Computer-aided medical image segmentation has been applied widely in diagnosis and treatment to obtain clinically useful information of shapes and volumes of target organs and tissues. In the past several years, convolutional neural network (CNN) based methods (e.g., U-Net) have dominated this area, but still suffered from inadequate long-range information capturing. Hence, recent work presented computer vision Transformer variants for medical image segmentation tasks and obtained promising performances. Such Transformers model long-range dependency by computing pair-wise patch relations. However, they incur prohibitive computational costs, especially on 3D medical images (e.g., CT and MRI). In this paper, we propose a new method called Dilated Transformer, which conducts self-attention for pair-wise patch relations captured alternately in local and global scopes. Inspired by dilated convolution kernels, we conduct the global self-attention in a dilated manner, enlarging receptive fields without increasing the patches involved and thus reducing computational costs. Based on this design of Dilated Transformer, we construct a U-shaped encoder-decoder hierarchical architecture called D-Former for 3D medical image segmentation. Experiments on the Synapse and ACDC datasets show that our D-Former model, trained from scratch, outperforms various competitive CNN-based or Transformer-based segmentation models at a low computational cost without time-consuming per-training process.
Most event extraction methods have traditionally relied on an annotated set of event types. However, creating event ontologies and annotating supervised training data are expensive and time-consuming. Previous work has proposed semi-supervised approaches which leverage seen (annotated) types to learn how to automatically discover new event types. State-of-the-art methods, both semi-supervised or fully unsupervised, use a form of reconstruction loss on specific tokens in a context. In contrast, we present a novel approach to semi-supervised new event type induction using a masked contrastive loss, which learns similarities between event mentions by enforcing an attention mechanism over the data minibatch. We further disentangle the discovered clusters by approximating the underlying manifolds in the data, which allows us to increase normalized mutual information and Fowlkes-Mallows scores by over 20% absolute. Building on these clustering results, we extend our approach to two new tasks: predicting the type name of the discovered clusters and linking them to FrameNet frames.
Radiology reports are unstructured and contain the imaging findings and corresponding diagnoses transcribed by radiologists which include clinical facts and negated and/or uncertain statements. Extracting pathologic findings and diagnoses from radiology reports is important for quality control, population health, and monitoring of disease progress. Existing works, primarily rely either on rule-based systems or transformer-based pre-trained model fine-tuning, but could not take the factual and uncertain information into consideration, and therefore generate false-positive outputs. In this work, we introduce three sedulous augmentation techniques which retain factual and critical information while generating augmentations for contrastive learning. We introduce RadBERT-CL, which fuses these information into BlueBert via a self-supervised contrastive loss. Our experiments on MIMIC-CXR show superior performance of RadBERT-CL on fine-tuning for multi-class, multi-label report classification. We illustrate that when few labeled data are available, RadBERT-CL outperforms conventional SOTA transformers (BERT/BlueBert) by significantly larger margins (6-11%). We also show that the representations learned by RadBERT-CL can capture critical medical information in the latent space.
We present novel active learning strategies dedicated to providing a solution to the cold start stage, i.e. initializing the classification of a large set of data with no attached labels. Moreover, proposed strategies are designed to handle an imbalanced context in which random selection is highly inefficient. Specifically, our active learning iterations address label scarcity and imbalance using element scores, combining information extracted from a clustering structure to a label propagation model. The strategy is illustrated by a case study on annotating Twitter content w.r.t. testimonies of a real flood event. We show that our method effectively copes with class imbalance, by boosting the recall of samples from the minority class.
We present a percolation inverse problem for diode networks: Given information about which pairs of nodes allow current to percolate from one to the other, can one construct a diode network consistent with the observed currents? We implement a divide-and-concur iterative projection method for solving the problem and demonstrate the supremacy of our method over an exhaustive approach for nontrivial instances of the problem. We find that the problem is most difficult when some but not all of the percolation data are hidden, and that the most difficult networks to reconstruct generally are those for which the currents are most sensitive to the addition or removal of a single diode.
The task of finding the best developer to fix a bug is called bug triage. Most of the existing approaches consider the bug triage task as a classification problem, however, classification is not appropriate when the sets of classes change over time (as developers often do in a project). Furthermore, to the best of our knowledge, all the existing models use textual sources of information, i.e., bug descriptions, which are not always available. In this work, we explore the applicability of existing solutions for the bug triage problem when stack traces are used as the main data source of bug reports. Additionally, we reformulate this task as a ranking problem and propose new deep learning models to solve it. The models are based on a bidirectional recurrent neural network with attention and on a convolutional neural network, with the weights of the models optimized using a ranking loss function. To improve the quality of ranking, we propose using additional information from version control system annotations. Two approaches are proposed for extracting features from annotations: manual and using an additional neural network. To evaluate our models, we collected two datasets of real-world stack traces. Our experiments show that the proposed models outperform existing models adapted to handle stack traces. To facilitate further research in this area, we publish the source code of our models and one of the collected datasets.
Message passing algorithms, whose iterative nature captures well complicated interactions among interconnected variables in complex systems and extracts information from the fixed point of iterated messages, provide a powerful toolkit in tackling hard computational tasks in optimization, inference, and learning problems. In the context of constraint satisfaction problems (CSPs), when a control parameter (such as constraint density) is tuned, multiple threshold phenomena emerge, signaling fundamental structural transitions in their solution space. Finding solutions around these transition points is exceedingly challenging for algorithm design, where message passing algorithms suffer from a large message fluctuation far from convergence. Here we introduce a residual-based updating step into message passing algorithms, in which messages varying large between consecutive steps are given high priority in the updating process. For the specific example of model RB, a typical prototype of random CSPs with growing domains, we show that our algorithm improves the convergence of message updating and increases the success probability in finding solutions around the satisfiability threshold with a low computational cost. Our approach to message passing algorithms should be of value for exploring their power in developing algorithms to find ground-state solutions and understand the detailed structure of solution space of hard optimization problems.
Wireless x-haul networks rely on microwave and millimeter-wave links between 4G and/or 5G base-stations to support ultra-high data rate and ultra-low latency. A major challenge associated with these high frequency links is their susceptibility to weather conditions. In particular, precipitation may cause severe signal attenuation, which significantly degrades the network performance. In this paper, we develop a Predictive Network Reconfiguration (PNR) framework that uses historical data to predict the future condition of each link and then prepares the network ahead of time for imminent disturbances. The PNR framework has two components: (i) an Attenuation Prediction (AP) mechanism; and (ii) a Multi-Step Network Reconfiguration (MSNR) algorithm. The AP mechanism employs an encoder-decoder Long Short-Term Memory (LSTM) model to predict the sequence of future attenuation levels of each link. The MSNR algorithm leverages these predictions to dynamically optimize routing and admission control decisions aiming to maximize network utilization, while preserving max-min fairness among the base-stations sharing the network and preventing transient congestion that may be caused by re-routing. We train, validate, and evaluate the PNR framework using a dataset containing over 2 million measurements collected from a real-world city-scale backhaul network. The results show that the framework: (i) predicts attenuation with high accuracy, with an RMSE of less than 0.4 dB for a prediction horizon of 50 seconds; and (ii) can improve the instantaneous network utilization by more than 200% when compared to reactive network reconfiguration algorithms that cannot leverage information about future disturbances.
Registration of longitudinal optical coherence tomography (OCT) images assists disease monitoring and is essential in image fusion applications. Mouse retinal OCT images are often collected for longitudinal study of eye disease models such as uveitis, but their quality is often poor compared with human imaging. This paper presents a novel but efficient framework involving an optimal transport based graph matching (OT-GM) method for 3D mouse OCT image registration. We first perform registration of fundus-like images obtained by projecting all b-scans of a volume on a plane orthogonal to them, hereafter referred to as the x-y plane. We introduce Adaptive Weighted Vessel Graph Descriptors (AWVGD) and 3D Cube Descriptors (CD) to identify the correspondence between nodes of graphs extracted from segmented vessels within the OCT projection images. The AWVGD comprises scaling, translation and rotation, which are computationally efficient, whereas CD exploits 3D spatial and frequency domain information. The OT-GM method subsequently performs the correct alignment in the x-y plane. Finally, registration along the direction orthogonal to the x-y plane (the z-direction) is guided by the segmentation of two important anatomical features peculiar to mouse b-scans, the Internal Limiting Membrane (ILM) and the hyaloid remnant (HR). Both subjective and objective evaluation results demonstrate that our framework outperforms other well-established methods on mouse OCT images within a reasonable execution time.
Since the beginning of information processing by electronic components, the nervous system has served as a metaphor for the organization of computational primitives. Brain-inspired computing today encompasses a class of approaches ranging from using novel nano-devices for computation to research into large-scale neuromorphic architectures, such as TrueNorth, SpiNNaker, BrainScaleS, Tianjic, and Loihi. While implementation details differ, spiking neural networks - sometimes referred to as the third generation of neural networks - are the common abstraction used to model computation with such systems. Here we describe the second generation of the BrainScaleS neuromorphic architecture, emphasizing applications enabled by this architecture. It combines a custom analog accelerator core supporting the accelerated physical emulation of bio-inspired spiking neural network primitives with a tightly coupled digital processor and a digital event-routing network.