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1. Inverse Design Framework With Invertible Neural Networks for Passive Vibration Suppression in Phononic Structures

   https://doi.org/10.1115/1.4052300  

   Oddiraju, Manaswin ; Behjat, Amir ; Nouh, Mostafa ; Chowdhury, Souma ( February 2022 , Journal of Mechanical Design)

   null (Ed.)

   Abstract Automated inverse design methods are critical to the development of metamaterial systems that exhibit special user-demanded properties. While machine learning approaches represent an emerging paradigm in the design of metamaterial structures, the ability to retrieve inverse designs on-demand remains lacking. Such an ability can be useful in accelerating optimization-based inverse design processes. This paper develops an inverse design framework that provides this capability through the novel usage of invertible neural networks (INNs). We exploit an INN architecture that can be trained to perform forward prediction over a set of high-fidelity samples and automatically learns the reverse mapping with guaranteed invertibility. We apply this INN for modeling the frequency response of periodic and aperiodic phononic structures, with the performance demonstrated on vibration suppression of drill pipes. Training and testing samples are generated by employing a transfer matrix method. The INN models provide competitive forward and inverse prediction performance compared to typical deep neural networks (DNNs). These INN models are used to retrieve approximate inverse designs for a queried non-resonant frequency range; the inverse designs are then used to initialize a constrained gradient-based optimization process to find a more accurate inverse design that also minimizes mass. The INN-initialized optimizations are found to be generally superior in terms of the queried property and mass compared to randomly initialized and inverse DNN-initialized optimizations. Particle swarm optimization with INN-derived initial points is then found to provide even better solutions, especially for the higher-dimensional aperiodic structures. 

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2. A Practical Algorithm Design and Evaluation for Heterogeneous Elastic Computing with Stragglers

   https://doi.org/10.1109/GLOBECOM46510.2021.9685714  

   Woolsey, Nicholas ; Kliewer, Jorg ; Chen, Rong-Rong ; Ji, Mingyue ( February 2022 , 2021 IEEE Global Communications Conference (GLOBECOM))

   Our extensive real measurements over Amazon EC2 show that the virtual instances often have different computing speeds even if they share the same configurations. This motivates us to study heterogeneous Coded Storage Elastic Computing (CSEC) systems where machines, with different computing speeds, join and leave the network arbitrarily over different computing steps. In CSEC systems, a Maximum Distance Separable (MDS) code is used for coded storage such that the file placement does not have to be re-defined with each elastic event. Computation assignment algorithms are used to minimize the computation time given computation speeds of different machines. While previous studies of heterogeneous CSEC do not include stragglers - the slow machines during the computation, we develop a new framework in heterogeneous CSEC that introduces straggler tolerance. Based on this framework, we design a novel algorithm using our previously proposed approach for heterogeneous CSEC such that the system can handle any subset of stragglers of a specified size while minimizing the computation time. Furthermore, we establish a trade-off in computation time and straggler tolerance. Another major limitation of existing CSEC designs is the lack of practical evaluations using real applications. In this paper, we evaluate the performance of our designs on Amazon EC2 for applications of the power iteration and linear regression. Evaluation results show that the proposed heterogeneous CSEC algorithms outperform the state-of-the-art designs by more than 30%. 

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3. Invertibility aware Integration of Static and Time-series data: An application to Lake Temperature Modeling

   https://doi.org/10.1137/1.9781611977172.79  

   Tayal, K. ; Jia X. ; Ghosh R. ; Willard J. ; Read J. ; Kumar V. ( April 2022 , 2022 SIAM International Conference on Data Mining (SDM))

   Accurate predictions of water temperature are the foundation for many decisions and regulations, with direct impacts on water quality, fishery yields, and power production. Building accurate broad-scale models for lake temperature prediction remains challenging in practice due to the variability in the data distribution across different lake systems monitored by static and time-series data. In this paper, to tackle the above challenges, we propose a novel machine learning based approach for integrating static and time-series data in deep recurrent models, which we call Invertibility-Aware-Long Short-Term Memory(IA-LSTM), and demonstrate its effectiveness in predicting lake temperature. Our proposed method integrates components of the Invertible Network and LSTM to better predict temperature profiles (forward modeling) and infer the static features (i.e., inverse modeling) that can eventually enhance the prediction when static variables are missing. We evaluate our method on predicting the temperature profile of 450 lakes in the Midwestern U.S. and report a relative improvement of 4\% to capture data heterogeneity and simultaneously outperform baseline predictions by 12\% when static features are unavailable. 

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4. Physically Invertible System Identification for Monitoring System Edges with Unobservability

   Jingyi Yuan and Yang Weng ( September 2022 , Machine Learning and Knowledge Discovery in Databases: European Conference)

   Nowadays, the data collected in physical/engineering systems allows various machine learning methods to conduct system monitoring and control, when the physical knowledge on the system edge is limited and challenging to recover completely. Solving such problems typically requires identifying forward system mapping rules, from system states to the output measurements. However, the forward system identification based on digital twin can hardly provide complete monitoring functions, such as state estimation, e.g., to infer the states from measurements. While one can directly learn the inverse mapping rule, it is more desirable to re-utilize the forward digital twin since it is relatively easy to embed physical law there to regularize the inverse process and avoid overfitting. For this purpose, this paper proposes an invertible learning structure based on designing parallel paths in structural neural networks with basis functionals and embedding virtual storage variables for information preservation. For such a two-way digital twin modeling, there is an additional challenge of multiple solutions for system inverse, which contradict the reality of one feasible solution for the current system. To avoid ambiguous inverse, the proposed model maximizes the physical likelihood to contract the original solution space, leading to the unique system operation status of interest. We validate the proposed method on various physical system monitoring tasks and scenarios, such as inverse kinematics problems, power system state estimation, etc. Furthermore, by building a perfect match of a forward-inverse pair, the proposed method obtains accurate and computation-efficient inverse predictions, given observations. Finally, the forward physical interpretation and small prediction errors guarantee the explainability of the invertible structure, compared to standard learning methods. 

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5. ExpertRNA: A New Framework for RNA Secondary Structure Prediction

   https://doi.org/10.1287/ijoc.2022.1188  

   Liu, Menghan ; Poppleton, Erik ; Pedrielli, Giulia ; Šulc, Petr ; Bertsekas, Dimitri P. ( September 2022 , INFORMS Journal on Computing)

   Ribonucleic acid (RNA) is a fundamental biological molecule that is essential to all living organisms, performing a versatile array of cellular tasks. The function of many RNA molecules is strongly related to the structure it adopts. As a result, great effort is being dedicated to the design of efficient algorithms that solve the “folding problem”—given a sequence of nucleotides, return a probable list of base pairs, referred to as the secondary structure prediction. Early algorithms largely rely on finding the structure with minimum free energy. However, the predictions rely on effective simplified free energy models that may not correctly identify the correct structure as the one with the lowest free energy. In light of this, new, data-driven approaches that not only consider free energy, but also use machine learning techniques to learn motifs are also investigated and recently been shown to outperform free energy–based algorithms on several experimental data sets. In this work, we introduce the new ExpertRNA algorithm that provides a modular framework that can easily incorporate an arbitrary number of rewards (free energy or nonparametric/data driven) and secondary structure prediction algorithms. We argue that this capability of ExpertRNA has the potential to balance out different strengths and weaknesses of state-of-the-art folding tools. We test ExpertRNA on several RNA sequence-structure data sets, and we compare the performance of ExpertRNA against a state-of-the-art folding algorithm. We find that ExpertRNA produces, on average, more accurate predictions of nonpseudoknotted secondary structures than the structure prediction algorithm used, thus validating the promise of the approach. Summary of Contribution: ExpertRNA is a new algorithm inspired by a biological problem. It is applied to solve the problem of secondary structure prediction for RNA molecules given an input sequence. The computational contribution is given by the design of a multibranch, multiexpert rollout algorithm that enables the use of several state-of-the-art approaches as base heuristics and allowing several experts to evaluate partial candidate solutions generated, thus avoiding assuming the reward being optimized by an RNA molecule when folding. Our implementation allows for the effective use of parallel computational resources as well as to control the size of the rollout tree as the algorithm progresses. The problem of RNA secondary structure prediction is of primary importance within the biology field because the molecule structure is strongly related to its functionality. Whereas the contribution of the paper is in the algorithm, the importance of the application makes ExpertRNA a showcase of the relevance of computationally efficient algorithms in supporting scientific discovery. 

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