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Creators/Authors contains: "Lin, Liang"

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  1. Abstract

    The large-scale simulation of dynamical systems is critical in numerous scientific and engineering disciplines. However, traditional numerical solvers are limited by the choice of step sizes when estimating integration, resulting in a trade-off between accuracy and computational efficiency. To address this challenge, we introduce a deep learning-based corrector called Neural Vector (NeurVec), which can compensate for integration errors and enable larger time step sizes in simulations. Our extensive experiments on a variety of complex dynamical system benchmarks demonstrate that NeurVec exhibits remarkable generalization capability on a continuous phase space, even when trained using limited and discrete data. NeurVec significantly accelerates traditional solvers, achieving speeds tens to hundreds of times faster while maintaining high levels of accuracy and stability. Moreover, NeurVec’s simple-yet-effective design, combined with its ease of implementation, has the potential to establish a new paradigm for fast-solving differential equations based on deep learning.

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  2. This article presents a semisupervised multilabel fully convolutional network (FCN) for hierarchical object parsing of images. We consider each object part (e.g., eye and head) as a class label and learn to assign every image pixel to multiple coherent part labels. Different from previous methods that consider part labels as independent classes, our method explicitly models the internal relationships between object parts, e.g., that a pixel highly scored for eyes should be highly scored for heads as well. Such relationships directly reflect the structure of the semantic space and thus should be respected while learning the deep representation. We achieve this objective by introducing a multilabel softmax loss function over both labeled and unlabeled images and regularizing it with two pairwise ranking constraints. The first constraint is based on a manifold assumption that image pixels being visually and spatially close to each other should be collaboratively classified as the same part label. The other constraint is used to enforce that no pixel receives significant scores from more than one label that are semantically conflicting with each other. The proposed loss function is differentiable with respect to network parameters and hence can be optimized by standard stochastic gradient methods. We evaluate the proposed method on two public image data sets for hierarchical object parsing and compare it with the alternative parsing methods. Extensive comparisons showed that our method can achieve state-of-the-art performance while using 50% less labeled training samples than the alternatives. 
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  3. Abstract

    Glycosylation plays important roles in cellular function and endows protein therapeutics with beneficial properties. However, constructing biosynthetic pathways to study and engineer precise glycan structures on proteins remains a bottleneck. Here, we report a modular, versatile cell-free platform forglycosylationpathway assembly byrapidin vitromixing andexpression (GlycoPRIME). In GlycoPRIME, glycosylation pathways are assembled by mixing-and-matching cell-free synthesized glycosyltransferases that can elaborate a glucose primer installed onto protein targets by anN-glycosyltransferase. We demonstrate GlycoPRIME by constructing 37 putative protein glycosylation pathways, creating 23 unique glycan motifs, 18 of which have not yet been synthesized on proteins. We use selected pathways to synthesize a protein vaccine candidate with an α-galactose adjuvant motif in a one-pot cell-free system and human antibody constant regions with minimal sialic acid motifs in glycoengineeredEscherichia coli. We anticipate that these methods and pathways will facilitate glycoscience and make possible new glycoengineering applications.

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  4. This paper presents a unified framework to learn to quantify perceptual attributes (e.g., safety, attractiveness) of physical urban environments using crowd-sourced street-view photos without human annotations. The efforts of this work include two folds. First, we collect a large-scale urban image dataset in multiple major cities in U.S.A., which consists of multiple street-view photos for every place. Instead of using subjective annotations as in previous works, which are neither accurate nor consistent, we collect for every place the safety score from government’s crime event records as objective safety indicators. Second, we observe that the place-centric perception task is by nature a multi-instance regression problem since the labels are only available for places (bags), rather than images or image regions (instances). We thus introduce a deep convolutional neural network (CNN) to parameterize the instance-level scoring function, and develop an EM algorithm to alternatively estimate the primary instances (images or image regions) which affect the safety scores and train the proposed network. Our method is capable of localizing interesting images and image regions for each place.We evaluate the proposed method on a newly created dataset and a public dataset. Results with comparisons showed that our method can clearly outperform the alternative perception methods and more importantly, is capable of generating region-level safety scores to facilitate interpretations of the perception process. 
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