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  1. Graph neural networks (GNNs) have achieved tremendous success on multiple graph-based learning tasks by fusing network structure and node features. Modern GNN models are built upon iterative aggregation of neighbor's/proximity features by message passing. Its prediction performance has been shown to be strongly bounded by assortative mixing in the graph, a key property wherein nodes with similar attributes mix/connect with each other. We observe that real world networks exhibit heterogeneous or diverse mixing patterns and the conventional global measurement of assortativity, such as global assortativity coefficient, may not be a representative statistic in quantifying this mixing. We adopt a generalized concept, node-level assortativity, one that is based at the node level to better represent the diverse patterns and accurately quantify the learnability of GNNs. We find that the prediction performance of a wide range of GNN models is highly correlated with the node level assortativity. To break this limit, in this work, we focus on transforming the input graph into a computation graph which contains both proximity and structural information as distinct type of edges. The resulted multi-relational graph has an enhanced level of assortativity and, more importantly, preserves rich information from the original graph. We then propose to run GNNs on this computation graph and show that adaptively choosing between structure and proximity leads to improved performance under diverse mixing. Empirically, we show the benefits of adopting our transformation framework for semi-supervised node classification task on a variety of real world graph learning benchmarks. 
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  5. Abstract

    The incorporation of high‐performance optoelectronic devices into photonic neuromorphic processors can substantially accelerate computationally intensive matrix multiplication operations in machine learning (ML) algorithms. However, the conventional designs of individual devices and system are largely disconnected, and the system optimization is limited to the manual exploration of a small design space. Here, a device‐system end‐to‐end design methodology is reported to optimize a free‐space optical general matrix multiplication (GEMM) hardware accelerator by engineering a spatially reconfigurable array made from chalcogenide phase change materials. With a highly parallelized integrated hardware emulator with experimental information, the design of unit device to directly optimize GEMM calculation accuracy is achieved by exploring a large parameter space through reinforcement learning algorithms, including deep Q‐learning neural network, Bayesian optimization, and their cascaded approach. The algorithm‐generated physical quantities show a clear correlation between system performance metrics and device specifications. Furthermore, physics‐aware training approaches are employed to deploy optimized hardware to the tasks of image classification, materials discovery, and a closed‐loop design of optical ML accelerators. The demonstrated framework offers insights into the end‐to‐end and co‐design of optoelectronic devices and systems with reduced human supervision and domain knowledge barriers.

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  6. Abstract Motivation

    Reconstructing the full-length expressed transcripts (a.k.a. the transcript assembly problem) from the short sequencing reads produced by RNA-seq protocol plays a central role in identifying novel genes and transcripts as well as in studying gene expressions and gene functions. A crucial step in transcript assembly is to accurately determine the splicing junctions and boundaries of the expressed transcripts from the reads alignment. In contrast to the splicing junctions that can be efficiently detected from spliced reads, the problem of identifying boundaries remains open and challenging, due to the fact that the signal related to boundaries is noisy and weak.


    We present DeepBound, an effective approach to identify boundaries of expressed transcripts from RNA-seq reads alignment. In its core DeepBound employs deep convolutional neural fields to learn the hidden distributions and patterns of boundaries. To accurately model the transition probabilities and to solve the label-imbalance problem, we novelly incorporate the AUC (area under the curve) score into the optimizing objective function. To address the issue that deep probabilistic graphical models requires large number of labeled training samples, we propose to use simulated RNA-seq datasets to train our model. Through extensive experimental studies on both simulation datasets of two species and biological datasets, we show that DeepBound consistently and significantly outperforms the two existing methods.

    Availability and implementation

    DeepBound is freely available at

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  7. Abstract Motivation

    Protein intrinsically disordered regions (IDRs) play an important role in many biological processes. Two key properties of IDRs are (i) the occurrence is proteome-wide and (ii) the ratio of disordered residues is about 6%, which makes it challenging to accurately predict IDRs. Most IDR prediction methods use sequence profile to improve accuracy, which prevents its application to proteome-wide prediction since it is time-consuming to generate sequence profiles. On the other hand, the methods without using sequence profile fare much worse than using sequence profile.


    This article formulates IDR prediction as a sequence labeling problem and employs a new machine learning method called Deep Convolutional Neural Fields (DeepCNF) to solve it. DeepCNF is an integration of deep convolutional neural networks (DCNN) and conditional random fields (CRF); it can model not only complex sequence–structure relationship in a hierarchical manner, but also correlation among adjacent residues. To deal with highly imbalanced order/disorder ratio, instead of training DeepCNF by widely used maximum-likelihood, we develop a novel approach to train it by maximizing area under the ROC curve (AUC), which is an unbiased measure for class-imbalanced data.


    Our experimental results show that our IDR prediction method AUCpreD outperforms existing popular disorder predictors. More importantly, AUCpreD works very well even without sequence profile, comparing favorably to or even outperforming many methods using sequence profile. Therefore, our method works for proteome-wide disorder prediction while yielding similar or better accuracy than the others.

    Availability and Implementation


    Supplementary information

    Supplementary data are available at Bioinformatics online.

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  8. Abstract Motivation

    As an increasing amount of protein–protein interaction (PPI) data becomes available, their computational interpretation has become an important problem in bioinformatics. The alignment of PPI networks from different species provides valuable information about conserved subnetworks, evolutionary pathways and functional orthologs. Although several methods have been proposed for global network alignment, there is a pressing need for methods that produce more accurate alignments in terms of both topological and functional consistency.


    In this work, we present a novel global network alignment algorithm, named ModuleAlign, which makes use of local topology information to define a module-based homology score. Based on a hierarchical clustering of functionally coherent proteins involved in the same module, ModuleAlign employs a novel iterative scheme to find the alignment between two networks. Evaluated on a diverse set of benchmarks, ModuleAlign outperforms state-of-the-art methods in producing functionally consistent alignments. By aligning Pathogen–Human PPI networks, ModuleAlign also detects a novel set of conserved human genes that pathogens preferentially target to cause pathogenesis.


    Contact or

    Supplementary information

    Supplementary data are available at Bioinformatics online.

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