Materials
A review on data-driven constitutive laws for solids
Fuhg, Jan Niklas, Padmanabha, Govinda Anantha, Bouklas, Nikolaos, Bahmani, Bahador, Sun, WaiChing, Vlassis, Nikolaos N., Flaschel, Moritz, Carrara, Pietro, De Lorenzis, Laura
This review article highlights state-of-the-art data-driven techniques to discover, encode, surrogate, or emulate constitutive laws that describe the path-independent and path-dependent response of solids. Our objective is to provide an organized taxonomy to a large spectrum of methodologies developed in the past decades and to discuss the benefits and drawbacks of the various techniques for interpreting and forecasting mechanics behavior across different scales. Distinguishing between machine-learning-based and model-free methods, we further categorize approaches based on their interpretability and on their learning process/type of required data, while discussing the key problems of generalization and trustworthiness. We attempt to provide a road map of how these can be reconciled in a data-availability-aware context. We also touch upon relevant aspects such as data sampling techniques, design of experiments, verification, and validation.
AdsorbDiff: Adsorbate Placement via Conditional Denoising Diffusion
Kolluru, Adeesh, Kitchin, John R
Determining the optimal configuration of adsorbates on a slab (adslab) is pivotal in the exploration of novel catalysts across diverse applications. Traditionally, the quest for the lowest energy adslab configuration involves placing the adsorbate onto the slab followed by an optimization process. Prior methodologies have relied on heuristics, problem-specific intuitions, or brute-force approaches to guide adsorbate placement. In this work, we propose a novel framework for adsorbate placement using denoising diffusion. The model is designed to predict the optimal adsorbate site and orientation corresponding to the lowest energy configuration. Further, we have an end-to-end evaluation framework where diffusion-predicted adslab configuration is optimized with a pretrained machine learning force field and finally evaluated with Density Functional Theory (DFT). Our findings demonstrate an acceleration of up to 5x or 3.5x improvement in accuracy compared to the previous best approach. Given the novelty of this framework and application, we provide insights into the impact of pre-training, model architectures, and conduct extensive experiments to underscore the significance of this approach.
Modern Information Technologies in Scientific Research and Educational Activities
Malakhov, Kyrylo, Kaverinskiy, Vadislav, Ivanova, Liliia, Romanyuk, Oleksandr, Romaniuk, Oksana, Voinova, Svitlana, Kotlyk, Sergii, Sokolova, Oksana
Nowadays, there is a rapid development of information technology, which entails the need to constantly improve and expand the capabilities of interactive artificial intelligence systems This monograph combines several current topics related to the field of information technology One of the key topics is the methodology for enhancing the capabilities of conversational systems, with a focus on ChatGPT, which represents the latest advance in the field of artificial intelligence The monograph also discusses text generation systems based on ontological representations, which open up wide opportunities for creating high-quality content A special place in the work is given to an automated computer system for diagnosing the competitiveness of specialists in the field of information technology This helps to effectively assess the professionalism of specialists and determine the need for advanced training Theoretical aspects of correct color rendering and informatization of educational and research work of graduate students are important in ensuring the quality of education and scientific research And finally, the use of technology for creating 3D models has become an integral part of the modern information environment, which makes it possible to bring the most daring ideas and projects to life Research and development in these areas contribute to the improvement of information technologies, finding application in various fields of activity The purpose of our monograph is to conduct analysis and research in these areas in order to promote the development of information technologies and increase their efficiency The monograph was compiled based on the results of the XVI international scientific and practical conference "Information technologies and automation -- 2023", which took place in October 2023 at Odessa National University of Technology
Contrastive Dual-Interaction Graph Neural Network for Molecular Property Prediction
Zhao, Zexing, Shi, Guangsi, Wu, Xiaopeng, Ren, Ruohua, Gao, Xiaojun, Li, Fuyi
Molecular property prediction is a key component of AI-driven drug discovery and molecular characterization learning. Despite recent advances, existing methods still face challenges such as limited ability to generalize, and inadequate representation of learning from unlabeled data, especially for tasks specific to molecular structures. To address these limitations, we introduce DIG-Mol, a novel self-supervised graph neural network framework for molecular property prediction. This architecture leverages the power of contrast learning with dual interaction mechanisms and unique molecular graph enhancement strategies. DIG-Mol integrates a momentum distillation network with two interconnected networks to efficiently improve molecular characterization. The framework's ability to extract key information about molecular structure and higher-order semantics is supported by minimizing loss of contrast. We have established DIG-Mol's state-of-the-art performance through extensive experimental evaluation in a variety of molecular property prediction tasks. In addition to demonstrating superior transferability in a small number of learning scenarios, our visualizations highlight DIG-Mol's enhanced interpretability and representation capabilities. These findings confirm the effectiveness of our approach in overcoming challenges faced by traditional methods and mark a significant advance in molecular property prediction.
Non-Destructive Peat Analysis using Hyperspectral Imaging and Machine Learning
Yan, Yijun, Ren, Jinchang, Harrison, Barry, Lewis, Oliver, Li, Yinhe, Ma, Ping
Peat, a crucial component in whisky production, imparts distinctive and irreplaceable flavours to the final product. However, the extraction of peat disrupts ancient ecosystems and releases significant amounts of carbon, contributing to climate change. This paper aims to address this issue by conducting a feasibility study on enhancing peat use efficiency in whisky manufacturing through non-destructive analysis using hyperspectral imaging. Results show that shot-wave infrared (SWIR) data is more effective for analyzing peat samples and predicting total phenol levels, with accuracies up to 99.81%.
The Download: Sam Altman on AI's killer function, and the problem with ethanol
Sam Altman, CEO of OpenAI, has a vision for how AI tools will become enmeshed in our daily lives. During a sit-down chat with MIT Technology Review in Cambridge, Massachusetts, he described how he sees the killer app for AI as a "super-competent colleague that knows absolutely everything about my whole life, every email, every conversation I've ever had, but doesn't feel like an extension." In the new paradigm, as Altman sees it, AI will be capable of helping us outside the chat interface and taking real-world tasks off our plates. Read more about Altman's thoughts on the future of AI hardware, where training data will come from next, and who is best poised to create AGI. Eliminating carbon pollution from aviation is one of the most challenging parts of the climate puzzle, simply because large commercial airlines are too heavy and need too much power during takeoff for today's batteries to do the job.
Generative Active Learning for the Search of Small-molecule Protein Binders
Korablyov, Maksym, Liu, Cheng-Hao, Jain, Moksh, van der Sloot, Almer M., Jolicoeur, Eric, Ruediger, Edward, Nica, Andrei Cristian, Bengio, Emmanuel, Lapchevskyi, Kostiantyn, St-Cyr, Daniel, Schuetz, Doris Alexandra, Butoi, Victor Ion, Rector-Brooks, Jarrid, Blackburn, Simon, Feng, Leo, Nekoei, Hadi, Gottipati, SaiKrishna, Vijayan, Priyesh, Gupta, Prateek, Rampášek, Ladislav, Avancha, Sasikanth, Bacon, Pierre-Luc, Hamilton, William L., Paige, Brooks, Misra, Sanchit, Jastrzebski, Stanislaw Kamil, Kaul, Bharat, Precup, Doina, Hernández-Lobato, José Miguel, Segler, Marwin, Bronstein, Michael, Marinier, Anne, Tyers, Mike, Bengio, Yoshua
Despite substantial progress in machine learning for scientific discovery in recent years, truly de novo design of small molecules which exhibit a property of interest remains a significant challenge. We introduce LambdaZero, a generative active learning approach to search for synthesizable molecules. Powered by deep reinforcement learning, LambdaZero learns to search over the vast space of molecules to discover candidates with a desired property. We apply LambdaZero with molecular docking to design novel small molecules that inhibit the enzyme soluble Epoxide Hydrolase 2 (sEH), while enforcing constraints on synthesizability and drug-likeliness. LambdaZero provides an exponential speedup in terms of the number of calls to the expensive molecular docking oracle, and LambdaZero de novo designed molecules reach docking scores that would otherwise require the virtual screening of a hundred billion molecules. Importantly, LambdaZero discovers novel scaffolds of synthesizable, drug-like inhibitors for sEH. In in vitro experimental validation, a series of ligands from a generated quinazoline-based scaffold were synthesized, and the lead inhibitor N-(4,6-di(pyrrolidin-1-yl)quinazolin-2-yl)-N-methylbenzamide (UM0152893) displayed sub-micromolar enzyme inhibition of sEH.
Extracting chemical food safety hazards from the scientific literature automatically using large language models
Özen, Neris, Mu, Wenjuan, van Asselt, Esther D., Bulk, Leonieke M. van den
The number of scientific articles published in the domain of food safety has consistently been increasing over the last few decades. It has therefore become unfeasible for food safety experts to read all relevant literature related to food safety and the occurrence of hazards in the food chain. However, it is important that food safety experts are aware of the newest findings and can access this information in an easy and concise way. In this study, an approach is presented to automate the extraction of chemical hazards from the scientific literature through large language models. The large language model was used out-of-the-box and applied on scientific abstracts; no extra training of the models or a large computing cluster was required. Three different styles of prompting the model were tested to assess which was the most optimal for the task at hand. The prompts were optimized with two validation foods (leafy greens and shellfish) and the final performance of the best prompt was evaluated using three test foods (dairy, maize and salmon). The specific wording of the prompt was found to have a considerable effect on the results. A prompt breaking the task down into smaller steps performed best overall. This prompt reached an average accuracy of 93% and contained many chemical contaminants already included in food monitoring programs, validating the successful retrieval of relevant hazards for the food safety domain. The results showcase how valuable large language models can be for the task of automatic information extraction from the scientific literature.
FOTS: A Fast Optical Tactile Simulator for Sim2Real Learning of Tactile-motor Robot Manipulation Skills
Zhao, Yongqiang, Qian, Kun, Duan, Boyi, Luo, Shan
Simulation is a widely used tool in robotics to reduce hardware consumption and gather large-scale data. Despite previous efforts to simulate optical tactile sensors, there remain challenges in efficiently synthesizing images and replicating marker motion under different contact loads. In this work, we propose a fast optical tactile simulator, named FOTS, for simulating optical tactile sensors. We utilize multi-layer perceptron mapping and planar shadow generation to simulate the optical response, while employing marker distribution approximation to simulate the motion of surface markers caused by the elastomer deformation. Experimental results demonstrate that FOTS outperforms other methods in terms of image generation quality and rendering speed, achieving 28.6 fps for optical simulation and 326.1 fps for marker motion simulation on a single CPU without GPU acceleration. In addition, we integrate the FOTS simulation model with physical engines like MuJoCo, and the peg-in-hole task demonstrates the effectiveness of our method in achieving zero-shot Sim2Real learning of tactile-motor robot manipulation skills. Our code is available at https://github.com/Rancho-zhao/FOTS.
Numeric Reward Machines
Levina, Kristina, Pappas, Nikolaos, Karapantelakis, Athanasios, Feljan, Aneta Vulgarakis, Seipp, Jendrik
Reward machines inform reinforcement learning agents about the reward structure of the environment and often drastically speed up the learning process. However, reward machines only accept Boolean features such as robot-reached-gold. Consequently, many inherently numeric tasks cannot profit from the guidance offered by reward machines. To address this gap, we aim to extend reward machines with numeric features such as distance-to-gold. For this, we present two types of reward machines: numeric-Boolean and numeric. In a numeric-Boolean reward machine, distance-to-gold is emulated by two Boolean features distance-to-gold-decreased and robot-reached-gold. In a numeric reward machine, distance-to-gold is used directly alongside the Boolean feature robot-reached-gold. We compare our new approaches to a baseline reward machine in the Craft domain, where the numeric feature is the agent-to-target distance. We use cross-product Q-learning, Q-learning with counter-factual experiences, and the options framework for learning. Our experimental results show that our new approaches significantly outperform the baseline approach. Extending reward machines with numeric features opens up new possibilities of using reward machines in inherently numeric tasks.