OpenRaiser/Intern-Atlas huggingface dataset:
Text Mining to Identify and Extract Novel Disease Treatments From Unstructured Datasets
Venue: arXiv cs.IR 2020
Year: 2020

Objective: We aim to learn potential novel cures for diseases from unstructured text sources. More specifically, we seek to extract drug-disease pairs of potential cures to diseases by a simple reasoning over the structure of spoken text. Materials and Methods: We use Google Cloud to transcribe podcast episodes of an NPR radio show. We then build a pipeline for systematically pre-processing the text to ensure quality input to the core classification model, which feeds to a series of post-processing steps for obtaining filtered results. Our classification model itself uses a language model pre-trained on PubMed text. The modular nature of our pipeline allows for ease of future developments in this area by substituting higher quality components at each stage of the pipeline. As a validation measure, we use ROBOKOP, an engine over a medical knowledge graph with only validated pathways, as a ground truth source for checking the existence of the proposed pairs. For the proposed pairs not found in ROBOKOP, we provide further verification using Chemotext. Results: We found 30.4% of our proposed pairs in the ROBOKOP database. For example, our model successfully identified that Omeprazole can help treat heartburn.We discuss the significance of this result, showing some examples of the proposed pairs. Discussion and Conclusion: The agreement of our results with the existing knowledge source indicates a step in the right direction. Given the plug-and-play nature of our framework, it is easy to add, remove, or modify parts to improve the model as necessary. We discuss the results showing some examples, and note that this is a potentially new line of research that has further scope to be explored. Although our approach was originally oriented on radio podcast transcripts, it is input-agnostic and could be applied to any source of textual data and to any problem of interest.
Combining the Mersenne Twister and the Xorgens Designs
Venue: arXiv cs.DS 2020
Year: 2020

We combine the design of two \emph{random number generators}, \emph{Mersenne Twister} and \emph{Xorgens}, to obtain a new class of generators with heavy-weight characteristic polynomials (exceeded only by the {\sc well} generators) and high speed (comparable with the originals). Tables with parameter combinations are included for state sizes ranging from 521 to 44497 bits and each of the word lengths 32, 64, 128. These generators passed all tests of the \emph{TestU01}-package for each 32-bit integer part and each 64-bit derived real part of the output. We determine \emph{dimension gaps} for 32-bit words, neglecting the non-linear tempering, and compare with an alternative experimental linear tempering.
Cycle-Consistent Generative Rendering for 2D-3D Modality Translation
Venue: arXiv cs.CV 2020
Year: 2020

For humans, visual understanding is inherently generative: given a 3D shape, we can postulate how it would look in the world; given a 2D image, we can infer the 3D structure that likely gave rise to it. We can thus translate between the 2D visual and 3D structural modalities of a given object. In the context of computer vision, this corresponds to a learnable module that serves two purposes: (i) generate a realistic rendering of a 3D object (shape-to-image translation) and (ii) infer a realistic 3D shape from an image (image-to-shape translation). In this paper, we learn such a module while being conscious of the difficulties in obtaining large paired 2D-3D datasets. By leveraging generative domain translation methods, we are able to define a learning algorithm that requires only weak supervision, with unpaired data. The resulting model is not only able to perform 3D shape, pose, and texture inference from 2D images, but can also generate novel textured 3D shapes and renders, similar to a graphics pipeline. More specifically, our method (i) infers an explicit 3D mesh representation, (ii) utilizes example shapes to regularize inference, (iii) requires only an image mask (no keypoints or camera extrinsics), and (iv) has generative capabilities. While prior work explores subsets of these properties, their combination is novel. We demonstrate the utility of our learned representation, as well as its performance on image generation and unpaired 3D shape inference tasks.
Mixing ADAM and SGD: a Combined Optimization Method
Venue: arXiv cs.LG 2020
Year: 2020

Optimization methods (optimizers) get special attention for the efficient training of neural networks in the field of deep learning. In literature there are many papers that compare neural models trained with the use of different optimizers. Each paper demonstrates that for a particular problem an optimizer is better than the others but as the problem changes this type of result is no longer valid and we have to start from scratch. In our paper we propose to use the combination of two very different optimizers but when used simultaneously they can overcome the performances of the single optimizers in very different problems. We propose a new optimizer called MAS (Mixing ADAM and SGD) that integrates SGD and ADAM simultaneously by weighing the contributions of both through the assignment of constant weights. Rather than trying to improve SGD or ADAM we exploit both at the same time by taking the best of both. We have conducted several experiments on images and text document classification, using various CNNs, and we demonstrated by experiments that the proposed MAS optimizer produces better performance than the single SGD or ADAM optimizers. The source code and all the results of the experiments are available online at the following link https://gitlab.com/nicolalandro/multi\_optimizer
The unreasonable effectiveness of Batch-Norm statistics in addressing catastrophic forgetting across medical institutions
Venue: arXiv cs.LG 2020
Year: 2020

Model brittleness is a primary concern when deploying deep learning models in medical settings owing to inter-institution variations, like patient demographics and intra-institution variation, such as multiple scanner types. While simply training on the combined datasets is fraught with data privacy limitations, fine-tuning the model on subsequent institutions after training it on the original institution results in a decrease in performance on the original dataset, a phenomenon called catastrophic forgetting. In this paper, we investigate trade-off between model refinement and retention of previously learned knowledge and subsequently address catastrophic forgetting for the assessment of mammographic breast density. More specifically, we propose a simple yet effective approach, adapting Elastic weight consolidation (EWC) using the global batch normalization (BN) statistics of the original dataset. The results of this study provide guidance for the deployment of clinical deep learning models where continuous learning is needed for domain expansion.
Cinematic-L1 Video Stabilization with a Log-Homography Model
Venue: arXiv cs.CV 2020
Year: 2020

We present a method for stabilizing handheld video that simulates the camera motions cinematographers achieve with equipment like tripods, dollies, and Steadicams. We formulate a constrained convex optimization problem minimizing the $\ell_1$-norm of the first three derivatives of the stabilized motion. Our approach extends the work of Grundmann et al. [9] by solving with full homographies (rather than affinities) in order to correct perspective, preserving linearity by working in log-homography space. We also construct crop constraints that preserve field-of-view; model the problem as a quadratic (rather than linear) program to allow for an $\ell_2$ term encouraging fidelity to the original trajectory; and add constraints and objectives to reduce distortion. Furthermore, we propose new methods for handling salient objects via both inclusion constraints and centering objectives. Finally, we describe a windowing strategy to approximate the solution in linear time and bounded memory. Our method is computationally efficient, running at 300fps on an iPhone XS, and yields high-quality results, as we demonstrate with a collection of stabilized videos, quantitative and qualitative comparisons to [9] and other methods, and an ablation study.
LUCIDGames: Online Unscented Inverse Dynamic Games for Adaptive Trajectory Prediction and Planning
Venue: arXiv cs.RO 2020
Year: 2020

Existing game-theoretic planning methods assume that the robot knows the objective functions of the other agents a priori while, in practical scenarios, this is rarely the case. This paper introduces LUCIDGames, an inverse optimal control algorithm that is able to estimate the other agents' objective functions in real time, and incorporate those estimates online into a receding-horizon game-theoretic planner. LUCIDGames solves the inverse optimal control problem by recasting it in a recursive parameter-estimation framework. LUCIDGames uses an unscented Kalman filter (UKF) to iteratively update a Bayesian estimate of the other agents' cost function parameters, improving that estimate online as more data is gathered from the other agents' observed trajectories. The planner then takes account of the uncertainty in the Bayesian parameter estimates of other agents by planning a trajectory for the robot subject to uncertainty ellipse constraints. The algorithm assumes no explicit communication or coordination between the robot and the other agents in the environment. An MPC implementation of LUCIDGames demonstrates real-time performance on complex autonomous driving scenarios with an update frequency of 40 Hz. Empirical results demonstrate that LUCIDGames improves the robot's performance over existing game-theoretic and traditional MPC planning approaches. Our implementation of LUCIDGames is available at https://github.com/RoboticExplorationLab/LUCIDGames.jl.
Uncertainty measures for probabilistic hesitant fuzzy sets in multiple criteria decision making
Venue: arXiv cs.AI 2020
Year: 2020

This contribution reviews critically the existing entropy measures for probabilistic hesitant fuzzy sets (PHFSs), and demonstrates that these entropy measures fail to effectively distinguish a variety of different PHFSs in some cases. In the sequel, we develop a new axiomatic framework of entropy measures for probabilistic hesitant fuzzy elements (PHFEs) by considering two facets of uncertainty associated with PHFEs which are known as fuzziness and nonspecificity. Respect to each kind of uncertainty, a number of formulae are derived to permit flexible selection of PHFE entropy measures. Moreover, based on the proposed PHFE entropy measures, we introduce some entropy-based distance measures which are used in the portion of comparative analysis.
Dialog Simulation with Realistic Variations for Training Goal-Oriented Conversational Systems
Venue: arXiv cs.CL 2020
Year: 2020

Goal-oriented dialog systems enable users to complete specific goals like requesting information about a movie or booking a ticket. Typically the dialog system pipeline contains multiple ML models, including natural language understanding, state tracking and action prediction (policy learning). These models are trained through a combination of supervised or reinforcement learning methods and therefore require collection of labeled domain specific datasets. However, collecting annotated datasets with language and dialog-flow variations is expensive, time-consuming and scales poorly due to human involvement. In this paper, we propose an approach for automatically creating a large corpus of annotated dialogs from a few thoroughly annotated sample dialogs and the dialog schema. Our approach includes a novel goal-sampling technique for sampling plausible user goals and a dialog simulation technique that uses heuristic interplay between the user and the system (Alexa), where the user tries to achieve the sampled goal. We validate our approach by generating data and training three different downstream conversational ML models. We achieve 18 ? 50% relative accuracy improvements on a held-out test set compared to a baseline dialog generation approach that only samples natural language and entity value variations from existing catalogs but does not generate any novel dialog flow variations. We also qualitatively establish that the proposed approach is better than the baseline. Moreover, several different conversational experiences have been built using this method, which enables customers to have a wide variety of conversations with Alexa.
ACCORDANT: A Domain Specific Model and DevOpsApproach for Big Data Analytics Architectures
Venue: arXiv cs.SE 2020
Year: 2020

Big data analytics (BDA) applications use machine learning algorithms to extract valuable insights from large, fast, and heterogeneous data sources. New software engineering challenges for BDA applications include ensuring performance levels of data-driven algorithms even in the presence of large data volume, velocity, and variety (3Vs). BDA software complexity frequently leads to delayed deployments, longer development cycles and challenging performance assessment. This paper proposes a Domain-Specific Model (DSM), and DevOps practices to design, deploy, and monitor performance metrics in BDA applications. Our proposal includes a design process, and a framework to define architectural inputs, software components, and deployment strategies through integrated high-level abstractions to enable QS monitoring. We evaluate our approach with four use cases from different domains to demonstrate a high level of generalization. Our results show a shorter deployment and monitoring times, and a higher gain factor per iteration compared to similar approaches.
Overcomplete Deep Subspace Clustering Networks
Venue: arXiv cs.CV 2020
Year: 2020

Deep Subspace Clustering Networks (DSC) provide an efficient solution to the problem of unsupervised subspace clustering by using an undercomplete deep auto-encoder with a fully-connected layer to exploit the self expressiveness property. This method uses undercomplete representations of the input data which makes it not so robust and more dependent on pre-training. To overcome this, we propose a simple yet efficient alternative method - Overcomplete Deep Subspace Clustering Networks (ODSC) where we use overcomplete representations for subspace clustering. In our proposed method, we fuse the features from both undercomplete and overcomplete auto-encoder networks before passing them through the self-expressive layer thus enabling us to extract a more meaningful and robust representation of the input data for clustering. Experimental results on four benchmark datasets show the effectiveness of the proposed method over DSC and other clustering methods in terms of clustering error. Our method is also not as dependent as DSC is on where pre-training should be stopped to get the best performance and is also more robust to noise. Code - \href{https://github.com/jeya-maria-jose/Overcomplete-Deep-Subspace-Clustering}{https://github.com/jeya-maria-jose/Overcomplete-Deep-Subspace-Clustering
Vis-CRF, A Classical Receptive Field Model for VISION
Venue: arXiv cs.CV 2020
Year: 2020

Over the last decade, a variety of new neurophysiological experiments have led to new insights as to how, when and where retinal processing takes place, and the nature of the retinal representation encoding sent to the cortex for further processing. Based on these neurobiological discoveries, in our previous work, we provided computer simulation evidence to suggest that Geometrical illusions are explained in part, by the interaction of multiscale visual processing performed in the retina. The output of our retinal stage model, named Vis-CRF, is presented here for a sample of natural image and for several types of Tilt Illusion, in which the final tilt percept arises from multiple scale processing of Difference of Gaussians (DoG) and the perceptual interaction of foreground and background elements (Nematzadeh and Powers, 2019; Nematzadeh, 2018; Nematzadeh, Powers and Lewis, 2017; Nematzadeh, Lewis and Powers, 2015).
Augmented Fairness: An Interpretable Model Augmenting Decision-Makers' Fairness
Venue: arXiv cs.LG 2020
Year: 2020

We propose a model-agnostic approach for mitigating the prediction bias of a black-box decision-maker, and in particular, a human decision-maker. Our method detects in the feature space where the black-box decision-maker is biased and replaces it with a few short decision rules, acting as a "fair surrogate". The rule-based surrogate model is trained under two objectives, predictive performance and fairness. Our model focuses on a setting that is common in practice but distinct from other literature on fairness. We only have black-box access to the model, and only a limited set of true labels can be queried under a budget constraint. We formulate a multi-objective optimization for building a surrogate model, where we simultaneously optimize for both predictive performance and bias. To train the model, we propose a novel training algorithm that combines a nondominated sorting genetic algorithm with active learning. We test our model on public datasets where we simulate various biased "black-box" classifiers (decision-makers) and apply our approach for interpretable augmented fairness.
Semi-Supervised Few-Shot Atomic Action Recognition
Venue: arXiv cs.CV 2020
Year: 2020

Despite excellent progress has been made, the performance on action recognition still heavily relies on specific datasets, which are difficult to extend new action classes due to labor-intensive labeling. Moreover, the high diversity in Spatio-temporal appearance requires robust and representative action feature aggregation and attention. To address the above issues, we focus on atomic actions and propose a novel model for semi-supervised few-shot atomic action recognition. Our model features unsupervised and contrastive video embedding, loose action alignment, multi-head feature comparison, and attention-based aggregation, together of which enables action recognition with only a few training examples through extracting more representative features and allowing flexibility in spatial and temporal alignment and variations in the action. Experiments show that our model can attain high accuracy on representative atomic action datasets outperforming their respective state-of-the-art classification accuracy in full supervision setting.
Transducer Adaptive Ultrasound Volume Reconstruction
Venue: arXiv cs.CV 2020
Year: 2020

Reconstructed 3D ultrasound volume provides more context information compared to a sequence of 2D scanning frames, which is desirable for various clinical applications such as ultrasound-guided prostate biopsy. Nevertheless, 3D volume reconstruction from freehand 2D scans is a very challenging problem, especially without the use of external tracking devices. Recent deep learning based methods demonstrate the potential of directly estimating inter-frame motion between consecutive ultrasound frames. However, such algorithms are specific to particular transducers and scanning trajectories associated with the training data, which may not be generalized to other image acquisition settings. In this paper, we tackle the data acquisition difference as a domain shift problem and propose a novel domain adaptation strategy to adapt deep learning algorithms to data acquired with different transducers. Specifically, feature extractors that generate transducer-invariant features from different datasets are trained by minimizing the discrepancy between deep features of paired samples in a latent space. Our results show that the proposed domain adaptation method can successfully align different feature distributions while preserving the transducer-specific information for universal freehand ultrasound volume reconstruction.
Weak Links in Authentication Chains: A Large-scale Analysis of Email Sender Spoofing Attacks
Venue: arXiv cs.CR 2020
Year: 2020

As a fundamental communicative service, email is playing an important role in both individual and corporate communications, which also makes it one of the most frequently attack vectors. An email's authenticity is based on an authentication chain involving multiple protocols, roles and services, the inconsistency among which creates security threats. Thus, it depends on the weakest link of the chain, as any failed part can break the whole chain-based defense. This paper systematically analyzes the transmission of an email and identifies a series of new attacks capable of bypassing SPF, DKIM, DMARC and user-interface protections. In particular, by conducting a "cocktail" joint attack, more realistic emails can be forged to penetrate the celebrated email services, such as Gmail and Outlook. We conduct a large-scale experiment on 30 popular email services and 23 email clients, and find that all of them are vulnerable to certain types of new attacks. We have duly reported the identified vulnerabilities to the related email service providers, and received positive responses from 11 of them, including Gmail, Yahoo, iCloud and Alibaba. Furthermore, we propose key mitigating measures to defend against the new attacks. Therefore, this work is of great value for identifying email spoofing attacks and improving the email ecosystem's overall security.
A Time-Frequency based Suspicious Activity Detection for Anti-Money Laundering
Venue: arXiv cs.LG 2020
Year: 2020

Money laundering is the crucial mechanism utilized by criminals to inject proceeds of crime to the financial system. The primary responsibility of the detection of suspicious activity related to money laundering is with the financial institutions. Most of the current systems in these institutions are rule-based and ineffective. The available data science-based anti-money laundering (AML) models in order to replace the existing rule-based systems work on customer relationship management (CRM) features and time characteristics of transaction behaviour. However, there is still a challenge on accuracy and problems around feature engineering due to thousands of possible features. Aiming to improve the detection performance of suspicious transaction monitoring systems for AML systems, in this article, we introduce a novel feature set based on time-frequency analysis, that makes use of 2-D representations of financial transactions. Random forest is utilized as a machine learning method, and simulated annealing is adopted for hyperparameter tuning. The designed algorithm is tested on real banking data, proving the efficacy of the results in practically relevant environments. It is shown that the time-frequency characteristics of suspicious and non-suspicious entities differentiate significantly, which would substantially improve the precision of data science-based transaction monitoring systems looking at only time-series transaction and CRM features.
MVP-BERT: Redesigning Vocabularies for Chinese BERT and Multi-Vocab Pretraining
Venue: arXiv cs.CL 2020
Year: 2020

Despite the development of pre-trained language models (PLMs) significantly raise the performances of various Chinese natural language processing (NLP) tasks, the vocabulary for these Chinese PLMs remain to be the one provided by Google Chinese Bert \cite{devlin2018bert}, which is based on Chinese characters. Second, the masked language model pre-training is based on a single vocabulary, which limits its downstream task performances. In this work, we first propose a novel method, \emph{seg\_tok}, to form the vocabulary of Chinese BERT, with the help of Chinese word segmentation (CWS) and subword tokenization. Then we propose three versions of multi-vocabulary pretraining (MVP) to improve the models expressiveness. Experiments show that: (a) compared with char based vocabulary, \emph{seg\_tok} does not only improves the performances of Chinese PLMs on sentence level tasks, it can also improve efficiency; (b) MVP improves PLMs' downstream performance, especially it can improve \emph{seg\_tok}'s performances on sequence labeling tasks.