pwc-archive/papers-with-abstracts huggingface dataset:
Controlled Molecule Generator for Optimizing Multiple Chemical Properties
Authors: Bonggun Shin, Sungsoo Park, JinYeong Bak, Joyce C. Ho
Date: 2020-10-26 00:00:00
Tasks: Drug Discovery, Property Prediction, Translation

Generating a novel and optimized molecule with desired chemical properties is an essential part of the drug discovery process. Failure to meet one of the required properties can frequently lead to failure in a clinical test which is costly. In addition, optimizing these multiple properties is a challenging task because the optimization of one property is prone to changing other properties. In this paper, we pose this multi-property optimization problem as a sequence translation process and propose a new optimized molecule generator model based on the Transformer with two constraint networks: property prediction and similarity prediction. We further improve the model by incorporating score predictions from these constraint networks in a modified beam search algorithm. The experiments demonstrate that our proposed model outperforms state-of-the-art models by a significant margin for optimizing multiple properties simultaneously.
T$^2$-Net: A Semi-supervised Deep Model for Turbulence Forecasting
Authors: Denghui Zhang, Yanchi Liu, Wei Cheng, Bo Zong, Jingchao Ni, Zhengzhang Chen, Haifeng Chen, Hui Xiong
Date: 2020-10-26 00:00:00
Tasks: Decoder

Accurate air turbulence forecasting can help airlines avoid hazardous turbulence, guide the routes that keep passengers safe, maximize efficiency, and reduce costs. Traditional turbulence forecasting approaches heavily rely on painstakingly customized turbulence indexes, which are less effective in dynamic and complex weather conditions. The recent availability of high-resolution weather data and turbulence records allows more accurate forecasting of the turbulence in a data-driven way. However, it is a non-trivial task for developing a machine learning based turbulence forecasting system due to two challenges: (1) Complex spatio-temporal correlations, turbulence is caused by air movement with complex spatio-temporal patterns, (2) Label scarcity, very limited turbulence labels can be obtained. To this end, in this paper, we develop a unified semi-supervised framework, T$^2$-Net, to address the above challenges. Specifically, we first build an encoder-decoder paradigm based on the convolutional LSTM to model the spatio-temporal correlations. Then, to tackle the label scarcity problem, we propose a novel Dual Label Guessing method to take advantage of massive unlabeled turbulence data. It integrates complementary signals from the main Turbulence Forecasting task and the auxiliary Turbulence Detection task to generate pseudo-labels, which are dynamically utilized as additional training data. Finally, extensive experimental results on a real-world turbulence dataset validate the superiority of our method on turbulence forecasting.
Expectile Neural Networks for Genetic Data Analysis of Complex Diseases
Authors: Jinghang Lin, Xiaoran Tong, Chenxi Li, Qing Lu
Date: 2020-10-26 00:00:00
Tasks: regression

The genetic etiologies of common diseases are highly complex and heterogeneous. Classic statistical methods, such as linear regression, have successfully identified numerous genetic variants associated with complex diseases. Nonetheless, for most complex diseases, the identified variants only account for a small proportion of heritability. Challenges remain to discover additional variants contributing to complex diseases. Expectile regression is a generalization of linear regression and provides completed information on the conditional distribution of a phenotype of interest. While expectile regression has many nice properties and holds great promise for genetic data analyses (e.g., investigating genetic variants predisposing to a high-risk population), it has been rarely used in genetic research. In this paper, we develop an expectile neural network (ENN) method for genetic data analyses of complex diseases. Similar to expectile regression, ENN provides a comprehensive view of relationships between genetic variants and disease phenotypes and can be used to discover genetic variants predisposing to sub-populations (e.g., high-risk groups). We further integrate the idea of neural networks into ENN, making it capable of capturing non-linear and non-additive genetic effects (e.g., gene-gene interactions). Through simulations, we showed that the proposed method outperformed an existing expectile regression when there exist complex relationships between genetic variants and disease phenotypes. We also applied the proposed method to the genetic data from the Study of Addiction: Genetics and Environment(SAGE), investigating the relationships of candidate genes with smoking quantity.
How We Refactor and How We Document it? On the Use of Supervised Machine Learning Algorithms to Classify Refactoring Documentation
Authors: Eman Abdullah AlOmar, Anthony Peruma, Mohamed Wiem Mkaouer, Christian Newman, Ali Ouni, Marouane Kessentini
Date: 2020-10-26 00:00:00

Refactoring is the art of improving the design of a system without altering its external behavior. Refactoring has become a well established and disciplined software engineering practice that has attracted a significant amount of research presuming that refactoring is primarily motivated by the need to improve system structures. However, recent studies have shown that developers may incorporate refactorings in other development activities that go beyond improving the design. Unfortunately, these studies are limited to developer interviews and a reduced set of projects. To cope with the above-mentioned limitations, we aim to better understand what motivates developers to apply refactoring by mining and classifying a large set of 111,884 commits containing refactorings, extracted from 800 Java projects. We trained a multi-class classifier to categorize these commits into 3 categories, namely, Internal QA, External QA, and Code Smell Resolution, along with the traditional BugFix and Functional categories. This classification challenges the original definition of refactoring, being exclusive to improving the design and fixing code smells. Further, to better understand our classification results, we analyzed commit messages to extract textual patterns that developers regularly use to describe their refactorings. The results show that (1) fixing code smells is not the main driver for developers to refactoring their codebases. Refactoring is solicited for a wide variety of reasons, going beyond its traditional definition; (2) the distribution of refactorings differs between production and test files; (3) developers use several patterns to purposefully target refactoring; (4) the textual patterns, extracted from commit messages, provide better coverage for how developers document their refactorings.
Versatile Verification of Tree Ensembles
Authors: Laurens Devos, Wannes Meert, Jesse Davis
Date: 2020-10-26 00:00:00
Tasks: Fairness

Machine learned models often must abide by certain requirements (e.g., fairness or legal). This has spurred interested in developing approaches that can provably verify whether a model satisfies certain properties. This paper introduces a generic algorithm called Veritas that enables tackling multiple different verification tasks for tree ensemble models like random forests (RFs) and gradient boosting decision trees (GBDTs). This generality contrasts with previous work, which has focused exclusively on either adversarial example generation or robustness checking. Veritas formulates the verification task as a generic optimization problem and introduces a novel search space representation. Veritas offers two key advantages. First, it provides anytime lower and upper bounds when the optimization problem cannot be solved exactly. In contrast, many existing methods have focused on exact solutions and are thus limited by the verification problem being NP-complete. Second, Veritas produces full (bounded suboptimal) solutions that can be used to generate concrete examples. We experimentally show that Veritas outperforms the previous state of the art by (a) generating exact solutions more frequently, (b) producing tighter bounds when (a) is not possible, and (c) offering orders of magnitude speed ups. Subsequently, Veritas enables tackling more and larger real-world verification scenarios.
Improved Neural Language Model Fusion for Streaming Recurrent Neural Network Transducer
Authors: Suyoun Kim, Yuan Shangguan, Jay Mahadeokar, Antoine Bruguier, Christian Fuegen, Michael L. Seltzer, Duc Le
Date: 2020-10-26 00:00:00
Tasks: Language Modeling, Language Modelling, speech-recognition, Speech Recognition

Recurrent Neural Network Transducer (RNN-T), like most end-to-end speech recognition model architectures, has an implicit neural network language model (NNLM) and cannot easily leverage unpaired text data during training. Previous work has proposed various fusion methods to incorporate external NNLMs into end-to-end ASR to address this weakness. In this paper, we propose extensions to these techniques that allow RNN-T to exploit external NNLMs during both training and inference time, resulting in 13-18% relative Word Error Rate improvement on Librispeech compared to strong baselines. Furthermore, our methods do not incur extra algorithmic latency and allow for flexible plug-and-play of different NNLMs without re-training. We also share in-depth analysis to better understand the benefits of the different NNLM fusion methods. Our work provides a reliable technique for leveraging unpaired text data to significantly improve RNN-T while keeping the system streamable, flexible, and lightweight.
Bayesian Importance of Features (BIF)
Authors: Kamil Adamczewski, Frederik Harder, Mijung Park
Date: 2020-10-26 00:00:00
Tasks: Bayesian Inference, BIG-bench Machine Learning, Fairness, Feature Importance, feature selection

We introduce a simple and intuitive framework that provides quantitative explanations of statistical models through the probabilistic assessment of input feature importance. The core idea comes from utilizing the Dirichlet distribution to define the importance of input features and learning it via approximate Bayesian inference. The learned importance has probabilistic interpretation and provides the relative significance of each input feature to a model's output, additionally assessing confidence about its importance quantification. As a consequence of using the Dirichlet distribution over the explanations, we can define a closed-form divergence to gauge the similarity between learned importance under different models. We use this divergence to study the feature importance explainability tradeoffs with essential notions in modern machine learning, such as privacy and fairness. Furthermore, BIF can work on two levels: global explanation (feature importance across all data instances) and local explanation (individual feature importance for each data instance). We show the effectiveness of our method on a variety of synthetic and real datasets, taking into account both tabular and image datasets. The code is available at https://github.com/kamadforge/featimp_dp.
Examining the causal structures of deep neural networks using information theory
Authors: Simon Mattsson, Eric J. Michaud, Erik Hoel
Date: 2020-10-26 00:00:00

Deep Neural Networks (DNNs) are often examined at the level of their response to input, such as analyzing the mutual information between nodes and data sets. Yet DNNs can also be examined at the level of causation, exploring "what does what" within the layers of the network itself. Historically, analyzing the causal structure of DNNs has received less attention than understanding their responses to input. Yet definitionally, generalizability must be a function of a DNN's causal structure since it reflects how the DNN responds to unseen or even not-yet-defined future inputs. Here, we introduce a suite of metrics based on information theory to quantify and track changes in the causal structure of DNNs during training. Specifically, we introduce the effective information (EI) of a feedforward DNN, which is the mutual information between layer input and output following a maximum-entropy perturbation. The EI can be used to assess the degree of causal influence nodes and edges have over their downstream targets in each layer. We show that the EI can be further decomposed in order to examine the sensitivity of a layer (measured by how well edges transmit perturbations) and the degeneracy of a layer (measured by how edge overlap interferes with transmission), along with estimates of the amount of integrated information of a layer. Together, these properties define where each layer lies in the "causal plane" which can be used to visualize how layer connectivity becomes more sensitive or degenerate over time, and how integration changes during training, revealing how the layer-by-layer causal structure differentiates. These results may help in understanding the generalization capabilities of DNNs and provide foundational tools for making DNNs both more generalizable and more explainable.
Word Frequency Does Not Predict Grammatical Knowledge in Language Models
Authors: Charles Yu, Ryan Sie, Nico Tedeschi, Leon Bergen
Date: 2020-10-26 00:00:00
Proceeding: EMNLP 2020 11

Neural language models learn, to varying degrees of accuracy, the grammatical properties of natural languages. In this work, we investigate whether there are systematic sources of variation in the language models' accuracy. Focusing on subject-verb agreement and reflexive anaphora, we find that certain nouns are systematically understood better than others, an effect which is robust across grammatical tasks and different language models. Surprisingly, we find that across four orders of magnitude, corpus frequency is unrelated to a noun's performance on grammatical tasks. Finally, we find that a novel noun's grammatical properties can be few-shot learned from various types of training data. The results present a paradox: there should be less variation in grammatical performance than is actually observed.
Improved Supervised Training of Physics-Guided Deep Learning Image Reconstruction with Multi-Masking
Authors: Burhaneddin Yaman, Seyed Amir Hossein Hosseini, Steen Moeller, Mehmet Akçakaya
Date: 2020-10-26 00:00:00
Tasks: Image Reconstruction, Rolling Shutter Correction

Physics-guided deep learning (PG-DL) via algorithm unrolling has received significant interest for improved image reconstruction, including MRI applications. These methods unroll an iterative optimization algorithm into a series of regularizer and data consistency units. The unrolled networks are typically trained end-to-end using a supervised approach. Current supervised PG-DL approaches use all of the available sub-sampled measurements in their data consistency units. Thus, the network learns to fit the rest of the measurements. In this study, we propose to improve the performance and robustness of supervised training by utilizing randomness by retrospectively selecting only a subset of all the available measurements for data consistency units. The process is repeated multiple times using different random masks during training for further enhancement. Results on knee MRI show that the proposed multi-mask supervised PG-DL enhances reconstruction performance compared to conventional supervised PG-DL approaches.
Computing Nash Equilibria in Multiplayer DAG-Structured Stochastic Games with Persistent Imperfect Information
Authors: Sam Ganzfried
Date: 2020-10-26 00:00:00

Many important real-world settings contain multiple players interacting over an unknown duration with probabilistic state transitions, and are naturally modeled as stochastic games. Prior research on algorithms for stochastic games has focused on two-player zero-sum games, games with perfect information, and games with imperfect-information that is local and does not extend between game states. We present an algorithm for approximating Nash equilibrium in multiplayer general-sum stochastic games with persistent imperfect information that extends throughout game play. We experiment on a 4-player imperfect-information naval strategic planning scenario. Using a new procedure, we are able to demonstrate that our algorithm computes a strategy that closely approximates Nash equilibrium in this game.
Data Troubles in Sentence Level Confidence Estimation for Machine Translation
Authors: Ciprian Chelba, Junpei Zhou, Yuezhang, Li, Hideto Kazawa, Jeff Klingner, Mengmeng Niu
Date: 2020-10-26 00:00:00
Tasks: Machine Translation, Sentence, Translation

The paper investigates the feasibility of confidence estimation for neural machine translation models operating at the high end of the performance spectrum. As a side product of the data annotation process necessary for building such models we propose sentence level accuracy $SACC$ as a simple, self-explanatory evaluation metric for quality of translation. Experiments on two different annotator pools, one comprised of non-expert (crowd-sourced) and one of expert (professional) translators show that $SACC$ can vary greatly depending on the translation proficiency of the annotators, despite the fact that both pools are about equally reliable according to Krippendorff's alpha metric; the relatively low values of inter-annotator agreement confirm the expectation that sentence-level binary labeling $good$ / $needs\ work$ for translation out of context is very hard. For an English-Spanish translation model operating at $SACC = 0.89$ according to a non-expert annotator pool we can derive a confidence estimate that labels 0.5-0.6 of the $good$ translations in an "in-domain" test set with 0.95 Precision. Switching to an expert annotator pool decreases $SACC$ dramatically: $0.61$ for English-Spanish, measured on the exact same data as above. This forces us to lower the CE model operating point to 0.9 Precision while labeling correctly about 0.20-0.25 of the $good$ translations in the data. We find surprising the extent to which CE depends on the level of proficiency of the annotator pool used for labeling the data. This leads to an important recommendation we wish to make when tackling CE modeling in practice: it is critical to match the end-user expectation for translation quality in the desired domain with the demands of annotators assigning binary quality labels to CE training data.
Multi-Class Zero-Shot Learning for Artistic Material Recognition
Authors: Alexander W Olson, Andreea Cucu, Tom Bock
Date: 2020-10-26 00:00:00
Tasks: Material Recognition, Transfer Learning, Zero-Shot Learning

Zero-Shot Learning (ZSL) is an extreme form of transfer learning, where no labelled examples of the data to be classified are provided during the training stage. Instead, ZSL uses additional information learned about the domain, and relies upon transfer learning algorithms to infer knowledge about the missing instances. ZSL approaches are an attractive solution for sparse datasets. Here we outline a model to identify the materials with which a work of art was created, by learning the relationship between English descriptions of the subject of a piece and its composite materials. After experimenting with a range of hyper-parameters, we produce a model which is capable of correctly identifying the materials used on pieces from an entirely distinct museum dataset. This model returned a classification accuracy of 48.42% on 5,000 artworks taken from the Tate collection, which is distinct from the Rijksmuseum network used to create and train our model.
Enhancing road signs segmentation using photometric invariants
Authors: Tarik Ayaou, Azeddine Beghdadi, Karim Afdel, Abdellah Amghar
Date: 2020-10-26 00:00:00
Tasks: Segmentation

Road signs detection and recognition in natural scenes is one of the most important tasksin the design of Intelligent Transport Systems (ITS). However, illumination changes remain a major problem. In this paper, an efficient ap-proach of road signs segmentation based on photometric invariants is proposed. This method is based on color in-formation using a hybrid distance, by exploiting the chro-matic distance and the red and blue ratio, on l Theta Phi color space which is invariant to highlight, shading and shadow changes. A comparative study is performed to demonstrate the robustness of this approach over the most frequently used methods for road sign segmentation. The experimental results and the detailed analysis show the high performance of the algorithm described in this paper.
Peak Detection On Data Independent Acquisition Mass Spectrometry Data With Semisupervised Convolutional Transformers
Authors: Leon L. Xu, Hannes L. Röst
Date: 2020-10-26 00:00:00
Tasks: image-classification, Image Classification, Time Series, Time Series Analysis

Liquid Chromatography coupled to Mass Spectrometry (LC-MS) based methods are commonly used for high-throughput, quantitative measurements of the proteome (i.e. the set of all proteins in a sample at a given time). Targeted LC-MS produces data in the form of a two-dimensional time series spectrum, with the mass to charge ratio of analytes (m/z) on one axis, and the retention time from the chromatography on the other. The elution of a peptide of interest produces highly specific patterns across multiple fragment ion traces (extracted ion chromatograms, or XICs). In this paper, we formulate this peak detection problem as a multivariate time series segmentation problem, and propose a novel approach based on the Transformer architecture. Here we augment Transformers, which are capable of capturing long distance dependencies with a global view, with Convolutional Neural Networks (CNNs), which can capture local context important to the task at hand, in the form of Transformers with Convolutional Self-Attention. We further train this model in a semisupervised manner by adapting state of the art semisupervised image classification techniques for multi-channel time series data. Experiments on a representative LC-MS dataset are benchmarked using manual annotations to showcase the encouraging performance of our method; it outperforms baseline neural network architectures and is competitive against the current state of the art in automated peak detection.
VisualHints: A Visual-Lingual Environment for Multimodal Reinforcement Learning
Authors: Thomas Carta, Subhajit Chaudhury, Kartik Talamadupula, Michiaki Tatsubori
Date: 2020-10-26 00:00:00
Tasks: Atari Games, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL), text-based games

We present VisualHints, a novel environment for multimodal reinforcement learning (RL) involving text-based interactions along with visual hints (obtained from the environment). Real-life problems often demand that agents interact with the environment using both natural language information and visual perception towards solving a goal. However, most traditional RL environments either solve pure vision-based tasks like Atari games or video-based robotic manipulation; or entirely use natural language as a mode of interaction, like Text-based games and dialog systems. In this work, we aim to bridge this gap and unify these two approaches in a single environment for multimodal RL. We introduce an extension of the TextWorld cooking environment with the addition of visual clues interspersed throughout the environment. The goal is to force an RL agent to use both text and visual features to predict natural language action commands for solving the final task of cooking a meal. We enable variations and difficulties in our environment to emulate various interactive real-world scenarios. We present a baseline multimodal agent for solving such problems using CNN-based feature extraction from visual hints and LSTMs for textual feature extraction. We believe that our proposed visual-lingual environment will facilitate novel problem settings for the RL community.