MHSnet: Multi-head and Spatial Attention Network with False-Positive Reduction for Pulmonary Nodules Detection

The mortality of lung cancer has ranked high among cancers for many years. Early detection of lung cancer is critical for disease prevention, cure, and mortality rate reduction. However, existing detection methods on pulmonary nodules introduce an excessive number of false positive proposals in order to achieve high sensitivity, which is not practical in clinical situations. In this paper, we propose the multi-head detection and spatial squeeze-and-attention network, MHSnet, to detect pulmonary nodules, in order to aid doctors in the early diagnosis of lung cancers. Specifically, we first introduce multi-head detectors and skip connections to customize for the variety of nodules in sizes, shapes and types and capture multi-scale features. Then, we implement a spatial attention module to enable the network to focus on different regions differently inspired by how experienced clinicians screen CT images, which results in fewer false positive proposals. Lastly, we present a lightweight but effective false positive reduction module with the Linear Regression model to cut down the number of false positive proposals, without any constraints on the front network. Extensive experimental results compared with the state-of-the-art models have shown the superiority of the MHSnet in terms of the average FROC, sensitivity and especially false discovery rate (2.98% and 2.18% improvement in terms of average FROC and sensitivity, 5.62% and 28.33% decrease in terms of false discovery rate and average candidates per scan). The false positive reduction module significantly decreases the average number of candidates generated per scan by 68.11% and the false discovery rate by 13.48%, which is promising to reduce distracted proposals for the downstream tasks based on the detection results.

A Coarse-to-fine Morphological Approach With Knowledge-based Rules and Self-adapting Correction for Lung Nodules Segmentation

The segmentation module which precisely outlines the nodules is a crucial step in a computer-aided diagnosis(CAD) system. The most challenging part of such a module is how to achieve high accuracy of the segmentation, especially for the juxtapleural, non-solid and small nodules. In this research, we present a coarse-to-fine methodology that greatly improves the thresholding method performance with a novel self-adapting correction algorithm and effectively removes noisy pixels with well-defined knowledge-based principles. Compared with recent strong morphological baselines, our algorithm, by combining dataset features, achieves state-of-the-art performance on both the public LIDC-IDRI dataset (DSC 0.699) and our private LC015 dataset (DSC 0.760) which closely approaches the SOTA deep learning-based models' performances. Furthermore, unlike most available morphological methods that can only segment the isolated and well-circumscribed nodules accurately, the precision of our method is totally independent of the nodule type or diameter, proving its applicability and generality.

Neural-FST Class Language Model for End-to-End Speech Recognition

We propose Neural-FST Class Language Model (NFCLM) for end-to-end speech recognition, a novel method that combines neural network language models (NNLMs) and finite state transducers (FSTs) in a mathematically consistent framework. Our method utilizes a background NNLM which models generic background text together with a collection of domain-specific entities modeled as individual FSTs. Each output token is generated by a mixture of these components; the mixture weights are estimated with a separately trained neural decider. We show that NFCLM significantly outperforms NNLM by 15.8% relative in terms of Word Error Rate. NFCLM achieves similar performance as traditional NNLM and FST shallow fusion while being less prone to overbiasing and 12 times more compact, making it more suitable for on-device usage.

Random cohort effects and age groups dependency structure for mortality modelling and forecasting: Mixed-effects time-series model approach

There have been significant efforts devoted to solving the longevity risk given that a continuous growth in population ageing has become a severe issue for many developed countries over the past few decades. The Cairns-Blake-Dowd (CBD) model, which incorporates cohort effects parameters in its parsimonious design, is one of the most well-known approaches for mortality modelling at higher ages and longevity risk. This article proposes a novel mixed-effects time-series approach for mortality modelling and forecasting with considerations of age groups dependence and random cohort effects parameters. The proposed model can disclose more mortality data information and provide a natural quantification of the model parameters uncertainties with no pre-specified constraint required for estimating the cohort effects parameters. The abilities of the proposed approach are demonstrated through two applications with empirical male and female mortality data. The proposed approach shows remarkable improvements in terms of forecast accuracy compared to the CBD model in the short-, mid-and long-term forecasting using mortality data of several developed countries in the numerical examples.

High-Fidelity Point Cloud Completion with Low-Resolution Recovery and Noise-Aware Upsampling

Completing an unordered partial point cloud is a challenging task. Existing approaches that rely on decoding a latent feature to recover the complete shape, often lead to the completed point cloud being over-smoothing, losing details, and noisy. Instead of decoding a whole shape, we propose to decode and refine a low-resolution (low-res) point cloud first, and then performs a patch-wise noise-aware upsampling rather than interpolating the whole sparse point cloud at once, which tends to lose details. Regarding the possibility of lacking details of the initially decoded low-res point cloud, we propose an iterative refinement to recover the geometric details and a symmetrization process to preserve the trustworthy information from the input partial point cloud. After obtaining a sparse and complete point cloud, we propose a patch-wise upsampling strategy. Patch-based upsampling allows to better recover fine details unlike decoding a whole shape, however, the existing upsampling methods are not applicable to completion task due to the data discrepancy (i.e., input sparse data here is not from ground-truth). Therefore, we propose a patch extraction approach to generate training patch pairs between the sparse and ground-truth point clouds, and an outlier removal step to suppress the noisy points from the sparse point cloud. Together with the low-res recovery, our whole method is able to achieve high-fidelity point cloud completion. Comprehensive evaluations are provided to demonstrate the effectiveness of the proposed method and its individual components.

MassFormer: Tandem Mass Spectrum Prediction with Graph Transformers

Mass spectrometry is a key tool in the study of small molecules, playing an important role in metabolomics, drug discovery, and environmental chemistry. Tandem mass spectra capture fragmentation patterns that provide key structural information about a molecule and help with its identification. Practitioners often rely on spectral library searches to match unknown spectra with known compounds. However, such search-based methods are limited by availability of reference experimental data. In this work we show that graph transformers can be used to accurately predict tandem mass spectra. Our model, MassFormer, outperforms competing deep learning approaches for spectrum prediction, and includes an interpretable attention mechanism to help explain predictions. We demonstrate that our model can be used to improve reference library coverage on a synthetic molecule identification task. Through quantitative analysis and visual inspection, we verify that our model recovers prior knowledge about the effect of collision energy on the generated spectrum. We evaluate our model on different types of mass spectra from two independent MS datasets and show that its performance generalizes. Code available at github.com/Roestlab/massformer.

Comparison between Time Shifting Deviation and Cross-correlation Methods

Time delay estimation (TDE) is an important step to identify and locate vibration source. The TDE result can be obtained by cross-correlation method through seeking the maximum correlation peak of two signals. However, the cross-correlation method will induce random error when dealing with the nonstationary signal. We propose a novel time shifting deviation (TSDEV) method to solve this problem, which has been proved to achieve ultrahigh precision localization result in the fiber vibration monitoring system. This paper compares TSDEV method with cross-correlation in detail by simulating TDE process in different conditions, such as signals with arbitrary intercepted length, nonstationary drift and correlated noise. Besides, experimental demonstration has been carried out on 60 km fiber to localize a wide band vibration signal. The typical localization error is 2 m with standard deviation of 21.4 m using TSDEV method. It stands in clear contrast to the result of cross-correlation method, whose localization error is 70 m and the standard deviation is 208.4 m. Compared with cross-correlation method, TSDEV has the same resistance to white noise, but has fewer boundary conditions and better suppression on linear drift or common noise, which leads to more precise TDE results.

Traffic4cast -- Large-scale Traffic Prediction using 3DResNet and Sparse-UNet

The IARAI competition Traffic4cast 2021 aims to predict short-term city-wide high-resolution traffic states given the static and dynamic traffic information obtained previously. The aim is to build a machine learning model for predicting the normalized average traffic speed and flow of the subregions of multiple large-scale cities using historical data points. The model is supposed to be generic, in a way that it can be applied to new cities. By considering spatiotemporal feature learning and modeling efficiency, we explore 3DResNet and Sparse-UNet approaches for the tasks in this competition. The 3DResNet based models use 3D convolution to learn the spatiotemporal features and apply sequential convolutional layers to enhance the temporal relationship of the outputs. The Sparse-UNet model uses sparse convolutions as the backbone for spatiotemporal feature learning. Since the latter algorithm mainly focuses on non-zero data points of the inputs, it dramatically reduces the computation time, while maintaining a competitive accuracy. Our results show that both of the proposed models achieve much better performance than the baseline algorithms. The codes and pretrained models are available at https://github.com/resuly/Traffic4Cast-2021.