Question: Algorithms to solve large and sparse network alignment issues.

This paper presents an extensive evaluation of various string similarity metrics for the purpose of name and record matching, utilizing an open-source Java toolkit. The study encompasses a wide range of distance metrics derived from diverse research domains, encompassing edit-distance measures, rapid string comparators, token-based approaches, and hybrid methodologies. The toolkit's capabilities are expanded to facilitate record comparisons, addressing complexities inherent in comparing structured data. The paper delves into the challenges associated with assessing record-matching techniques and offers baseline outcomes for select algorithms that employ string comparisons across record fields. The comprehensive analysis highlights the effectiveness of different metrics in tackling the intricacies of name and record matching, providing insights into optimal algorithm selection for specific applications.

The Floyd-Warshall algorithm is a simple and widely used algorithm to compute shortest paths between all pairs of vertices in an edge weighted directed graph. It can also be used to detect the presence of negative cycles. We will show that for this task many existing implementations of the Floyd-Warshall algorithm will fail because exponentially large numbers can appear during its execution.

Interaction between users in online social networks plays a key role in social network analysis. One on important types of social group is full connected relation between some users, which known as clique structure. Therefore finding a maximum clique is essential for some analysis. In this paper, we proposed a new method using ant colony optimization algorithm and particle swarm optimization algorithm. In the proposed method, in order to attain better results, it is improved process of pheromone update by particle swarm optimization. Simulation results on popular standard social network benchmarks in comparison standard ant colony optimization algorithm are shown a relative enhancement of proposed algorithm. Keywordssocial network analysis; clique problem; ACO; PSO.

Parallel matrix multiplication is one of the most studied fundamental problems in distributed and high performance computing. We obtain a new parallel algorithm that is based on Strassen's fast matrix multiplication and minimizes communication. The algorithm outperforms all known parallel matrix multiplication algorithms, classical and Strassen-based, both asymptotically and in practice. A critical bottleneck in parallelizing Strassen's algorithm is the communication between the processors. Ballard, Demmel, Holtz, and Schwartz (SPAA '11) prove lower bounds on these communication costs, using expansion properties of the underlying computation graph. Our algorithm matches these lower bounds, and so is communication-optimal. It exhibits perfect strong scaling within the maximum possible range.
 Benchmarking our implementation on a Cray XT4, we obtain speedups over classical and Strassen-based algorithms ranging from 24% to 184% for a fixed matrix dimension n=94080, where the number of processors ranges from 49 to 7203.
 Our parallelization approach generalizes to other fast matrix multiplication algorithms.

This article maybe used for research, teaching and private study purposes. Any substantial or systematic reproduction, redistribution , reselling , loan or sub-licensing, systematic supply or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. The accuracy of any instructions, formulae and drug doses should be independently verified with primary sources. The publisher shall not be liable for any loss, actions, claims, proceedings, demand or costs or damages whatsoever or howsoever caused arising directly or indirectly in connection with or arising out of the use of this material. Identification algorithms based on the well-known linear least squares methods of gaussian elimination, Cholesky decomposition, classical Gram-Schmidt, modified Gram-Schmidt, Householder transformation, Givens method, and singular value decomposition are reviewed. The classical Gram-Schmidt, modified Gram-Schmidt,and Householder transformation algorithms are then extended to combine structure determination, or which terms to include in the model, and parameter estimation in a very simple and efficient manner for a class of multivariable discrete-time non-linear stochastic systems which are linear in the parameters.

Given a large graph, how can we calculate the relevance between nodes fast and accurately? Random walk with restart (RWR) provides a good measure for this purpose and has been applied to diverse data mining applications including ranking, community detection, link prediction, and anomaly detection. Since calculating RWR from scratch takes a long time, various preprocessing methods, most of which are related to inverting adjacency matrices, have been proposed to speed up the calculation. However, these methods do not scale to large graphs because they usually produce large dense matrices that do not fit into memory. In addition, the existing methods are inappropriate when graphs dynamically change because the expensive preprocessing task needs to be computed repeatedly.
 In this article, we propose Bear, a fast, scalable, and accurate method for computing RWR on large graphs. Bear has two versions: a preprocessing method BearS for static graphs and an incremental update method BearD for dynamic graphs. BearS consists of the preprocessing step and the query step. In the preprocessing step, BearS reorders the adjacency matrix of a given graph so that it contains a large and easy-to-invert submatrix, and precomputes several matrices including the Schur complement of the submatrix. In the query step, BearS quickly computes the RWR scores for a given query node using a block elimination approach with the matrices computed in the preprocessing step. For dynamic graphs, BearD efficiently updates the changed parts in the preprocessed matrices of BearS based on the observation that only small parts of the preprocessed matrices change when few edges are inserted or deleted. Through extensive experiments, we show that BearS significantly outperforms other state-of-the-art methods in terms of preprocessing and query speed, space efficiency, and accuracy. We also show that BearD quickly updates the preprocessed matrices and immediately computes queries when the graph changes.

A recent paper posed the question: “Graph Matching: What are we really talking about?”. Far from providing a definite answer to that question, in this paper we will try to characterize the role that graphs play within the Pattern Recognition field. To this aim two taxonomies are presented and discussed. The first includes almost all the graph matching algorithms proposed from the late seventies, and describes the different classes of algorithms. The second taxonomy considers the types of common applications of graph-based techniques in the Pattern Recognition and Machine Vision field.

This paper introduces a linear time graph-based soft clustering algorithm. The algorithm applies a simple idea: given a graph, vertex pairs are assigned to the same cluster if either vertex has maximal affinity to the other. Clusters of varying size, shape, and density are found automatically making the algorithm suited to tasks such Word Sense Induction (WSI), where the number of classes is unknown and where class distributions may be skewed. The algorithm is applied to two WSI tasks, obtaining results comparable with those of systems adopting existing, state-of-the-art methods.

Greedy approximation algorithms have been frequently used to obtain sparse solutions to learning problems. In this paper, we present a general greedy algorithm for solving a class of convex optimization problems. We derive a bound on the rate of approximation for this algorithm, and show that our algorithm includes a number of earlier studies as special cases.

Given a parallel program represented by a task graph, the objective of a scheduling algorithm is to minimize the overall execution time of the program by properly assigning the nodes of the graph to the processors. This multiprocessor scheduling problem is NP-complete even with simplifying assumptions and becomes more complex under relaxed assumptions such as arbitrary precedence constraints, and arbitrary task execution and communication times. The present literature on this topic is a large repertoire of heuristics that produce good solutions in a reasonable amount of time. These heuristics, however, have restricted applicability in a practical environment because they have a number of fundamental problems including high time complexity, lack of scalability, and no performance guarantee with respect to optimal solutions. Recently, genetic algorithms (GAs) have been widely reckoned as a useful vehicle for obtaining high quality or even optimal solutions for a broad range of combinatorial optimization problems. While a few GAs for scheduling have already been suggested, in this paper we propose a novel GA-based algorithm with an objective to simultaneously meet the goals of high performance, scalability, and fast running time. The proposed parallel genetic scheduling (PGS) algorithm itself is a parallel algorithm which generates high quality solutions in a short time. By encoding the scheduling list as a chromosome, the PGS algorithm can potentially generate an optimal scheduling list which in turn leads to an optimal schedule. The major strength of the PGS algorithm lies in its two efficient genetic operators: the order crossover and mutation. These operators effectively combine the building-blocks of good scheduling lists to construct better lists. The proposed algorithm is evaluated through a robust comparison with two heuristics best known in terms of performance and time complexity. It outperforms both heuristics while taking considerably less running time. When evaluated with random task graphs for which optimal solutions are known, the PGS algorithm generates optimal solutions for more than half of the test cases and close-to-optimal for the other half. © 1997 Academic Press

Common-neighbor-based method is simple yet effective to predict missing links, which assume that two nodes are more likely to be connected if they have more common neighbors. In such method, each common neighbor of two nodes contributes equally to the connection likelihood. In this Letter, we argue that different common neighbors may play different roles and thus lead to different contributions, and propose a local näıve Bayes model accordingly. Extensive experiments were carried out on eight real networks. Compared with the common-neighbor-based methods, the present method can provide more accurate predictions. Finally, we gave a detailed case study on the US air transportation network. Introduction. – The problem of link prediction aims at estimating the likelihood of the existence of a link between two nodes in a given network, based on the observed links [1]. Recently, the study of link prediction has attracted much attention from disparate scientific communities. In the theoretical aspect, accurate prediction indeed gives evidence to some underlying mechanisms that drives the network evolution [2]. Moveover, it is very possible to build a fair evaluation platform for network modeling under the framework of link prediction, which might be interested by network scientists [1, 3]. In the practical aspect, for biological networks such as protein-protein interaction networks and metabolic networks [4–6], the experiments of uncovering the new links or interactions are costly, and thus to predict in advance and focus on the links most likely to exist can sharply reduce the experimental costs [7]. In addition, some of the representative methods of link prediction have been successfully applied to address the classification problem in partially labeled networks [8, 9], as well as identified the spurious links resulted from the inaccurate information in the data [10]. Motivated by the theoretical interests and practical significance, many methods for link predication have been proposed. Therein some algorithms are based on Markov chains [11–13] and machine learning [14, 15]. Another group of algorithms are based on node similarity [1, 16]. (a)Corresponding author:linyuan.lue@unifr.ch Common Neighbors (CN) is one of the simplest similarity indices. Empirically, Kossinets and Watts [17] analyzed a large-scale social network, suggesting that two students having many mutual friends are very probable to be friend in the future. Also in online society like Facebook, the users tend to be friend if they have common friends and therefore form a community. Extensive analysis on disparate networks suggests that CN index is of good performance on predicting the missing links [16, 18]. Lü et al. [19] suggested that in a network with large clustering coefficient, CN can provide competitively accurate predictions compared with the indices making use of global information. Very recently, Cui et al. [20] revealed that the nodes with more common neighbors are more likely to form new links in a growing network. The basic assumption of CN is that two nodes are more likely to be connected if they have more common neighbors. Simply counting the number of common neighbors indicates that each common neighbor gives equal contribution to the connection likelihood. However, sometimes different common neighbors may play different roles. For instance, the common close friends of two people who don’t know each other may contribute more to their possibly future friendship than their common nodding acquaintances. In this Letter, we propose a probabilistic model based on the Bayesian theory, called Local Näıve Bayes (LNB) model, to predict the missing links in complex networks. Based on the LNB model,


Question: Methods for solving large-scale, sparse network alignment issues.

Over the course of three decades, graph matching has evolved significantly within the realm of Pattern Recognition, with a multitude of algorithms being developed. This paper aims to elucidate the significance of graphs in this domain by presenting and analyzing two comprehensive taxonomies. The first taxonomy encompasses the vast majority of graph matching algorithms introduced since the late seventies, offering a detailed categorization of these algorithms into distinct classes. The second taxonomy shifts focus to the practical applications of graph-based methodologies, highlighting their prevalence and utility in Pattern Recognition and Machine Vision tasks. This systematic approach not only provides a historical perspective but also underscores the versatility and adaptability of graph matching techniques in addressing complex pattern recognition challenges. Through these taxonomies, the paper endeavors to contribute to the ongoing dialogue on the essence and scope of graph matching within the Pattern Recognition community.

Search-based graph queries, such as finding short paths and isomorphic subgraphs, are dominated by memory latency. If input graphs can be partitioned appropriately, large cluster-based computing platforms can run these queries. However, the lack of compute-bound processing at each vertex of the input graph and the constant need to retrieve neighbors implies low processor utilization. Furthermore, graph classes such as scale-free social networks lack the locality to make partitioning clearly effective. Massive multithreading is an alternative architectural paradigm, in which a large shared memory is combined with processors that have extra hardware to support many thread contexts. The processor speed is typically slower than normal, and there is no data cache. Rather than mitigating memory latency, multithreaded machines tolerate it. This paradigm is well aligned with the problem of graph search, as the high ratio of memory requests to computation can be tolerated via multithreading. In this paper, we introduce the multithreaded graph library (MTGL), generic graph query software for processing semantic graphs on multithreaded computers. This library currently runs on serial machines and the Cray MTA-2, but Sandia is developing a run-time system that will make it possible to run MTGL-based code on symmetric multiprocessors. We also introduce a multithreaded algorithm for connected components and a new heuristic for inexact subgraph isomorphism We explore the performance of these and other basic graph algorithms on large scale-free graphs. We conclude with a performance comparison between the Cray MTA-2 and Blue Gene/Light for s-t connectivity.

We propose a semiparametric approach called the nonparanormal SKEPTIC for efficiently and robustly estimating high-dimensional undirected graphical models. To achieve modeling flexibility, we consider the nonparanormal graphical models proposed by Liu, Lafferty and Wasserman [J. Mach. Learn. Res. 10 (2009) 2295–2328]. To achieve estimation robustness, we exploit nonparametric rank-based correlation coefficient estimators, including Spearman’s rho and Kendall’s tau. We prove that the nonparanormal SKEPTIC achieves the optimal parametric rates of convergence for both graph recovery and parameter estimation. This result suggests that the nonparanormal graphical models can be used as a safe replacement of the popular Gaussian graphical models, even when the data are truly Gaussian. Besides theoretical analysis, we also conduct thorough numerical simulations to compare the graph recovery performance of different estimators under both ideal and noisy settings. The proposed methods are then applied on a large-scale genomic data set to illustrate their empirical usefulness. The R package huge implementing the proposed methods is available on the Comprehensive R Archive Network: http://cran.r-project.org/.

We study an acceleration method for point-to-point shortest-path computations in large and sparse directed graphs with given nonnegative arc weights. The acceleration method is called the arc-flag approach and is based on Dijkstra's algorithm. In the arc-flag approach, we allow a preprocessing of the network data to generate additional information, which is then used to speedup shortest-path queries. In the preprocessing phase, the graph is divided into regions and information is gathered on whether an arc is on a shortest path into a given region. The arc-flag method combined with an appropriate partitioning and a bidirected search achieves an average speedup factor of more than 500 compared to the standard algorithm of Dijkstra on large networks (1 million nodes, 2.5 million arcs). This combination narrows down the search space of Dijkstra's algorithm to almost the size of the corresponding shortest path for long-distance shortest-path queries. We conduct an experimental study that evaluates which partitionings are best suited for the arc-flag method. In particular, we examine partitioning algorithms from computational geometry and a multiway arc separator partitioning. The evaluation was done on German road networks. The impact of different partitions on the speedup of the shortest path algorithm are compared. Furthermore, we present an extension of the speedup technique to multiple levels of partitions. With this multilevel variant, the same speedup factors can be achieved with smaller space requirements. It can, therefore, be seen as a compression of the precomputed data that preserves the correctness of the computed shortest paths.

Applications in biotechnology such as gene expression analysis and image processing have led to a tremendous development of statistical methods with emphasis on reliable solutions to severely underdetermined systems. Furthermore, interpretations of such solutions are of importance, meaning that the surplus of inputs has been reduced to a concise model. At the core of this development are methods which augment the standard linear models for regression, classification and decomposition such that sparse solutions are obtained. This toolbox aims at making public available carefully implemented and well-tested variants of the most popular of such methods for the MATLAB programming environment. These methods consist of easy-to-read yet efficient implementations of various coefficient-path following algorithms and implementations of sparse principal component analysis and sparse discriminant analysis which are not available in MATLAB. The toolbox builds on code made public in 2005 and which has since been used in several studies.

Compressed representations have become effective to store and access large Web and social graphs, in order to support various graph querying and mining tasks. The existing representations exploit various typical patterns in those networks and provide basic navigation support. In this paper we obtain unprecedented results by finding “dense subgraph” patterns and combining them with techniques such as node orderings and compact data structures. On those representations we support out-neighbor and out/in-neighbor queries, as well as mining queries based on dense subgraphs. First, we propose a compression scheme for Web graphs that reduces edges by representing dense subgraphs with “virtual nodes”; over this scheme we apply node orderings and other compression techniques. With this approach we match the best current compression ratios that support out-neighbor queries (i.e., nodes pointed from a given node), using 1.0–1.8 bits per edge (bpe) on large Web graphs, and retrieving each neighbor of a node in 0.6–1.0 microseconds (μsec). When supporting both outand in-neighbor queries, instead, our technique generally offers the best time when using little space. If the reduced graph, instead, is represented with a compact data structure that supports bidirectional navigation, we obtain the most compact Web graph representations (0.9–1.5 bpe) that support out/in-neighbor navigation, yet the time per neighbor extracted raises to around 5–20 μsec. We also propose a compact data structure that represents dense subgraphs without using virtual nodes. It allows us to recover out/in-neighbors and answer other more complex queries on the dense subgraphs identified. This structure is not competitive on Web graphs, but on social networks it achieves 4–13 bpe and 8–12 μsec per out/in-neighbor retrieved, which improves upon all existing representations.

Alignment-free sequence analysis approaches provide important alternatives over multiple sequence alignment (MSA) in biological sequence analysis because alignment-free approaches have low computation complexity and are not dependent on high level of sequence identity. However, most of the existing alignment-free methods do not employ true full information content of sequences and thus can not accurately reveal similarities and differences among DNA sequences. We present a novel alignment-free computational method for sequence analysis based on Ramanujan-Fourier transform (RFT), in which complete information of DNA sequences is retained. We represent DNA sequences as four binary indicator sequences and apply RFT on the indicator sequences to convert them into frequency domain. The Euclidean distance of the complete RFT coefficients of DNA sequences are used as similarity measures. To address the different lengths of RFT coefficients in Euclidean space, we pad zeros to short DNA binary sequences so that the binary sequences equal the longest length in the comparison sequence data. Thus, the DNA sequences are compared in the same dimensional frequency space without information loss. We demonstrate the usefulness of the proposed method by presenting experimental results on hierarchical clustering of genes and genomes. The proposed method opens a new channel to biological sequence analysis, classification, and structural module identification.

The mechanisms underlying life machinery are still not completely understood. Something is known, something is “probably” known, other things are still unknown. Scientists all over the world are working very hard to clarify the processes regulating the cell life cycle and bioinformaticians try to support them by developing specialized automated tools. Within the plethora of applications devoted to the study of life mechanisms, tools for the analysis and comparison of biological networks are catching the attention of many researchers. It is interesting to investigate why.

Efficient enumeration of all maximal cliques in a given graph has many applications in graph theory, data mining and bio informatics. However, the exponentially increasing computation time of this problem confines the scale of the graph. Meanwhile, recent researches show that many networks in our world are complex networks involving massive data. To solve the maximal clique problem in the real-world scenarios, this paper presents a parallel algorithm Peamc (parallel enumeration of all maximal cliques) which exploits several new and effective techniques to enumerate all maximal cliques in a complex network. Furthermore, we provide a performance study on a true-life call graph with up to 2,423,807 vertices and 5,317,183 edges. The experimental results show that Peamc can find all the maximal cliques in a complex network with high efficiency and scalability

It is shown how to construct a clique graph in which properties of cliques of a fixed order in a given graph are represented by vertices in a weighted graph. Various definitions and motivations for these weights are given. The detection of communities or clusters is used to illustrate how a clique graph may be exploited. In particular a benchmark network is shown where clique graphs find the overlapping communities accurately while vertex partition methods fail. PACS numbers: 89.75.Hc, 89.75.Fb, 89.75.-k

The proliferation of online social networks, and the concomitant accumulation of user data, give rise to hotly debated issues of privacy, security, and control. One specific challenge is the sharing or public release of anonymized data without accidentally leaking personally identifiable information (PII). Unfortunately, it is often difficult to ascertain that sophisticated statistical techniques, potentially employing additional external data sources, are unable to break anonymity. In this paper, we consider an instance of this problem, where the object of interest is the structure of a social network, i.e., a graph describing users and their links. Recent work demonstrates that anonymizing node identities may not be sufficient to keep the network private: the availability of node and link data from another domain, which is correlated with the anonymized network, has been used to re-identify the anonymized nodes. This paper is about conditions under which such a de-anonymization process is possible.
 We attempt to shed light on the following question: can we assume that a sufficiently sparse network is inherently anonymous, in the sense that even with unlimited computational power, de-anonymization is impossible? Our approach is to introduce a random graph model for a version of the de-anonymization problem, which is parameterized by the expected node degree and a similarity parameter that controls the correlation between two graphs over the same vertex set. We find simple conditions on these parameters delineating the boundary of privacy, and show that the mean node degree need only grow slightly faster than log n with network size n for nodes to be identifiable. Our results have policy implications for sharing of anonymized network information.


Question: MDU-Net: A multi-scale densely connected U-Net architecture for biomedical image segmentation tasks.

This paper introduces a significant advancement in deep learning architecture, focusing on the training of deeper neural networks, which have traditionally posed challenges due to their complexity. We propose a novel framework, residual learning, designed to facilitate the training of networks with unprecedented depth. The core idea involves reformulating the network layers to learn residual functions relative to the input layers, as opposed to learning functions independently. This approach has been empirically validated through extensive experiments, demonstrating that residual networks are more amenable to optimization and can achieve higher accuracy as depth increases. On the ImageNet dataset, we have successfully trained residual networks with up to 152 layers, which is 8 times deeper than the VGG nets, yet with lower complexity. An ensemble of these residual networks achieved a remarkable 3.57% error rate on the ImageNet test set, securing the first place in the ILSVRC 2015 classification task. Additionally, we conducted analyses on CIFAR-10 with 100 and 1000 layers. The depth of representations plays a pivotal role in visual recognition tasks, and our extremely deep representations have led to a 28% relative improvement in the COCO object detection dataset. The deep residual networks serve as the cornerstone of our submissions to the ILSVRC & COCO 2015 competitions, where we secured the top positions in ImageNet detection, ImageNet localization, COCO detection, and COCO segmentation tasks.

Tumor segmentation from magnetic resonance imaging (MRI) data is an important but time consuming manual task performed by medical experts. Automating this process is a challenging task because of the high diversity in the appearance of tumor tissues among different patients and in many cases similarity with the normal tissues. MRI is an advanced medical imaging technique providing rich information about the human soft-tissue anatomy. There are different brain tumor detection and segmentation methods to detect and segment a brain tumor from MRI images. These detection and segmentation approaches are reviewed with an importance placed on enlightening the advantages and drawbacks of these methods for brain tumor detection and segmentation. The use of MRI image detection and segmentation in different procedures are also described. Here a brief review of different segmentation for detection of brain tumor from MRI of brain has been discussed.

3D Convolutional Neural Networks are sensitive to transformations applied to their input. This is a problem because a voxelized version of a 3D object, and its rotated clone, will look unrelated to each other after passing through to the last layer of a network. Instead, an idealized model would preserve a meaningful representation of the voxelized object, while explaining the pose-difference between the two inputs. An equivariant representation vector has two components: the invariant identity part, and a discernable encoding of the transformation. Models that can’t explain pose-differences risk “diluting” the representation, in pursuit of optimizing a classification or regression loss function. We introduce a Group Convolutional Neural Network with linear equivariance to translations and right angle rotations in three dimensions. We call this network CubeNet, reflecting its cube-like symmetry. By construction, this network helps preserve a 3D shape’s global and local signature, as it is transformed through successive layers. We apply this network to a variety of 3D inference problems, achieving state-of-the-art on the ModelNet10 classification challenge, and comparable performance on the ISBI 2012 Connectome Segmentation Benchmark. To the best of our knowledge, this is the first 3D rotation equivariant CNN for voxel representations.

Multilabel image annotation is one of the most important open problems in computer vision field. Unlike existing works that usually use conventional visual features to annotate images, features based on deep learning have shown potential to achieve outstanding performance. In this work, we propose a multimodal deep learning framework, which aims to optimally integrate multiple deep neural networks pretrained with convolutional neural networks. In particular, the proposed framework explores a unified two-stage learning scheme that consists of (i) learning to fune-tune the parameters of deep neural network with respect to each individual modality, and (ii) learning to find the optimal combination of diverse modalities simultaneously in a coherent process. Experiments conducted on the NUS-WIDE dataset evaluate the performance of the proposed framework for multilabel image annotation, in which the encouraging results validate the effectiveness of the proposed algorithms.

Standard 3D convolution operations require much larger amounts of memory and computation cost than 2D convolution operations. The fact has hindered the development of deep neural nets in many 3D vision tasks. In this paper, we investigate the possibility of applying depthwise separable convolutions in 3D scenario and introduce the use of 3D depthwise convolution. A 3D depthwise convolution splits a single standard 3D convolution into two separate steps, which would drastically reduce the number of parameters in 3D convolutions with more than one order of magnitude. We experiment with 3D depthwise convolution on popular CNN architectures and also compare it with a similar structure called pseudo-3D convolution. The results demonstrate that, with 3D depthwise convolutions, 3D vision tasks like classification and reconstruction can be carried out with more light-weighted neural networks while still delivering comparable performances.

Early diagnosis of treatable diseases is essential for improving healthcare, and many diseases’ onsets are predictable from annual lab tests and their temporal trends. We introduce a multi-resolution convolutional neural network for early detection of multiple diseases from irregularly measured sparse lab values. Our novel architecture takes as input both an imputed version of the data and a binary observation matrix. For imputing the temporal sparse observations, we develop a flexible, fast to train method for differentiable multivariate kernel regression. Our experiments on data from 298K individuals over 8 years, 18 common lab measurements, and 171 diseases show that the temporal signatures learned via convolution are significantly more predictive than baselines commonly used for early disease diagnosis.

OBJECTIVE
Brain-computer interfaces (BCI) enable direct communication with a computer, using neural activity as the control signal. This neural signal is generally chosen from a variety of well-studied electroencephalogram (EEG) signals. For a given BCI paradigm, feature extractors and classifiers are tailored to the distinct characteristics of its expected EEG control signal, limiting its application to that specific signal. Convolutional neural networks (CNNs), which have been used in computer vision and speech recognition to perform automatic feature extraction and classification, have successfully been applied to EEG-based BCIs; however, they have mainly been applied to single BCI paradigms and thus it remains unclear how these architectures generalize to other paradigms. Here, we ask if we can design a single CNN architecture to accurately classify EEG signals from different BCI paradigms, while simultaneously being as compact as possible.

APPROACH
In this work we introduce EEGNet, a compact convolutional neural network for EEG-based BCIs. We introduce the use of depthwise and separable convolutions to construct an EEG-specific model which encapsulates well-known EEG feature extraction concepts for BCI. We compare EEGNet, both for within-subject and cross-subject classification, to current state-of-the-art approaches across four BCI paradigms: P300 visual-evoked potentials, error-related negativity responses (ERN), movement-related cortical potentials (MRCP), and sensory motor rhythms (SMR).

MAIN RESULTS
We show that EEGNet generalizes across paradigms better than, and achieves comparably high performance to, the reference algorithms when only limited training data is available across all tested paradigms. In addition, we demonstrate three different approaches to visualize the contents of a trained EEGNet model to enable interpretation of the learned features.

SIGNIFICANCE
Our results suggest that EEGNet is robust enough to learn a wide variety of interpretable features over a range of BCI tasks. Our models can be found at: https://github.com/vlawhern/arl-eegmodels.

We present a deep learning framework for computer-aided lung cancer diagnosis. Our multi-stage framework detects nodules in 3D lung CAT scans, determines if each nodule is malignant, and nally assigns a cancer probability based on these results. We discuss the challenges and advantages of our framework. In the Kaggle Data Science Bowl 2017, our framework ranked 41st out of 1972 teams.

Convolutional neural networks (CNNs) have demonstrated superior performance in super-resolution (SR). However, most CNN-based SR methods neglect the different importance among feature channels or fail to take full advantage of the hierarchical features. To address these issues, this paper presents a novel recursive unit. Firstly, at the beginning of each unit, we adopt a compact channel attention mechanism to adaptively recalibrate the channel importance of input features. Then, the multi-level features, rather than only deep-level features, are extracted and fused. Additionally, we find that it will force our model to learn more details by using the learnable upsampling method (i.e., transposed convolution) only on residual branch (instead of using it both on residual branch and identity branch) while using the bicubic interpolation on the other branch. Analytic experiments show that our method achieves competitive results compared with the state-of-the-art methods and maintains faster speed as well.

As a widely used non-linear activation, Rectified Linear Unit (ReLU) separates noise and signal in a feature map by learning a threshold or bias. However, we argue that the classification of noise and signal not only depends on the magnitude of responses, but also the context of how the feature responses would be used to detect more abstract patterns in higher layers. In order to output multiple response maps with magnitude in different ranges for a particular visual pattern, existing networks employing ReLU and its variants have to learn a large number of redundant filters. In this paper, we propose a multi-bias non-linear activation (MBA) layer to explore the information hidden in the magnitudes of responses. It is placed after the convolution layer to decouple the responses to a convolution kernel into multiple maps by multi-thresholding magnitudes, thus generating more patterns in the feature space at a low computational cost. It provides great flexibility of selecting responses to different visual patterns in different magnitude ranges to form rich representations in higher layers. Such a simple and yet effective scheme achieves the stateof-the-art performance on several benchmarks.

PURPOSE
To allow fast and high-quality reconstruction of clinical accelerated multi-coil MR data by learning a variational network that combines the mathematical structure of variational models with deep learning.

THEORY AND METHODS
Generalized compressed sensing reconstruction formulated as a variational model is embedded in an unrolled gradient descent scheme. All parameters of this formulation, including the prior model defined by filter kernels and activation functions as well as the data term weights, are learned during an offline training procedure. The learned model can then be applied online to previously unseen data.

RESULTS
The variational network approach is evaluated on a clinical knee imaging protocol for different acceleration factors and sampling patterns using retrospectively and prospectively undersampled data. The variational network reconstructions outperform standard reconstruction algorithms, verified by quantitative error measures and a clinical reader study for regular sampling and acceleration factor 4.

CONCLUSION
Variational network reconstructions preserve the natural appearance of MR images as well as pathologies that were not included in the training data set. Due to its high computational performance, that is, reconstruction time of 193 ms on a single graphics card, and the omission of parameter tuning once the network is trained, this new approach to image reconstruction can easily be integrated into clinical workflow. Magn Reson Med 79:3055-3071, 2018. © 2017 International Society for Magnetic Resonance in Medicine.


Question: MDU-Net: A multi-scale densely connected U-Net for the segmentation of biomedical images.

Introducing the MDU-Net: A Multi-scale Densely Connected U-Net Architecture for Enhanced Biomedical Image Segmentation

Innovative models for semantic segmentation, particularly in the biomedical domain, have evolved from adaptations of convolutional networks initially designed for image classification. However, dense prediction tasks like biomedical image segmentation present unique challenges that differ significantly from image classification. This paper presents a novel convolutional network module, the MDU-Net (Multi-scale Densely Connected U-Net), specifically engineered for dense prediction tasks. The MDU-Net leverages dilated convolutions to systematically aggregate multi-scale contextual information, thereby enhancing the network's ability to capture fine-grained details without sacrificing resolution. The core of the MDU-Net's design lies in the fact that dilated convolutions enable exponential expansion of the receptive field without compromising resolution or coverage. We demonstrate that incorporating the MDU-Net's context module into state-of-the-art semantic segmentation systems leads to a significant boost in accuracy. Moreover, we explore the adaptation of image classification networks to dense prediction tasks and reveal that simplifying these networks can further enhance accuracy, making the MDU-Net a promising solution for advancing biomedical image segmentation capabilities.

The objective of this paper is the unsupervised segmentation of image training sets into foreground and background in order to improve image classification performance. To this end we introduce a new scalable, alternation-based algorithm for co-segmentation, BiCoS, which is simpler than many of its predecessors, and yet has superior performance on standard benchmark image datasets.

Convolutional Neural Network (CNN)-based machine learning systems have made breakthroughs in feature extraction and image recognition tasks in two dimensions (2D). Although there is significant ongoing work to apply CNN technology to domains involving complex 3D data, the success of such efforts has been constrained, in part, by limitations in data representation techniques. Most current approaches rely upon low-resolution 3D models, strategic limitation of scope in the 3D space, or the application of lossy projection techniques to allow for the use of 2D CNNs. To address this issue, we present a mapping algorithm that converts 3D structures to 2D and 1D data grids by mapping a traversal of a 3D space-filling curve to the traversal of corresponding 2D and 1D curves. We explore the performance of 2D and 1D CNNs trained on data encoded with our method versus comparable volumetric CNNs operating upon raw 3D data from a popular benchmarking dataset. Our experiments demonstrate that both 2D and 1D representations of 3D data generated via our method preserve a significant proportion of the 3D data’s features in forms learnable by CNNs. Furthermore, we demonstrate that our method of encoding 3D data into lower-dimensional representations allows for decreased CNN training time cost, increased original 3D model rendering resolutions, and supports increased numbers of data channels when compared to purely volumetric approaches. This demonstration is accomplished in the context of a structural biology classification task wherein we train 3D, 2D, and 1D CNNs on examples of two homologous branches within the Ras protein family. The essential contribution of this paper is the introduction of a dimensionality-reduction method that may ease the application of powerful deep learning tools to domains characterized by complex structural data.

We propose a hierarchical segmentation algorithm that starts with a very fine over segmentation and gradually merges regions using a cascade of boundary classifiers. This approach allows the weights of region and boundary features to adapt to the segmentation scale at which they are applied. The stages of the cascade are trained sequentially, with asymetric loss to maximize boundary recall. On six segmentation data sets, our algorithm achieves best performance under most region-quality measures, and does it with fewer segments than the prior work. Our algorithm is also highly competitive in a dense over segmentation (super pixel) regime under boundary-based measures.

Deep learning approaches have shown promising performance for compressed sensing-based Magnetic Resonance Imaging. While deep neural networks trained with mean squared error (MSE) loss functions can achieve high peak signal to noise ratio, the reconstructed images are often blurry and lack sharp details, especially for higher undersampling rates. Recently, adversarial and perceptual loss functions have been shown to achieve more visually appealing results. However, it remains an open question how to (1) optimally combine these loss functions with the MSE loss function and (2) evaluate such a perceptual enhancement. In this work, we propose a hybrid method, in which a visual refinement component is learnt on top of an MSE loss-based reconstruction network. In addition, we introduce a semantic interpretability score, measuring the visibility of the region of interest in both ground truth and reconstructed images, which allows us to objectively quantify the usefulness of the image quality for image post-processing and analysis. Applied on a large cardiac MRI dataset simulated with 8-fold undersampling, we demonstrate significant improvements (p < 0.01) over the state-of-the-art in both a human observer study and the semantic interpretability score.

Hematoxylin and Eosin stained histopathology image analysis is essential for the diagnosis and study of complicated diseases such as cancer. Existing state-of-the-art approaches demand extensive amount of supervised training data from trained pathologists. In this work we synthesize in an unsupervised manner, large histopathology image datasets, suitable for supervised training tasks. We propose a unified pipeline that: a) generates a set of initial synthetic histopathology images with paired information about the nuclei such as segmentation masks; b) refines the initial synthetic images through a Generative Adversarial Network (GAN) to reference styles; c) trains a task-specific CNN and boosts the performance of the task-specific CNN with onthe-fly generated adversarial examples. Our main contribution is that the synthetic images are not only realistic, but also representative (in reference styles) and relatively challenging for training task-specific CNNs. We test our method for nucleus segmentation using images from four cancer types. When no supervised data exists for a cancer type, our method without supervision cost significantly outperforms supervised methods which perform across-cancer generalization. Even when supervised data exists for all cancer types, our approach without supervision cost performs better than supervised methods.

The Deep Convolutional Neural Network (DCNN) is one of the most powerful and successful deep learning approaches. DCNNs have already provided superior performance in different modalities of medical imaging including breast cancer classification, segmentation, and detection. Breast cancer is one of the most common and dangerous cancers impacting women worldwide. In this paper, we have proposed a method for breast cancer classification with the Inception Recurrent Residual Convolutional Neural Network (IRRCNN) model. The IRRCNN is a powerful DCNN model that combines the strength of the Inception Network (Inception-v4), the Residual Network (ResNet), and the Recurrent Convolutional Neural Network (RCNN). The IRRCNN shows superior performance against equivalent Inception Networks, Residual Networks, and RCNNs for object recognition tasks. In this paper, the IRRCNN approach is applied for breast cancer classification on two publicly available datasets including BreakHis and Breast Cancer (BC) classification challenge 2015. The experimental results are compared against the existing machine learning and deep learning–based approaches with respect to image-based, patch-based, image-level, and patient-level classification. The IRRCNN model provides superior classification performance in terms of sensitivity, area under the curve (AUC), the ROC curve, and global accuracy compared to existing approaches for both datasets.

Automated breast cancer multi-classification from histopathological images plays a key role in computer-aided breast cancer diagnosis or prognosis. Breast cancer multi-classification is to identify subordinate classes of breast cancer (Ductal carcinoma, Fibroadenoma, Lobular carcinoma, etc.). However, breast cancer multi-classification from histopathological images faces two main challenges from: (1) the great difficulties in breast cancer multi-classification methods contrasting with the classification of binary classes (benign and malignant), and (2) the subtle differences in multiple classes due to the broad variability of high-resolution image appearances, high coherency of cancerous cells, and extensive inhomogeneity of color distribution. Therefore, automated breast cancer multi-classification from histopathological images is of great clinical significance yet has never been explored. Existing works in literature only focus on the binary classification but do not support further breast cancer quantitative assessment. In this study, we propose a breast cancer multi-classification method using a newly proposed deep learning model. The structured deep learning model has achieved remarkable performance (average 93.2% accuracy) on a large-scale dataset, which demonstrates the strength of our method in providing an efficient tool for breast cancer multi-classification in clinical settings.

Liver tumors segmentation from computed tomography (CT) images is an essential task for diagnosis and treatments of liver cancer. However, it is difficult owing to the variability of appearances, fuzzy boundaries, heterogeneous densities, shapes and sizes of lesions. In this paper, an automatic method based on convolutional neural networks (CNNs) is presented to segment lesions from CT images. The CNNs is one of deep learning models with some convolutional filters which can learn hierarchical features from data. We compared the CNNs model to popular machine learning algorithms: AdaBoost, Random Forests (RF), and support vector machine (SVM). These classifiers were trained by handcrafted features containing mean, variance, and contextual features. Experimental evaluation was performed on 30 portal phase enhanced CT images using leave-one-out cross validation. The average Dice Similarity Coefficient (DSC), precision, and recall achieved of 80.06% ± 1.63%, 82.67% ± 1.43%, and 84.34% ± 1.61%, respectively. The results show that the CNNs method has better performance than other methods and is promising in liver tumor segmentation.

We consider the problem of localizing and segmenting individual teeth inside 3D Cone-Beam Computed Tomography (CBCT) images. To handle large image sizes we approach this task with a coarse-to-fine framework, where the whole volume is first analyzed as a 33-class semantic segmentation (adults have up to 32 teeth) in coarse resolution, followed by binary semantic segmentation of the cropped region of interest in original resolution. To improve the performance of the challenging 33-class segmentation, we first train the Coarse step model on a large weakly labeled dataset, then fine-tune it on a smaller precisely labeled dataset. The Fine step model is trained with precise labels only. Experiments using our inhouse dataset show significant improvement for both weaklysupervised pretraining and for the addition of the Fine step. Empirically, this framework yields precise teeth masks with low localization errors sufficient for many real-world applications.

The technology of image segmentation is widely used in medical image processing, face recognition pedestrian detection, etc. The current image segmentation techniques include region-based segmentation, edge detection segmentation, segmentation based on clustering, segmentation based on weakly-supervised learning in CNN, etc. This paper analyzes and summarizes these algorithms of image segmentation, and compares the advantages and disadvantages of different algorithms. Finally, we make a prediction of the development trend of image segmentation with the combination of these algorithms.


Question: MDU-Net: A Multi-scale, densely connected U-Net architecture for biomedical image segmentation tasks.

This paper introduces Incremental Network Quantization (INQ), a pioneering method designed to efficiently transform any pre-trained full-precision Convolutional Neural Network (CNN) model into a low-precision variant, where weights are restricted to powers of two or zero. Unlike conventional methods that often suffer from significant accuracy loss, INQ aims to mitigate this challenge through a combination of innovations. Firstly, it implements three interconnected processes: weight partitioning, group-wise quantization, and re-training. A validated technique is used to segregate the weights in each layer of a pre-trained CNN into two distinct groups. The weights in the first group are tasked with establishing a low-precision foundation and are quantized using a variable-length encoding method. Conversely, the weights in the second group are re-trained to offset any accuracy loss resulting from quantization. Secondly, these three processes are iteratively applied to the most recently re-trained group until all weights are converted into low-precision formats, a strategy that enhances accuracy incrementally. Comprehensive experiments on the ImageNet classification task, utilizing a wide range of deep CNN architectures such as AlexNet, VGG-16, GoogleNet, and ResNets, substantiate the effectiveness of INQ. Specifically, at 5-bit quantization (employing 1 bit for zero representation and the remaining 4 bits for up to 16 distinct values of powers of two), INQ models outperform their 32-bit floating-point counterparts in terms of accuracy. Using ResNet-18 as a case study, it is demonstrated that quantized models with 4-bit, 3-bit, and even 2-bit ternary weights either match or slightly exceed the accuracy of their 32-bit floating-point baseline. Additionally, the paper reports exceptional outcomes from combining network pruning with INQ. It is argued that INQ offers novel insights into making deep CNNs suitable for deployment on mobile or embedded devices. The source code for INQ is publicly accessible at https://github.com/Zhouaojun/IncrementalNetwork-Quantization.

We propose a deep learning-based framework for instance-level object segmentation. Our method mainly consists of three steps. First, We train a generic model based on ResNet-101 for foreground/background segmentations. Second, based on this generic model, we fine-tune it to learn instance-level models and segment individual objects by using augmented object annotations in first frames of test videos. To distinguish different instances in the same video, we compute a pixel-level score map for each object from these instance-level models. Each score map indicates the objectness likelihood and is only computed within the foreground mask obtained in the first step. To further refine this per frame score map, we learn a spatial propagation network. This network aims to learn how to propagate a coarse segmentation mask spatially based on the pairwise similarities in each frame. In addition, we apply a filter on the refined score map that aims to recognize the best connected region using spatial and temporal consistencies in the video. Finally, we decide the instance-level object segmentation in each video by comparing score maps of different instances.

The Deep Convolutional Neural Network (DCNN) is one of the most powerful and successful deep learning approaches. DCNNs have already provided superior performance in different modalities of medical imaging including breast cancer classification, segmentation, and detection. Breast cancer is one of the most common and dangerous cancers impacting women worldwide. In this paper, we have proposed a method for breast cancer classification with the Inception Recurrent Residual Convolutional Neural Network (IRRCNN) model. The IRRCNN is a powerful DCNN model that combines the strength of the Inception Network (Inception-v4), the Residual Network (ResNet), and the Recurrent Convolutional Neural Network (RCNN). The IRRCNN shows superior performance against equivalent Inception Networks, Residual Networks, and RCNNs for object recognition tasks. In this paper, the IRRCNN approach is applied for breast cancer classification on two publicly available datasets including BreakHis and Breast Cancer (BC) classification challenge 2015. The experimental results are compared against the existing machine learning and deep learning–based approaches with respect to image-based, patch-based, image-level, and patient-level classification. The IRRCNN model provides superior classification performance in terms of sensitivity, area under the curve (AUC), the ROC curve, and global accuracy compared to existing approaches for both datasets.

Training robust deep learning (DL) systems for medical image classification or segmentation is challenging due to limited images covering different disease types and severity. We propose an active learning (AL) framework to select most informative samples and add to the training data. We use conditional generative adversarial networks (cGANs) to generate realistic chest xray images with different disease characteristics by conditioning its generation on a real image sample. Informative samples to add to the training set are identified using a Bayesian neural network. Experiments show our proposed AL framework is able to achieve state of the art performance by using about 35% of the full dataset, thus saving significant time and effort over conventional methods.

Computerized Tomography Angiography (CTA) based follow-up of Abdominal Aortic Aneurysms (AAA) treated with Endovascular Aneurysm Repair (EVAR) is essential to evaluate the progress of the patient and detect complications. In this context, accurate quantification of post-operative thrombus volume is required. However, a proper evaluation is hindered by the lack of automatic, robust and reproducible thrombus segmentation algorithms. We propose a new fully automatic approach based on Deep Convolutional Neural Networks (DCNN) for robust and reproducible thrombus region of interest detection and subsequent fine thrombus segmentation. The DetecNet detection network is adapted to perform region of interest extraction from a complete CTA and a new segmentation network architecture, based on Fully Convolutional Networks and a Holistically-Nested Edge Detection Network, is presented. These networks are trained, validated and tested in 13 post-operative CTA volumes of different patients using a 4-fold cross-validation approach to provide more robustness to the results. Our pipeline achieves a Dice score of more than 82% for post-operative thrombus segmentation and provides a mean relative volume difference between ground truth and automatic segmentation that lays within the experienced human observer variance without the need of human intervention in most common cases.

Recent advances in semantic image segmentation have mostly been achieved by training deep convolutional neural networks (CNNs). We show how to improve semantic segmentation through the use of contextual information, specifically, we explore 'patch-patch' context between image regions, and 'patch-background' context. For learning from the patch-patch context, we formulate Conditional Random Fields (CRFs) with CNN-based pairwise potential functions to capture semantic correlations between neighboring patches. Efficient piecewise training of the proposed deep structured model is then applied to avoid repeated expensive CRF inference for back propagation. For capturing the patch-background context, we show that a network design with traditional multi-scale image input and sliding pyramid pooling is effective for improving performance. Our experimental results set new state-of-the-art performance on a number of popular semantic segmentation datasets, including NYUDv2, PASCAL VOC 2012, PASCAL-Context, and SIFT-flow. In particular, we achieve an intersection-overunion score of 78:0 on the challenging PASCAL VOC 2012 dataset.

To improve the diagnostic accuracy of cervical dysplasia, it is important to fuse multimodal information collected during a patient’s screening visit. However, current multimodal frameworks suffer from low sensitivity at high specificity levels, due to their limitations in learning correlations among highly heterogeneous modalities. In this paper, we design a deep learning framework for cervical dysplasia diagnosis by leveraging multimodal information. We first employ the convolutional neural network (CNN) to convert the low-level image data into a feature vector fusible with other non-image modalities. We then jointly learn the non-linear correlations among all modalities in a deep neural network. Our multimodal framework is an end-to-end deep network which can learn better complementary features from the image and non-image modalities. It automatically gives the final diagnosis for cervical dysplasia with 87.83% sensitivity at 90% specificity on a large dataset, which significantly outperforms methods using any single source of information alone and previous multimodal frameworks.

Deep Convolutional Neural Networks (DCNN) have recently emerged as superior for many image segmentation tasks. The DCNN performance is however heavily dependent on the availability of large amounts of problem-specific training samples. Here we show that DCNNs trained on ground truth created automatically using fluorescently labeled cells, perform similar to manual annotations.

For the task of subdecimeter aerial imagery segmentation, fine-grained semantic segmentation results are usually difficult to obtain because of complex remote sensing content and optical conditions. Recently, convolutional neural networks (CNNs) have shown outstanding performance on this task. Although many deep neural network structures and techniques have been applied to improve the accuracy, few have paid attention to better differentiating the easily confused classes. In this paper, we propose TreeSegNet which adopts an adaptive network to increase the classification rate at the pixelwise level. Specifically, based on the infrastructure of DeepUNet, a Tree-CNN block in which each node represents a ResNeXt unit is constructed adaptively according to the confusion matrix and the proposed TreeCutting algorithm. By transporting feature maps through concatenating connections, the Tree-CNN block fuses multiscale features and learns best weights for the model. In experiments on the ISPRS 2D semantic labeling Potsdam dataset, the results obtained by TreeSegNet are better than those of other  Corresponding author. Tel.: +86 18911938368. E-mail address: ilydouble@gmail.com TreeSegNet: Adaptive Tree CNNs for Subdecimeter Aerial Image Segmentation 2 published state-of-the-art methods. Detailed comparison and analysis show that the improvement brought by the adaptive Tree-CNN block is significant.

We introduce BranchGAN , a novel training method that enables unconditioned generative adversarial networks (GANs) to learn image manifolds at multiple scales. The key novel feature of BranchGAN is that it is trained in multiple branches, progressively covering both the breadth and depth of the network, as resolutions of the training images increase to reveal finer-scale features. Specifically, each noise vector, as input to the generator network, is explicitly split into several sub-vectors, each corresponding to, and is trained to learn, image representations at a particular scale. During training, we progressively “defreeze” the sub-vectors, one at a time, as a new set of higher-resolution images is employed for training and more network layers are added. A consequence of such an explicit sub-vector designation is that we can directly manipulate and even combine latent (sub-vector) codes which model different feature scales. Experiments demonstrate the effectiveness of our training method in scale-disentangled learning of image manifolds and synthesis, without any extra labels and without compromising quality of the synthesized high-resolution images. We further demonstrate three applications enabled or improved by BranchGAN.

As a widely used non-linear activation, Rectified Linear Unit (ReLU) separates noise and signal in a feature map by learning a threshold or bias. However, we argue that the classification of noise and signal not only depends on the magnitude of responses, but also the context of how the feature responses would be used to detect more abstract patterns in higher layers. In order to output multiple response maps with magnitude in different ranges for a particular visual pattern, existing networks employing ReLU and its variants have to learn a large number of redundant filters. In this paper, we propose a multi-bias non-linear activation (MBA) layer to explore the information hidden in the magnitudes of responses. It is placed after the convolution layer to decouple the responses to a convolution kernel into multiple maps by multi-thresholding magnitudes, thus generating more patterns in the feature space at a low computational cost. It provides great flexibility of selecting responses to different visual patterns in different magnitude ranges to form rich representations in higher layers. Such a simple and yet effective scheme achieves the stateof-the-art performance on several benchmarks.


Question: MDU-Net: A multi-scale densely connected U-Net architecture for biomedical image segmentation tasks.

Introducing MIMO-Net: An Enhanced Multi-Input Multi-Output Convolutional Neural Network for Robust Cell Segmentation in Fluorescence Microscopy

In this work, we unveil MIMO-Net, an innovative multi-input multi-output convolutional neural network designed specifically for the task of cell segmentation in fluorescence microscopy images. The network's architecture is crafted to tackle the inherent challenges in such images, including variable intensity cell boundaries and significant cell size variability, particularly in mouse pancreatic tissue. MIMO-Net achieves this by incorporating multiple resolutions of the input image during training, linking intermediate layers for improved localization and context, and employing multi-resolution deconvolution filters for the output generation.

A key feature of MIMO-Net is its ability to handle the complexity of cell boundaries and sizes through the addition of extra convolutional layers that bypass the max-pooling operation. This mechanism enables the network to capture a richer set of features and enhance its robustness in dealing with diverse cell characteristics. Our experimental results demonstrate that MIMO-Net outperforms other cutting-edge deep learning-based segmentation approaches, showcasing its effectiveness and superiority in the field of biomedical image analysis.

We propose a novel attention network, which accurately attends to target objects of various scales and shapes in images through multiple stages. The proposed network enables multiple layers to estimate attention in a convolutional neural network (CNN). The hierarchical attention model gradually suppresses irrelevant regions in an input image using a progressive attentive process over multiple CNN layers. The attentive process in each layer determines whether to pass or suppress feature maps for use in the next convolution. We employ local contexts to estimate attention probability at each location since it is difficult to infer accurate attention by observing a feature vector from a single location only. The experiments on synthetic and real datasets show that the proposed attention network outperforms traditional attention methods in various attribute prediction tasks.

Vasculature is known to be of key biological significance, especially in the study of cancer. As such, considerable effort has been focused on the automated measurement and analysis of vasculature in medical and pre-clinical images. In tumors in particular, the vascular networks may be extremely irregular and the appearance of the individual vessels may not conform to classical descriptions of vascular appearance. Typically, vessels are extracted by either a segmentation and thinning pipeline, or by direct tracking. Neither of these methods are well suited to microscopy images of tumor vasculature. In order to address this we propose a method to directly extract a medial representation of the vessels using Convolutional Neural Networks. We then show that these two-dimensional centerlines can be meaningfully extended into 3D in anisotropic and complex microscopy images using the recently popularized Convolutional Long Short-Term Memory units (ConvLSTM). We demonstrate the effectiveness of this hybrid convolutional-recurrent architecture over both 2D and 3D convolutional comparators.

Image segmentation is one of the basic concepts widely used in each and every fields of image processing. The entire process of the proposed work for image segmentation comprises of 3 phases: Threshold generation with dynamic Modified Region Growing phase (DMRG), texture feature generation phase and region merging phase. by dynamically changing two thresholds, the given input image can be performed as DMRG, in which the cuckoo search optimization algorithm helps to optimize the two thresholds in modified region growing. after obtaining the region growth segmented image, the edges are detected with edge detection algorithm. In the second phase, the texture feature is extracted using entropy based operation from the input image. In region merging phase, the results obtained from the texture feature generation phase is combined with the results of DMRG phase and similar regions are merged by using a distance comparison between regions. The proposed work is implemented using Mat lab platform with several medical images. the performance of the proposed work is evaluated using the metrics sensitivity, specificity and accuracy. the results show that this proposed work provides very good accuracy for the segmentation process in images.

In this work, we examine the strength of deep learning approaches for pathology detection in chest radiographs. Convolutional neural networks (CNN) deep architecture classification approaches have gained popularity due to their ability to learn mid and high level image representations. We explore the ability of CNN learned from a non-medical dataset to identify different types of pathologies in chest x-rays. We tested our algorithm on a 433 image dataset. The best performance was achieved using CNN and GIST features. We obtained an area under curve (AUC) of 0.87-0.94 for the different pathologies. The results demonstrate the feasibility of detecting pathology in chest x-rays using deep learning approaches based on non-medical learning. This is a first-of-its-kind experiment that shows that Deep learning with ImageNet, a large scale non-medical image database may be a good substitute to domain specific representations, which are yet to be available, for general medical image recognition tasks.

Convolutional neural networks (CNNs) are usually built by stacking convolutional operations layer-by-layer. Although CNN has shown strong capability to extract semantics from raw pixels, its capacity to capture spatial relationships of pixels across rows and columns of an image is not fully explored. These relationships are important to learn semantic objects with strong shape priors but weak appearance coherences, such as traffic lanes, which are often occluded or not even painted on the road surface as shown in Fig. 1 (a). In this paper, we propose Spatial CNN (SCNN), which generalizes traditional deep layer-by-layer convolutions to slice-byslice convolutions within feature maps, thus enabling message passings between pixels across rows and columns in a layer. Such SCNN is particular suitable for long continuous shape structure or large objects, with strong spatial relationship but less appearance clues, such as traffic lanes, poles, and wall. We apply SCNN on a newly released very challenging traffic lane detection dataset and Cityscapse dataset. The results show that SCNN could learn the spatial relationship for structure output and significantly improves the performance. We show that SCNN outperforms the recurrent neural network (RNN) based ReNet and MRF+CNN (MRFNet) in the lane detection dataset by 8.7% and 4.6% respectively. Moreover, our SCNN won the 1st place on the TuSimple Benchmark Lane Detection Challenge, with an accuracy of 96.53%.

OBJECTIVE
Brain-computer interfaces (BCI) enable direct communication with a computer, using neural activity as the control signal. This neural signal is generally chosen from a variety of well-studied electroencephalogram (EEG) signals. For a given BCI paradigm, feature extractors and classifiers are tailored to the distinct characteristics of its expected EEG control signal, limiting its application to that specific signal. Convolutional neural networks (CNNs), which have been used in computer vision and speech recognition to perform automatic feature extraction and classification, have successfully been applied to EEG-based BCIs; however, they have mainly been applied to single BCI paradigms and thus it remains unclear how these architectures generalize to other paradigms. Here, we ask if we can design a single CNN architecture to accurately classify EEG signals from different BCI paradigms, while simultaneously being as compact as possible.

APPROACH
In this work we introduce EEGNet, a compact convolutional neural network for EEG-based BCIs. We introduce the use of depthwise and separable convolutions to construct an EEG-specific model which encapsulates well-known EEG feature extraction concepts for BCI. We compare EEGNet, both for within-subject and cross-subject classification, to current state-of-the-art approaches across four BCI paradigms: P300 visual-evoked potentials, error-related negativity responses (ERN), movement-related cortical potentials (MRCP), and sensory motor rhythms (SMR).

MAIN RESULTS
We show that EEGNet generalizes across paradigms better than, and achieves comparably high performance to, the reference algorithms when only limited training data is available across all tested paradigms. In addition, we demonstrate three different approaches to visualize the contents of a trained EEGNet model to enable interpretation of the learned features.

SIGNIFICANCE
Our results suggest that EEGNet is robust enough to learn a wide variety of interpretable features over a range of BCI tasks. Our models can be found at: https://github.com/vlawhern/arl-eegmodels.

Modern deep neural networks have a large number of parameters, making them very hard to train. We propose DSD, a dense-sparse-dense training flow, for regularizing deep neural networks and achieving better optimization performance. In the first D (Dense) step, we train a dense network to learn connection weights and importance. In the S (Sparse) step, we regularize the network by pruning the unimportant connections with small weights and retraining the network given the sparsity constraint. In the final D (re-Dense) step, we increase the model capacity by removing the sparsity constraint, re-initialize the pruned parameters from zero and retrain the whole dense network. Experiments show that DSD training can improve the performance for a wide range of CNNs, RNNs and LSTMs on the tasks of image classification, caption generation and speech recognition. On ImageNet, DSD improved the Top1 accuracy of GoogLeNet by 1.1%, VGG-16 by 4.3%, ResNet-18 by 1.2% and ResNet-50 by 1.1%, respectively. On the WSJ’93 dataset, DSD improved DeepSpeech and DeepSpeech2 WER by 2.0% and 1.1%. On the Flickr-8K dataset, DSD improved the NeuralTalk BLEU score by over 1.7. DSD is easy to use in practice: at training time, DSD incurs only one extra hyper-parameter: the sparsity ratio in the S step. At testing time, DSD doesn’t change the network architecture or incur any inference overhead. The consistent and significant performance gain of DSD experiments shows the inadequacy of the current training methods for finding the best local optimum, while DSD effectively achieves superior optimization performance for finding a better solution. DSD models are available to download at https://songhan.github.io/DSD.

For the task of subdecimeter aerial imagery segmentation, fine-grained semantic segmentation results are usually difficult to obtain because of complex remote sensing content and optical conditions. Recently, convolutional neural networks (CNNs) have shown outstanding performance on this task. Although many deep neural network structures and techniques have been applied to improve the accuracy, few have paid attention to better differentiating the easily confused classes. In this paper, we propose TreeSegNet which adopts an adaptive network to increase the classification rate at the pixelwise level. Specifically, based on the infrastructure of DeepUNet, a Tree-CNN block in which each node represents a ResNeXt unit is constructed adaptively according to the confusion matrix and the proposed TreeCutting algorithm. By transporting feature maps through concatenating connections, the Tree-CNN block fuses multiscale features and learns best weights for the model. In experiments on the ISPRS 2D semantic labeling Potsdam dataset, the results obtained by TreeSegNet are better than those of other  Corresponding author. Tel.: +86 18911938368. E-mail address: ilydouble@gmail.com TreeSegNet: Adaptive Tree CNNs for Subdecimeter Aerial Image Segmentation 2 published state-of-the-art methods. Detailed comparison and analysis show that the improvement brought by the adaptive Tree-CNN block is significant.

Automated breast cancer multi-classification from histopathological images plays a key role in computer-aided breast cancer diagnosis or prognosis. Breast cancer multi-classification is to identify subordinate classes of breast cancer (Ductal carcinoma, Fibroadenoma, Lobular carcinoma, etc.). However, breast cancer multi-classification from histopathological images faces two main challenges from: (1) the great difficulties in breast cancer multi-classification methods contrasting with the classification of binary classes (benign and malignant), and (2) the subtle differences in multiple classes due to the broad variability of high-resolution image appearances, high coherency of cancerous cells, and extensive inhomogeneity of color distribution. Therefore, automated breast cancer multi-classification from histopathological images is of great clinical significance yet has never been explored. Existing works in literature only focus on the binary classification but do not support further breast cancer quantitative assessment. In this study, we propose a breast cancer multi-classification method using a newly proposed deep learning model. The structured deep learning model has achieved remarkable performance (average 93.2% accuracy) on a large-scale dataset, which demonstrates the strength of our method in providing an efficient tool for breast cancer multi-classification in clinical settings.

In this paper we address the problem of semantic labeling of indoor scenes on RGB-D data. With the availability of RGB-D cameras, it is expected that additional depth measurement will improve the accuracy. Here we investigate a solution how to incorporate complementary depth information into a semantic segmentation framework by making use of convolutional neural networks (CNNs). Recently encoder-decoder type fully convolutional CNN architectures have achieved a great success in the field of semantic segmentation. Motivated by this observation we propose an encoder-decoder type network, where the encoder part is composed of two branches of networks that simultaneously extract features from RGB and depth images and fuse depth features into the RGB feature maps as the network goes deeper. Comprehensive experimental evaluations demonstrate that the proposed fusion-based architecture achieves competitive results with the state-of-the-art methods on the challenging SUN RGB-D benchmark obtaining 76.27% global accuracy, 48.30% average class accuracy and 37.29% average intersectionover-union score.


Question: MDU-Net: A multi-scale densely connected U-Net architecture for biomedical image segmentation tasks.

This paper presents a novel framework, "DeepLab," which integrates Deep Convolutional Neural Networks (DCNNs) with fully connected Conditional Random Fields (CRFs) for achieving high precision in semantic image segmentation. While DCNNs have proven their prowess in high-level vision tasks like image classification and object detection, they have been found lacking in accurately localizing objects at the pixel level. This is primarily due to the very invariance properties that make DCNNs excel in abstract tasks. To rectify this issue, our "DeepLab" system merges the responses from the final layer of DCNNs with a fully connected CRF. This approach not only refines the localization of segment boundaries to a degree unattainable by previous methods but also sets a new benchmark in the PASCAL VOC-2012 semantic image segmentation challenge, achieving an IOU accuracy of 71.6% in the test set. Moreover, the efficiency of our method is noteworthy: by employing network re-purposing techniques and leveraging the 'hole' algorithm from the wavelet domain, we are able to compute dense neural net responses at a rate of 8 frames per second on a contemporary GPU. This fusion of DCNNs and CRFs in "DeepLab" not only enhances the accuracy of semantic segmentation but also demonstrates the potential of combining different computational models to address complex image processing tasks.

Image reconstruction under multiple light scattering is crucial for a number of important applications in cell microscopy and tissue imaging. The reconstruction problem is often formulated as a nonconvex optimization, where a nonlinear measurement model is used to account for multiple scattering and a regularizer is used to enforce the prior on the object. In this letter, We propose a powerful alternative to this optimization-based view of image reconstruction by designing and training a deep convolutional neural network (CNN) for inverting multiple scattering. Simulations show that the proposed formulation is substantially faster and achieves higher imaging quality compared to the state-of-the-art methods based on optimization.

Deep Neural Networks (DNNs) have recently shown outstanding performance on image classification tasks [14]. In this paper we go one step further and address the problem of object detection using DNNs, that is not only classifying but also precisely localizing objects of various classes. We present a simple and yet powerful formulation of object detection as a regression problem to object bounding box masks. We define a multi-scale inference procedure which is able to produce high-resolution object detections at a low cost by a few network applications. State-of-the-art performance of the approach is shown on Pascal VOC.

Segmentation of lungs with (large) lung cancer regions is a nontrivial problem. We present a new fully automated approach for segmentation of lungs with such high-density pathologies. Our method consists of two main processing steps. First, a novel robust active shape model (RASM) matching method is utilized to roughly segment the outline of the lungs. The initial position of the RASM is found by means of a rib cage detection method. Second, an optimal surface finding approach is utilized to further adapt the initial segmentation result to the lung. Left and right lungs are segmented individually. An evaluation on 30 data sets with 40 abnormal (lung cancer) and 20 normal left/right lungs resulted in an average Dice coefficient of 0.975±0.006 and a mean absolute surface distance error of 0.84±0.23 mm, respectively. Experiments on the same 30 data sets showed that our methods delivered statistically significant better segmentation results, compared to two commercially available lung segmentation approaches. In addition, our RASM approach is generally applicable and suitable for large shape models.

Semantic segmentation, as dense pixel-wise classification task, played an important tache in scene understanding. There are two main challenges in many state-of-the-art works: 1) most backbone of segmentation models that often were extracted from pretrained classification models generated poor performance in small categories because they were lacking in spatial information and 2) the gap of combination between high-level and low-level features in segmentation models has led to inaccurate predictions. To handle these challenges, in this paper, we proposed a new tailored backbone and attention select module for segmentation tasks. Specifically, our new backbone was modified from the original Resnet, which can yield better segmentation performance. Attention select module employed spatial and channel self-attention mechanism to reinforce the propagation of contextual features, which can aggregate semantic and spatial information simultaneously. In addition, based on our new backbone and attention select module, we further proposed our segmentation model for street scenes understanding. We conducted a series of ablation studies on two public benchmarks, including Cityscapes and CamVid dataset to demonstrate the effectiveness of our proposals. Our model achieved a mIoU score of 71.5% on the Cityscapes test set with only fine annotation data and 60.1% on the CamVid test set.

Considerable practical interest exists in being able to automatically determine whether a recorded magnetic resonance image is affected by motion artifacts caused by patient movements during scanning. Existing approaches usually rely on the use of navigators or external sensors to detect and track patient motion during image acquisition. In this work, we present an algorithm based on convolutional neural networks that enables fully automated detection of motion artifacts in MR scans without special hardware requirements. The approach is data driven and uses the magnitude of MR images in the spatial domain as input. We evaluate the performance of our algorithm on both synthetic and real data and observe adequate performance in terms of accuracy and generalization to different types of data. Our proposed approach could potentially be used in clinical practice to tag an MR image as motion-free or motion-corrupted immediately after a scan is finished. This process would facilitate the acquisition of high-quality MR images that are often indispensable for accurate medical diagnosis.

Brain segmentation is an important part of medical image processing. Most commonly, it aims at locating various lesions and pathologies inside the human brain. In this paper, a new brain segmentation algorithm is proposed. The method is seeded region growing approach which was developed to segment the area of the brain affected by a tumor. The proposed algorithm was described. Results of testing the developed method on real MRI data set are presented and discussed.

Crowd counting in varying density scenes is a challenging problem in artificial intelligence (AI) and pattern recognition. Recently, deep convolutional neural networks (CNNs) are used to tackle this problem. However, the single-column CNN cannot achieve high accuracy and robustness in diverse density scenes. Meanwhile, multi-column CNNs lack effective way to accurately learn the features of different scales for estimating crowd density. To address these issues, we propose a novel pan-density level deep learning model, named as Pan-Density Network (PaDNet). Specifically, the PaDNet learns multi-scale features by three steps. First, several sub-networks are pre-trained on crowd images with different density-levels. Then, a Scale Reinforcement Net (SRN) is utilized to reinforce the scale features. Finally, a Fusion Net fuses all of the scale features to generate the final density map. Experiments on four crowd counting benchmark datasets, the ShanghaiTech, the UCF CC 50, the UCSD, and the UCF-QRNF, indicate that the PaDNet achieves the best performance and has high robustness in pan-density crowd counting compared with other state-of-the-art algorithms.

Recent advances in semantic image segmentation have mostly been achieved by training deep convolutional neural networks (CNNs). We show how to improve semantic segmentation through the use of contextual information, specifically, we explore 'patch-patch' context between image regions, and 'patch-background' context. For learning from the patch-patch context, we formulate Conditional Random Fields (CRFs) with CNN-based pairwise potential functions to capture semantic correlations between neighboring patches. Efficient piecewise training of the proposed deep structured model is then applied to avoid repeated expensive CRF inference for back propagation. For capturing the patch-background context, we show that a network design with traditional multi-scale image input and sliding pyramid pooling is effective for improving performance. Our experimental results set new state-of-the-art performance on a number of popular semantic segmentation datasets, including NYUDv2, PASCAL VOC 2012, PASCAL-Context, and SIFT-flow. In particular, we achieve an intersection-overunion score of 78:0 on the challenging PASCAL VOC 2012 dataset.

Leveraging on the recent developments in convolutional neural networks (CNNs), matching dense correspondence from a stereo pair has been cast as a learning problem, with performance exceeding traditional approaches. However, it remains challenging to generate high-quality disparities for the inherently ill-posed regions. To tackle this problem, we propose a novel cascade CNN architecture composing of two stages. The first stage advances the recently proposed DispNet by equipping it with extra up-convolution modules, leading to disparity images with more details. The second stage explicitly rectifies the disparity initialized by the first stage; it couples with the first-stage and generates residual signals across multiple scales. The summation of the outputs from the two stages gives the final disparity. As opposed to directly learning the disparity at the second stage, we show that residual learning provides more effective refinement. Moreover, it also benefits the training of the overall cascade network. Experimentation shows that our cascade residual learning scheme provides state-of-the-art performance for matching stereo correspondence. By the time of the submission of this paper, our method ranks first in the KITTI 2015 stereo benchmark, surpassing the prior works by a noteworthy margin.

With the rapid growth of medical and biomedical image data, energy-efficient solutions for analyzing such image data that can be processed fast and accurately on platforms with low power budget are highly desirable. This paper uses segmenting glial cells in brain microscopy images as a case study to demonstrate how to achieve biomedical image segmentation with significant energy saving and minimal comprise in accuracy. Specifically, we design, train, implement, and evaluate Fully Convolutional Networks (FCNs) for biomedical image segmentation on IBM's neurosynaptic DNN processor — TrueNorth (TN). Comparisons in terms of accuracy and energy dissipation of TN with that of a low power NVIDIA TX2 mobile GPU platform have been conducted. Experimental results show that TN can offer at least two orders of magnitude improvement in energy efficiency when compared to TX2 GPU for the same workload.