OpenRaiser/Intern-Atlas huggingface dataset:
Unsupervised Extraction of Phenotypes from Cancer Clinical Notes for Association Studies
Venue: arXiv cs.LG 2019
Year: 2019

The recent adoption of Electronic Health Records (EHRs) by health care providers has introduced an important source of data that provides detailed and highly specific insights into patient phenotypes over large cohorts. These datasets, in combination with machine learning and statistical approaches, generate new opportunities for research and clinical care. However, many methods require the patient representations to be in structured formats, while the information in the EHR is often locked in unstructured texts designed for human readability. In this work, we develop the methodology to automatically extract clinical features from clinical narratives from large EHR corpora without the need for prior knowledge. We consider medical terms and sentences appearing in clinical narratives as atomic information units. We propose an efficient clustering strategy suitable for the analysis of large text corpora and to utilize the clusters to represent information about the patient compactly. To demonstrate the utility of our approach, we perform an association study of clinical features with somatic mutation profiles from 4,007 cancer patients and their tumors. We apply the proposed algorithm to a dataset consisting of about 65 thousand documents with a total of about 3.2 million sentences. We identify 341 significant statistical associations between the presence of somatic mutations and clinical features. We annotated these associations according to their novelty, and report several known associations. We also propose 32 testable hypotheses where the underlying biological mechanism does not appear to be known but plausible. These results illustrate that the automated discovery of clinical features is possible and the joint analysis of clinical and genetic datasets can generate appealing new hypotheses.
Community Detection and Growth Potential Prediction Using the Stochastic Block Model and the Long Short-term Memory from Patent Citation Networks
Venue: arXiv cs.DL 2019
Year: 2019

Scoring patent documents is very useful for technology management. However, conventional methods are based on static models and, thus, do not reflect the growth potential of the technology cluster of the patent. Because even if the cluster of a patent has no hope of growing, we recognize the patent is important if PageRank or other ranking score is high. Therefore, there arises a necessity of developing citation network clustering and prediction of future citations. In our research, clustering of patent citation networks by Stochastic Block Model was done with the aim of enabling corporate managers and investors to evaluate the scale and life cycle of technology. As a result, we confirmed nested SBM is appropriate for graph clustering of patent citation networks. Also, a high MAPE value was obtained and the direction accuracy achieved a value greater than 50% when predicting growth potential for each cluster by using LSTM.
On the 2-adic complexity of a class of binary sequences of period $4p$ with optimal autocorrelation magnitude
Venue: arXiv cs.IT 2019
Year: 2019

Via interleaving Ding-Helleseth-Lam sequences, a class of binary sequences of period $4p$ with optimal autocorrelation magnitude was constructed in \cite{W. Su}. Later, Fan showed that the linear complexity of this class of sequences is quite good \cite{C. Fan}. Recently, Sun et al. determined the upper and lower bounds of the 2-adic complexity of such sequences \cite{Y. Sun3}. We determine the exact value of the 2-adic complexity of this class of sequences. The results show that the 2-adic complexity of this class of binary sequences is close to the maximum.
A self-attention based deep learning method for lesion attribute detection from CT reports
Venue: arXiv cs.CL 2019
Year: 2019

In radiology, radiologists not only detect lesions from the medical image, but also describe them with various attributes such as their type, location, size, shape, and intensity. While these lesion attributes are rich and useful in many downstream clinical applications, how to extract them from the radiology reports is less studied. This paper outlines a novel deep learning method to automatically extract attributes of lesions of interest from the clinical text. Different from classical CNN models, we integrated the multi-head self-attention mechanism to handle the long-distance information in the sentence, and to jointly correlate different portions of sentence representation subspaces in parallel. Evaluation on an in-house corpus demonstrates that our method can achieve high performance with 0.848 in precision, 0.788 in recall, and 0.815 in F-score. The new method and constructed corpus will enable us to build automatic systems with a higher-level understanding of the radiological world.
Wearable Travel Aid for Environment Perception and Navigation of Visually Impaired People
Venue: arXiv cs.CV 2019
Year: 2019

This paper presents a wearable assistive device with the shape of a pair of eyeglasses that allows visually impaired people to navigate safely and quickly in unfamiliar environment, as well as perceive the complicated environment to automatically make decisions on the direction to move. The device uses a consumer Red, Green, Blue and Depth (RGB-D) camera and an Inertial Measurement Unit (IMU) to detect obstacles. As the device leverages the ground height continuity among adjacent image frames, it is able to segment the ground from obstacles accurately and rapidly. Based on the detected ground, the optimal walkable direction is computed and the user is then informed via converted beep sound. Moreover, by utilizing deep learning techniques, the device can semantically categorize the detected obstacles to improve the users' perception of surroundings. It combines a Convolutional Neural Network (CNN) deployed on a smartphone with a depth-image-based object detection to decide what the object type is and where the object is located, and then notifies the user of such information via speech. We evaluated the device's performance with different experiments in which 20 visually impaired people were asked to wear the device and move in an office, and found that they were able to avoid obstacle collisions and find the way in complicated scenarios.
Estimating the Frequency of a Clustered Signal
Venue: arXiv cs.DS 2019
Year: 2019

We consider the problem of locating a signal whose frequencies are "off grid" and clustered in a narrow band. Given noisy sample access to a function $g(t)$ with Fourier spectrum in a narrow range $[f_0 - Δ, f_0 + Δ]$, how accurately is it possible to identify $f_0$? We present generic conditions on $g$ that allow for efficient, accurate estimates of the frequency. We then show bounds on these conditions for $k$-Fourier-sparse signals that imply recovery of $f_0$ to within $Δ+ \tilde{O}(k^3)$ from samples on $[-1, 1]$. This improves upon the best previous bound of $O\big( Δ+ \tilde{O}(k^5) \big)^{1.5}$. We also show that no algorithm can do better than $Δ+ \tilde{O}(k^2)$. In the process we provide a new $\tilde{O}(k^3)$ bound on the ratio between the maximum and average value of continuous $k$-Fourier-sparse signals, which has independent application.
Early Action Prediction with Generative Adversarial Networks
Venue: arXiv cs.CV 2019
Year: 2019

Action Prediction is aimed to determine what action is occurring in a video as early as possible, which is crucial to many online applications, such as predicting a traffic accident before it happens and detecting malicious actions in the monitoring system. In this work, we address this problem by developing an end-to-end architecture that improves the discriminability of features of partially observed videos by assimilating them to features from complete videos. For this purpose, the generative adversarial network is introduced for tackling action prediction problem, which improves the recognition accuracy of partially observed videos though narrowing the feature difference of partially observed videos from complete ones. Specifically, its generator comprises of two networks: a CNN for feature extraction and an LSTM for estimating residual error between features of the partially observed videos and complete ones, and then the features from CNN adds the residual error from LSTM, which is regarded as the enhanced feature to fool a competing discriminator. Meanwhile, the generator is trained with an additional perceptual objective, which forces the enhanced features of partially observed videos are discriminative enough for action prediction. Extensive experimental results on UCF101, BIT and UT-Interaction datasets demonstrate that our approach outperforms the state-of-the-art methods, especially for videos that less than 50% portion of frames is observed.
Elastic-TCP: Flexible Congestion Control Algorithm to Adapt for High-BDP Networks
Venue: arXiv cs.NI 2019
Year: 2019

In the last decade, the demand for Internet applications has been increased, which increases the number of data centers across the world. These data centers are usually connected to each other using long-distance and high-speed networks. As known, the Transmission Control Protocol (TCP) is the predominant protocol used to provide such connectivity among these data centers. Unfortunately, the huge bandwidth-delay product (BDP) of these networks hinders TCP from achieving full bandwidth utilization. In order to increase TCP flexibility to adapt for high-BDP networks, we propose a new delay-based and RTT-independent congestion control algorithm (CCA), namely Elastic-TCP. It mainly contributes the novel window-correlated weighting function (WWF) to increase TCP bandwidth utilization over high-BDP networks. Extensive simulation and testbed experiments have been carried out to evaluate the proposed Elastic-TCP by comparing its performance to the commonly used TCPs developed by Microsoft, Linux, and Google. The results show that the proposed Elastic-TCP achieves higher average throughput than the other TCPs, while it maintains the sharing fairness and the loss ratio. Moreover, it is worth noting that the new Elastic-TCP presents lower sensitivity to the variation of buffer size and packet error rate than the other TCPs, which grants high efficiency and stability.
Facial Expressions Analysis Under Occlusions Based on Specificities of Facial Motion Propagation
Venue: arXiv cs.CV 2019
Year: 2019

Although much progress has been made in the facial expression analysis field, facial occlusions are still challenging. The main innovation brought by this contribution consists in exploiting the specificities of facial movement propagation for recognizing expressions in presence of important occlusions. The movement induced by an expression extends beyond the movement epicenter. Thus, the movement occurring in an occluded region propagates towards neighboring visible regions. In presence of occlusions, per expression, we compute the importance of each unoccluded facial region and we construct adapted facial frameworks that boost the performance of per expression binary classifier. The output of each expression-dependant binary classifier is then aggregated and fed into a fusion process that aims constructing, per occlusion, a unique model that recognizes all the facial expressions considered. The evaluations highlight the robustness of this approach in presence of significant facial occlusions.
Topic Classification Method for Analyzing Effect of eWOM on Consumer Game Sales
Venue: arXiv cs.IR 2019
Year: 2019

Electronic word-of-mouth (eWOM) has become an important resource for the analysis of marketing research. In this study, in order to analyze user needs for consumer game software, we focus on tweet data. And we proposed topic extraction method using entropy-based feature selection based feature expansion. We also applied it to the classification of the data extracted from tweet data by using SVM. As a result, we achieved a 0.63 F-measure.
Fourier Transform Approach to Machine Learning II: Fourier Clustering
Venue: arXiv cs.LG 2019
Year: 2019

We propose a Fourier-based approach for optimization of several clustering algorithms. Mathematically, clusters data can be described by a density function represented by the Dirac mixture distribution. The density function can be smoothed by applying the Fourier transform and a Gaussian filter. The determination of the optimal standard deviation of the Gaussian filter will be accomplished by the use of a convergence criterion related to the correlation between the smoothed and the original density functions. In principle, the optimal smoothed density function exhibits local maxima, which correspond to the cluster centroids. Thus, the complex task of finding the centroids of the clusters is simplified by the detection of the peaks of the smoothed density function. A multiple sliding windows procedure is used to detect the peaks. The remarkable accuracy of the proposed algorithm demonstrates its capability as a reliable general method for enhancement of the clustering performance, its global optimization and also removing the initialization problem in many clustering methods.
On Social Machines for Algorithmic Regulation
Venue: arXiv cs.CY 2019
Year: 2019

Autonomous mechanisms have been proposed to regulate certain aspects of society and are already being used to regulate business organisations. We take seriously recent proposals for algorithmic regulation of society, and we identify the existing technologies that can be used to implement them, most of them originally introduced in business contexts. We build on the notion of 'social machine' and we connect it to various ongoing trends and ideas, including crowdsourced task-work, social compiler, mechanism design, reputation management systems, and social scoring. After showing how all the building blocks of algorithmic regulation are already well in place, we discuss possible implications for human autonomy and social order. The main contribution of this paper is to identify convergent social and technical trends that are leading towards social regulation by algorithms, and to discuss the possible social, political, and ethical consequences of taking this path.
Effective and Efficient Indexing in Cross-Modal Hashing-Based Datasets
Venue: arXiv cs.IR 2019
Year: 2019

To overcome the barrier of storage and computation, the hashing technique has been widely used for nearest neighbor search in multimedia retrieval applications recently. Particularly, cross-modal retrieval that searches across different modalities becomes an active but challenging problem. Although dozens of cross-modal hashing algorithms are proposed to yield compact binary codes, the exhaustive search is impractical for the real-time purpose, and Hamming distance computation suffers inaccurate results. In this paper, we propose a novel search method that utilizes a probability-based index scheme over binary hash codes in cross-modal retrieval. The proposed hash code indexing scheme exploits a few binary bits of the hash code as the index code. We construct an inverted index table based on index codes and train a neural network to improve the indexing accuracy and efficiency. Experiments are performed on two benchmark datasets for retrieval across image and text modalities, where hash codes are generated by three cross-modal hashing methods. Results show the proposed method effectively boost the performance on these hash methods.
PYRO-NN: Python Reconstruction Operators in Neural Networks
Venue: arXiv cs.CV 2019
Year: 2019

Purpose: Recently, several attempts were conducted to transfer deep learning to medical image reconstruction. An increasingly number of publications follow the concept of embedding the CT reconstruction as a known operator into a neural network. However, most of the approaches presented lack an efficient CT reconstruction framework fully integrated into deep learning environments. As a result, many approaches are forced to use workarounds for mathematically unambiguously solvable problems. Methods: PYRO-NN is a generalized framework to embed known operators into the prevalent deep learning framework Tensorflow. The current status includes state-of-the-art parallel-, fan- and cone-beam projectors and back-projectors accelerated with CUDA provided as Tensorflow layers. On top, the framework provides a high level Python API to conduct FBP and iterative reconstruction experiments with data from real CT systems. Results: The framework provides all necessary algorithms and tools to design end-to-end neural network pipelines with integrated CT reconstruction algorithms. The high level Python API allows a simple use of the layers as known from Tensorflow. To demonstrate the capabilities of the layers, the framework comes with three baseline experiments showing a cone-beam short scan FDK reconstruction, a CT reconstruction filter learning setup, and a TV regularized iterative reconstruction. All algorithms and tools are referenced to a scientific publication and are compared to existing non deep learning reconstruction frameworks. The framework is available as open-source software at \url{https://github.com/csyben/PYRO-NN}. Conclusions: PYRO-NN comes with the prevalent deep learning framework Tensorflow and allows to setup end-to-end trainable neural networks in the medical image reconstruction context. We believe that the framework will be a step towards reproducible research
Object Contour and Edge Detection with RefineContourNet
Venue: arXiv cs.CV 2019
Year: 2019

A ResNet-based multi-path refinement CNN is used for object contour detection. For this task, we prioritise the effective utilization of the high-level abstraction capability of a ResNet, which leads to state-of-the-art results for edge detection. Keeping our focus in mind, we fuse the high, mid and low-level features in that specific order, which differs from many other approaches. It uses the tensor with the highest-levelled features as the starting point to combine it layer-by-layer with features of a lower abstraction level until it reaches the lowest level. We train this network on a modified PASCAL VOC 2012 dataset for object contour detection and evaluate on a refined PASCAL-val dataset reaching an excellent performance and an Optimal Dataset Scale (ODS) of 0.752. Furthermore, by fine-training on the BSDS500 dataset we reach state-of-the-art results for edge-detection with an ODS of 0.824.
Risk-Averse Explore-Then-Commit Algorithms for Finite-Time Bandits
Venue: arXiv cs.LG 2019
Year: 2019

In this paper, we study multi-armed bandit problems in explore-then-commit setting. In our proposed explore-then-commit setting, the goal is to identify the best arm after a pure experimentation (exploration) phase and exploit it once or for a given finite number of times. We identify that although the arm with the highest expected reward is the most desirable objective for infinite exploitations, it is not necessarily the one that is most probable to have the highest reward in a single or finite-time exploitations. Alternatively, we advocate the idea of risk-aversion where the objective is to compete against the arm with the best risk-return trade-off. Then, we propose two algorithms whose objectives are to select the arm that is most probable to reward the most. Using a new notion of finite-time exploitation regret, we find an upper bound for the minimum number of experiments before commitment, to guarantee an upper bound for the regret. As compared to existing risk-averse bandit algorithms, our algorithms do not rely on hyper-parameters, resulting in a more robust behavior in practice, which is verified by the numerical evaluation.
Simpler and Better Algorithms for Minimum-Norm Load Balancing
Venue: arXiv cs.DS 2019
Year: 2019

Recently, Chakrabarty and Swamy (STOC 2019) introduced the {\em minimum-norm load-balancing} problem on unrelated machines, wherein we are given a set $J$ of jobs that need to be scheduled on a set of $m$ unrelated machines, and a monotone, symmetric norm; We seek an assignment $\sg:J\mapsto[m]$ that minimizes the norm of the resulting load vector $\lvec_\sg\in\R_+^m$, where $\lvec_\sg(i)$ is the load on machine $i$ under the assignment $\sg$. Besides capturing all $\ell_p$ norms, symmetric norms also capture other norms of interest including top-$\ell$ norms, and ordered norms. Chakrabarty and Swamy (STOC 2019) give a $(38+\ve)$-approximation algorithm for this problem via a general framework they develop for minimum-norm optimization that proceeds by first carefully reducing this problem (in a series of steps) to a problem called \minmax ordered load balancing, and then devising a so-called deterministic oblivious LP-rounding algorithm for ordered load balancing. We give a direct, and simple $4$-approximation algorithm for the minimum-norm load balancing based on rounding a (near-optimal) solution to a novel convex-programming relaxation for the problem. Whereas the natural convex program encoding minimum-norm load balancing problem has a large non-constant integrality gap, we show that this issue can be remedied by including a key constraint that bounds the "norm of the job-cost vector." Our techniques also yield a (essentially) $4$-approximation for: (a) {\em multi-norm load balancing}, wherein we are given multiple monotone symmetric norms, and we seek an assignment respecting a given budget for each norm; (b) the best {\em simultaneous approximation factor} achievable for all symmetric norms for a given instance.
Personalized Ranking in eCommerce Search
Venue: arXiv cs.IR 2019
Year: 2019

We address the problem of personalization in the context of eCommerce search. Specifically, we develop personalization ranking features that use in-session context to augment a generic ranker optimized for conversion and relevance. We use a combination of latent features learned from item co-clicks in historic sessions and content-based features that use item title and price. Personalization in search has been discussed extensively in the existing literature. The novelty of our work is combining and comparing content-based and content-agnostic features and showing that they complement each other to result in a significant improvement of the ranker. Moreover, our technique does not require an explicit re-ranking step, does not rely on learning user profiles from long term search behavior, and does not involve complex modeling of query-item-user features. Our approach captures item co-click propensity using lightweight item embeddings. We experimentally show that our technique significantly outperforms a generic ranker in terms of Mean Reciprocal Rank (MRR). We also provide anecdotal evidence for the semantic similarity captured by the item embeddings on the eBay search engine.
Deep Learning for Audio Signal Processing
Venue: arXiv cs.SD 2019
Year: 2019

Given the recent surge in developments of deep learning, this article provides a review of the state-of-the-art deep learning techniques for audio signal processing. Speech, music, and environmental sound processing are considered side-by-side, in order to point out similarities and differences between the domains, highlighting general methods, problems, key references, and potential for cross-fertilization between areas. The dominant feature representations (in particular, log-mel spectra and raw waveform) and deep learning models are reviewed, including convolutional neural networks, variants of the long short-term memory architecture, as well as more audio-specific neural network models. Subsequently, prominent deep learning application areas are covered, i.e. audio recognition (automatic speech recognition, music information retrieval, environmental sound detection, localization and tracking) and synthesis and transformation (source separation, audio enhancement, generative models for speech, sound, and music synthesis). Finally, key issues and future questions regarding deep learning applied to audio signal processing are identified.