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  1. Free, publicly-accessible full text available May 1, 2024
  2. Atomic force microscopy (AFM) provides a platform for high-resolution topographical imaging and the mechanical characterization of a wide range of samples, including live cells, proteins, and other biomolecules. AFM is also instrumental for measuring interaction forces and binding kinetics for protein–protein or receptor–ligand interactions on live cells at a single-molecule level. However, performing force measurements and high-resolution imaging with AFM and data analytics are time-consuming and require special skill sets and continuous human supervision. Recently, researchers have explored the applications of artificial intelligence (AI) and deep learning (DL) in the bioimaging field. However, the applications of AI to AFM operations for live-cell characterization are little-known. In this work, we implemented a DL framework to perform automatic sample selection based on the cell shape for AFM probe navigation during AFM biomechanical mapping. We also established a closed-loop scanner trajectory control for measuring multiple cell samples at high speed for automated navigation. With this, we achieved a 60× speed-up in AFM navigation and reduced the time involved in searching for the particular cell shape in a large sample. Our innovation directly applies to many bio-AFM applications with AI-guided intelligent automation through image data analysis together with smart navigation. 
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  3. In this paper we propose a new framework—MoViLan (Modular Vision and Language) for execution of visually grounded natural language instructions for day to day indoor household tasks. While several data-driven, end-to-end learning frameworks have been proposed for targeted navigation tasks based on the vision and language modalities, performance on recent benchmark data sets revealed the gap in developing comprehensive techniques for long horizon, compositional tasks (involving manipulation and navigation) with diverse object categories, realistic instructions and visual scenarios with non reversible state changes. We propose a modular approach to deal with the combined navigation and object interaction problem without the need for strictly aligned vision and language training data (e.g., in the form of expert demonstrated trajectories). Such an approach is a significant departure from the traditional end-to-end techniques in this space and allows for a more tractable training process with separate vision and language data sets. Specifically, we propose a novel geometry-aware mapping technique for cluttered indoor environments, and a language understanding model generalized for household instruction following. We demonstrate a significant increase in success rates for long horizon, compositional tasks over recent works on the recently released benchmark data set -ALFRED. 
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  4. Using a reliable and accurate method to phenotype disease incidence and severity is essential to unravel the complex genetic architecture of disease resistance in plants, and to develop disease resistant cultivars. Genome-wide association studies (GWAS) involve phenotyping large numbers of accessions, and have been used for a myriad of traits. In field studies, genetic accessions are phenotyped across multiple environments and replications, which takes a significant amount of labor and resources. Deep Learning (DL) techniques can be effective for analyzing image-based tasks; thus DL methods are becoming more routine for phenotyping traits to save time and effort. This research aims to conduct GWAS on sudden death syndrome (SDS) of soybean [ Glycine max L. (Merr.)] using disease severity from both visual field ratings and DL-based (using images) severity ratings collected from 473 accessions. Images were processed through a DL framework that identified soybean leaflets with SDS symptoms, and then quantified the disease severity on those leaflets into a few classes with mean Average Precision of 0.34 on unseen test data. Both visual field ratings and image-based ratings identified significant single nucleotide polymorphism (SNP) markers associated with disease resistance. These significant SNP markers are either in the proximity of previously reported candidate genes for SDS or near potentially novel candidate genes. Four previously reported SDS QTL were identified that contained a significant SNPs, from this study, from both a visual field rating and an image-based rating. The results of this study provide an exciting avenue of using DL to capture complex phenotypic traits from images to get comparable or more insightful results compared to subjective visual field phenotyping of traits for disease symptoms. 
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  5. We propose a novel policy gradient method for multi-agent reinforcement learning, which leverages two different variance-reduction techniques and does not require large batches over iterations. Specifically, we propose a momentum-based decentralized policy gradient tracking (MDPGT) where a new momentum-based variance reduction technique is used to approximate the local policy gradient surrogate with importance sampling, and an intermediate parameter is adopted to track two consecutive policy gradient surrogates. MDPGT provably achieves the best available sample complexity of O(N -1 e -3) for converging to an e-stationary point of the global average of N local performance functions (possibly nonconcave). This outperforms the state-of-the-art sample complexity in decentralized model-free reinforcement learning and when initialized with a single trajectory, the sample complexity matches those obtained by the existing decentralized policy gradient methods. We further validate the theoretical claim for the Gaussian policy function. When the required error tolerance e is small enough, MDPGT leads to a linear speed up, which has been previously established in decentralized stochastic optimization, but not for reinforcement learning. Lastly, we provide empirical results on a multi-agent reinforcement learning benchmark environment to support our theoretical findings. 
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