision, consistency, and sensitivity. However, a deeper understanding of enzymes and their roles would be beneficial in a number of disciplines, including genetics, chemistry, pharmaceuticals, medicine, and industrial materials. The scientists are using the protein language to forecast their performance, similar to how ChatGPT uses written language data to generate predictive phrases. Almost all scientists desire to comprehend the purpose of a protein as soon as they encounter a new protein sequence.


Brace Yourself for a Tidal Wave of ChatGPT Email Scams

WIRED

Here's an experiment being run by undergraduate computer science students everywhere: Ask ChatGPT to generate phishing emails, and test whether these are better at persuading victims to respond or click on the link than the usual spam. It's an interesting experiment, and the results are likely to vary wildly based on the details of the experiment. Bruce Schneier is a lecturer and fellow at the Harvard Kennedy School and chief of security architecture at Inrupt. His latest book is A Hacker's Mind. Barath Raghavan is a professor of computer science at USC and cofounder of INVISV.


Adaptive learning of effective dynamics: Adaptive real-time, online modeling for complex systems

arXiv.org Artificial Intelligence

Predictive simulations are essential for applications ranging from weather forecasting to material design. The veracity of these simulations hinges on their capacity to capture the effective system dynamics. Massively parallel simulations predict the systems dynamics by resolving all spatiotemporal scales, often at a cost that prevents experimentation. On the other hand, reduced order models are fast but often limited by the linearization of the system dynamics and the adopted heuristic closures. We propose a novel systematic framework that bridges large scale simulations and reduced order models to extract and forecast adaptively the effective dynamics (AdaLED) of multiscale systems. AdaLED employs an autoencoder to identify reduced-order representations of the system dynamics and an ensemble of probabilistic recurrent neural networks (RNNs) as the latent time-stepper. The framework alternates between the computational solver and the surrogate, accelerating learned dynamics while leaving yet-to-be-learned dynamics regimes to the original solver. AdaLED continuously adapts the surrogate to the new dynamics through online training. The transitions between the surrogate and the computational solver are determined by monitoring the prediction accuracy and uncertainty of the surrogate. The effectiveness of AdaLED is demonstrated on three different systems - a Van der Pol oscillator, a 2D reaction-diffusion equation, and a 2D Navier-Stokes flow past a cylinder for varying Reynolds numbers (400 up to 1200), showcasing its ability to learn effective dynamics online, detect unseen dynamics regimes, and provide net speed-ups. To the best of our knowledge, AdaLED is the first framework that couples a surrogate model with a computational solver to achieve online adaptive learning of effective dynamics. It constitutes a potent tool for applications requiring many expensive simulations.


When Robotics Meets Wireless Communications: An Introductory Tutorial

arXiv.org Artificial Intelligence

The importance of ground Mobile Robots (MRs) and Unmanned Aerial Vehicles (UAVs) within the research community, industry, and society is growing fast. Many of these agents are nowadays equipped with communication systems that are, in some cases, essential to successfully achieve certain tasks. In this context, we have begun to witness the development of a new interdisciplinary research field at the intersection of robotics and communications. This research field has been boosted by the intention of integrating UAVs within the 5G and 6G communication networks. This research will undoubtedly lead to many important applications in the near future. Nevertheless, one of the main obstacles to the development of this research area is that most researchers address these problems by oversimplifying either the robotics or the communications aspect. This impedes the ability of reaching the full potential of this new interdisciplinary research area. In this tutorial, we present some of the modelling tools necessary to address problems involving both robotics and communication from an interdisciplinary perspective. As an illustrative example of such problems, we focus in this tutorial on the issue of communication-aware trajectory planning.


Crafting with a Robot Assistant: Use Social Cues to Inform Adaptive Handovers in Human-Robot Collaboration

arXiv.org Artificial Intelligence

We study human-robot handovers in a naturalistic collaboration scenario, where a mobile manipulator robot assists a person during a crafting session by providing and retrieving objects used for wooden piece assembly (functional activities) and painting (creative activities). We collect quantitative and qualitative data from 20 participants in a Wizard-of-Oz study, generating the Functional And Creative Tasks Human-Robot Collaboration dataset (the FACT HRC dataset), available to the research community. This work illustrates how social cues and task context Figure 1: Experimental space layout: the participant and inform the temporal-spatial coordination in human-robot the experimenter sat at the work space and storage space, handovers, and how human-robot collaboration is shaped by and respectively. The Fetch robot moves in between to pass in turn influences people's functional and creative activities.


Transformer visualization via dictionary learning: contextualized embedding as a linear superposition of transformer factors

arXiv.org Artificial Intelligence

Transformer networks have revolutionized NLP representation learning since they were introduced. Though a great effort has been made to explain the representation in transformers, it is widely recognized that our understanding is not sufficient. One important reason is that there lack enough visualization tools for detailed analysis. In this paper, we propose to use dictionary learning to open up these "black boxes" as linear superpositions of transformer factors. Through visualization, we demonstrate the hierarchical semantic structures captured by the transformer factors, e.g., word-level polysemy disambiguation, sentence-level pattern formation, and long-range dependency. While some of these patterns confirm the conventional prior linguistic knowledge, the rest are relatively unexpected, which may provide new insights. We hope this visualization tool can bring further knowledge and a better understanding of how transformer networks work. The code is available at https://github.com/zeyuyun1/TransformerVis


Reusable Options through Gradient-based Meta Learning

arXiv.org Artificial Intelligence

Hierarchical methods in reinforcement learning have the potential to reduce the amount of decisions that the agent needs to perform when learning new tasks. However, finding reusable useful temporal abstractions that facilitate fast learning remains a challenging problem. Recently, several deep learning approaches were proposed to learn such temporal abstractions in the form of options in an end-to-end manner. In this work, we point out several shortcomings of these methods and discuss their potential negative consequences. Subsequently, we formulate the desiderata for reusable options and use these to frame the problem of learning options as a gradient-based meta-learning problem. This allows us to formulate an objective that explicitly incentivizes options which allow a higher-level decision maker to adjust in few steps to different tasks. Experimentally, we show that our method is able to learn transferable components which accelerate learning and performs better than existing prior methods developed for this setting. Additionally, we perform ablations to quantify the impact of using gradient-based meta-learning as well as other proposed changes.


Adaptive Multi-Agent Continuous Learning System

arXiv.org Artificial Intelligence

We propose an adaptive multi-agent clustering recognition system that can be self-supervised driven, based on a temporal sequences continuous learning mechanism with adaptability. The system is designed to use some different functional agents to build up a connection structure to improve adaptability to cope with environmental diverse demands, by predicting the input of the agent to drive the agent to achieve the act of clustering recognition of sequences using the traditional algorithmic approach. Finally, the feasibility experiments of video behavior clustering demonstrate the feasibility of the system to cope with dynamic situations. Our work is placed here\footnote{https://github.com/qian-git/MAMMALS}.


A Probabilistic Framework for Lifelong Test-Time Adaptation

arXiv.org Artificial Intelligence

Test-time adaptation (TTA) is the problem of updating a pre-trained source model at inference time given test input(s) from a different target domain. Most existing TTA approaches assume the setting in which the target domain is stationary, i.e., all the test inputs come from a single target domain. However, in many practical settings, the test input distribution might exhibit a lifelong/continual shift over time. Moreover, existing TTA approaches also lack the ability to provide reliable uncertainty estimates, which is crucial when distribution shifts occur between the source and target domain. To address these issues, we present PETAL (Probabilistic lifElong Test-time Adaptation with seLf-training prior), which solves lifelong TTA using a probabilistic approach, and naturally results in (1) a student-teacher framework, where the teacher model is an exponential moving average of the student model, and (2) regularizing the model updates at inference time using the source model as a regularizer. To prevent model drift in the lifelong/continual TTA setting, we also propose a data-driven parameter restoration technique which contributes to reducing the error accumulation and maintaining the knowledge of recent domains by restoring only the irrelevant parameters. In terms of predictive error rate as well as uncertainty based metrics such as Brier score and negative log-likelihood, our method achieves better results than the current state-of-the-art for online lifelong test-time adaptation across various benchmarks, such as CIFAR-10C, CIFAR-100C, ImageNetC, and ImageNet3DCC datasets. The source code for our approach is accessible at https://github.com/dhanajitb/petal.


One Small Step for Generative AI, One Giant Leap for AGI: A Complete Survey on ChatGPT in AIGC Era

arXiv.org Artificial Intelligence

OpenAI has recently released GPT-4 (a.k.a. ChatGPT plus), which is demonstrated to be one small step for generative AI (GAI), but one giant leap for artificial general intelligence (AGI). Since its official release in November 2022, ChatGPT has quickly attracted numerous users with extensive media coverage. Such unprecedented attention has also motivated numerous researchers to investigate ChatGPT from various aspects. According to Google scholar, there are more than 500 articles with ChatGPT in their titles or mentioning it in their abstracts. Considering this, a review is urgently needed, and our work fills this gap. Overall, this work is the first to survey ChatGPT with a comprehensive review of its underlying technology, applications, and challenges. Moreover, we present an outlook on how ChatGPT might evolve to realize general-purpose AIGC (a.k.a. AI-generated content), which will be a significant milestone for the development of AGI.