pwc-archive/papers-with-abstracts huggingface dataset:
ALBRT: Cellular Composition Prediction in Routine Histology Images
Authors: Muhammad Dawood, Kim Branson, Nasir M. Rajpoot, Fayyaz ul Amir Afsar Minhas
Date: 2021-08-18 00:00:00
Tasks: Contrastive Learning, Prediction, Survival Analysis

Cellular composition prediction, i.e., predicting the presence and counts of different types of cells in the tumor microenvironment from a digitized image of a Hematoxylin and Eosin (H&E) stained tissue section can be used for various tasks in computational pathology such as the analysis of cellular topology and interactions, subtype prediction, survival analysis, etc. In this work, we propose an image-based cellular composition predictor (ALBRT) which can accurately predict the presence and counts of different types of cells in a given image patch. ALBRT, by its contrastive-learning inspired design, learns a compact and rotation-invariant feature representation that is then used for cellular composition prediction of different cell types. It offers significant improvement over existing state-of-the-art approaches for cell classification and counting. The patch-level feature representation learned by ALBRT is transferrable for cellular composition analysis over novel datasets and can also be utilized for downstream prediction tasks in CPath as well. The code and the inference webserver for the proposed method are available at the URL: https://github.com/engrodawood/ALBRT.
Denoising ECG by Adaptive Filter with Empirical Mode Decomposition
Authors: Bingze Dai, Wen Bai
Date: 2021-08-18 00:00:00
Tasks: Denoising

Electrocardiogram (ECG) signal is an important physiological signal which contains cardiac information and is the basis to diagnosis cardiac related diseases. In this paper, several innovative and efficient methods based on adaptive filter and empirical mode decomposition (EMD) to denoise ECG signal contaminated by various kinds of noise, including baseline wander (BW), power line interference (PLI), electrode motion artifact (EM) and muscle artifact (MA), are proposed. We first present a novel method based on EMD and adaptive filter for the removal of BW and PLI in ECG signal. We then extend the method to the complex scenario where four most common noises, PLI, BW, EM and MA are present. The proposed Parallel EMD adaptive filter structure yields the best SNR improvement on the MIT-BIH arrhythmia database, corrupted by the four types of noises.
Designing drug regimens that mitigate nonadherence
Authors: Elijah D Counterman, Sean D Lawley
Date: 2021-08-18 00:00:00
Tasks: Ethics

Medication adherence is a well-known problem for pharmaceutical treatment of chronic diseases. Understanding how nonadherence affects treatment efficacy is made difficult by the ethics of clinical trials that force patients to skip doses of the medication being tested, the unpredictable timing of missed doses by actual patients, and the many competing variables that can either mitigate or magnify the deleterious effects of nonadherence, such as pharmacokinetic absorption and elimination rates, dosing intervals, dose sizes, adherence rates, etc. In this paper, we formulate and analyze a mathematical model of the drug concentration in an imperfectly adherent patient. Our model takes the form of the standard single compartment pharmacokinetic model with first order absorption and elimination, except that the patient takes medication only at a given proportion of the prescribed dosing times. Doses are missed randomly, and we use stochastic analysis to study the resulting random drug level in the body. We then use our mathematical results to propose principles for designing drug regimens that are robust to nonadherence. In particular, we quantify the resilience of extended release drugs to nonadherence, which is quite significant in some circumstances, and we show the benefit of taking a double dose following a missed dose if the drug absorption or elimination rate is slow compared to the dosing interval. We further use our results to compare some antiepileptic and antipsychotic drug regimens.
Music to My Ears: Neural modularity and flexibility differ in response to real-world music stimuli
Authors: Melia E. Bonomo, Anthony K. Brandt, J. Todd Frazier, Christof Karmonik
Date: 2020-10-08 00:00:00

Music listening involves many simultaneous neural operations, including auditory processing, working memory, temporal sequencing, pitch tracking, anticipation, reward, and emotion, and thus, a full investigation of music cognition would benefit from whole-brain analyses. Here, we quantify whole-brain activity while participants listen to a variety of music and speech auditory pieces using two network measures that are grounded in complex systems theory: modularity, which measures the degree to which brain regions are interacting in communities, and flexibility, which measures the rate that brain regions switch the communities to which they belong. In a music and brain connectivity study that is part of a larger clinical investigation into music listening and stroke recovery, fMRI was performed on healthy participants while they listened to self-selected music to which they felt a positive emotional attachment, as well as culturally familiar music (J.S. Bach), culturally unfamiliar music (Gagaku court music of medieval Japan), and several excerpts of speech. There was a marked contrast among the whole-brain networks during the different types of auditory pieces, in particular for the unfamiliar music. During the self-selected and Bach tracks, participants' whole-brain networks exhibited modular organization that was significantly coordinated with the network flexibility. Meanwhile, when the Gagaku music was played, this relationship between brain network modularity and flexibility largely disappeared. In addition, while the auditory cortex's flexibility during the self-selected piece was equivalent to that during Bach, it was more flexible during Gagaku. The results suggest that the modularity and flexibility measures of whole-brain activity have the potential to lead to new insights into the complex neural function that occurs during music perception of real-world songs.
IT2CFNN: An Interval Type-2 Correlation-Aware Fuzzy Neural Network to Construct Non-Separable Fuzzy Rules with Uncertain and Adaptive Shapes for Nonlinear Function Approximation
Authors: Armin Salimi-Badr
Date: 2021-08-11 00:00:00
Tasks: Time Series, Time Series Analysis, Vocal Bursts Type Prediction

In this paper, a new interval type-2 fuzzy neural network able to construct non-separable fuzzy rules with adaptive shapes is introduced. To reflect the uncertainty, the shape of fuzzy sets considered to be uncertain. Therefore, a new form of interval type-2 fuzzy sets based on a general Gaussian model able to construct different shapes (including triangular, bell-shaped, trapezoidal) is proposed. To consider the interactions among input variables, input vectors are transformed to new feature spaces with uncorrelated variables proper for defining each fuzzy rule. Next, the new features are fed to a fuzzification layer using proposed interval type-2 fuzzy sets with adaptive shape. Consequently, interval type-2 non-separable fuzzy rules with proper shapes, considering the local interactions of variables and the uncertainty are formed. For type reduction the contribution of the upper and lower firing strengths of each fuzzy rule are adaptively selected separately. To train different parameters of the network, the Levenberg-Marquadt optimization method is utilized. The performance of the proposed method is investigated on clean and noisy datasets to show the ability to consider the uncertainty. Moreover, the proposed paradigm, is successfully applied to real-world time-series predictions, regression problems, and nonlinear system identification. According to the experimental results, the performance of our proposed model outperforms other methods with a more parsimonious structure.
Attribute-based Explanations of Non-Linear Embeddings of High-Dimensional Data
Authors: Jan-Tobias Sohns, Michaela Schmitt, Fabian Jirasek, Hans Hasse, Heike Leitte
Date: 2021-07-28 00:00:00
Tasks: Attribute, Matrix Completion, Vocal Bursts Intensity Prediction

Embeddings of high-dimensional data are widely used to explore data, to verify analysis results, and to communicate information. Their explanation, in particular with respect to the input attributes, is often difficult. With linear projects like PCA the axes can still be annotated meaningfully. With non-linear projections this is no longer possible and alternative strategies such as attribute-based color coding are required. In this paper, we review existing augmentation techniques and discuss their limitations. We present the Non-Linear Embeddings Surveyor (NoLiES) that combines a novel augmentation strategy for projected data (rangesets) with interactive analysis in a small multiples setting. Rangesets use a set-based visualization approach for binned attribute values that enable the user to quickly observe structure and detect outliers. We detail the link between algebraic topology and rangesets and demonstrate the utility of NoLiES in case studies with various challenges (complex attribute value distribution, many attributes, many data points) and a real-world application to understand latent features of matrix completion in thermodynamics.
GSVMA: A Genetic-Support Vector Machine-Anova method for CAD diagnosis based on Z-Alizadeh Sani dataset
Authors: Javad Hassannataj Joloudari, Faezeh Azizi, Mohammad Ali Nematollahi, Roohallah Alizadehsani, Edris Hassannataj, Amir Mosavi
Date: 2021-07-23 00:00:00
Tasks: BIG-bench Machine Learning, Hybrid Machine Learning

Coronary heart disease (CAD) is one of the crucial reasons for cardiovascular mortality in middle-aged people worldwide. The most typical tool is angiography for diagnosing CAD. The challenges of CAD diagnosis using angiography are costly and have side effects. One of the alternative solutions is the use of machine learning-based patterns for CAD diagnosis. Hence, this paper provides a new hybrid machine learning model called Genetic Support Vector Machine and Analysis of Variance (GSVMA). The ANOVA is known as the kernel function for SVM. The proposed model is performed based on the Z-Alizadeh Sani dataset. A genetic optimization algorithm is used to select crucial features. In addition, SVM with Anova, Linear SVM, and LibSVM with radial basis function methods were applied to classify the dataset. As a result, the GSVMA hybrid method performs better than other methods. This proposed method has the highest accuracy of 89.45% through a 10-fold cross-validation technique with 35 selected features on the Z-Alizadeh Sani dataset. Therefore, the genetic optimization algorithm is very effective for improving accuracy. The computer-aided GSVMA method can be helped clinicians with CAD diagnosis.
Automatic differentiation as a tool in engineering design
Authors: J. -F. M. Barthelemy, L. E. Hall
Date: 1995-04-01 00:00:00
Proceeding: Springer 1995 4
Tasks: Sensitivity

Automatic Differentiation (AD) is a tool that systematically implements the chain rule of differentiation to obtain the derivatives of functions calculated by computer programs. In this paper, it is assessed as a tool for engineering design. The paper discusses the forward and reverse modes of AD, their computing requirements, as well as approaches to implementing AD. It continues with the application of two different tools to two medium-size structural analysis problems to generate sensitivity information typically necessary in an optimization or design situation. The paper concludes with the observation that AD is to be preferred to finite differencing in most cases, as long as sufficient computer storage is available; in some instances, AD may be the alternative to consider in lieu of analytical sensitivity analysis.
Trees with Attention for Set Prediction Tasks
Authors: Roy Hirsch, Ran Gilad-Bachrach
Date: 2021-07-01 00:00:00
Proceeding: International Conference on Machine Learning 2021 7
Tasks: BIG-bench Machine Learning, Interpretable Machine Learning, Prediction

In many machine learning applications, each record represents a set of items. For example, when making predictions from medical records, the medications prescribed to a patient are a set whose size is not fixed and whose order is arbitrary. However, most machine learning algorithms are not designed to handle set structures and are limited to processing records of fixed size. Set-Tree, presented in this work, extends the support for sets to tree-based models, such as Random-Forest and Gradient-Boosting, by introducing an attention mechanism and set-compatible split criteria. We evaluate the new method empirically on a wide range of problems ranging from making predictions on sub-atomic particle jets to estimating the redshift of galaxies. The new method outperforms existing tree-based methods consistently and significantly. Moreover, it is competitive and often outperforms Deep Learning. We also discuss the theoretical properties of Set-Trees and explain how they enable item-level explainability.
Attribute-Based Classification for Zero-Shot Visual Object Categorization
Authors: Christoph H. Lampert, Hannes Nickisch, Stefan Harmeling
Date: 2013-07-30 00:00:00
Proceeding: IEEE Transactions on Pattern Analysis and Machine Intelligence 2013 7
Tasks: Attribute, Classification, Object, Object Categorization, Object Recognition, Zero-Shot Learning

We study the problem of object recognition for categories for which we have no training examples, a task also called
zero-data or zero-shot learning. This situation has hardly been studied in computer vision research, even though it occurs frequently;
the world contains tens of thousands of different object classes, and image collections have been formed and suitably annotated for
only a few of them. To tackle the problem, we introduce attribute-based classification: Objects are identified based on a high-level
description that is phrased in terms of semantic attributes, such as the object’s color or shape. Because the identification of each such
property transcends the specific learning task at hand, the attribute classifiers can be prelearned independently, for example, from
existing image data sets unrelated to the current task. Afterward, new classes can be detected based on their attribute representation,
without the need for a new training phase. In this paper, we also introduce a new data set, Animals with Attributes, of over 30,000
images of 50 animal classes, annotated with 85 semantic attributes. Extensive experiments on this and two more data sets show that
attribute-based classification indeed is able to categorize images without access to any training images of the target classes.
Efficient Online Estimation of Causal Effects by Deciding What to Observe
Authors: Shantanu Gupta, Zachary C. Lipton, David Childers
Date: 2021-08-20 00:00:00
Proceeding: NeurIPS 2021 12

Researchers often face data fusion problems, where multiple data sources are available, each capturing a distinct subset of variables. While problem formulations typically take the data as given, in practice, data acquisition can be an ongoing process. In this paper, we aim to estimate any functional of a probabilistic model (e.g., a causal effect) as efficiently as possible, by deciding, at each time, which data source to query. We propose online moment selection (OMS), a framework in which structural assumptions are encoded as moment conditions. The optimal action at each step depends, in part, on the very moments that identify the functional of interest. Our algorithms balance exploration with choosing the best action as suggested by current estimates of the moments. We propose two selection strategies: (1) explore-then-commit (OMS-ETC) and (2) explore-then-greedy (OMS-ETG), proving that both achieve zero asymptotic regret as assessed by MSE. We instantiate our setup for average treatment effect estimation, where structural assumptions are given by a causal graph and data sources may include subsets of mediators, confounders, and instrumental variables.
Uniformity Testing in the Shuffle Model: Simpler, Better, Faster
Authors: Clément L. Canonne, Hongyi Lyu
Date: 2021-08-20 00:00:00

Uniformity testing, or testing whether independent observations are uniformly distributed, is the prototypical question in distribution testing. Over the past years, a line of work has been focusing on uniformity testing under privacy constraints on the data, and obtained private and data-efficient algorithms under various privacy models such as central differential privacy (DP), local privacy (LDP), pan-privacy, and, very recently, the shuffle model of differential privacy. In this work, we considerably simplify the analysis of the known uniformity testing algorithm in the shuffle model, and, using a recent result on "privacy amplification via shuffling," provide an alternative algorithm attaining the same guarantees with an elementary and streamlined argument.
Multi-functional microwave photonic radar system for simultaneous distance and velocity measurement and high-resolution microwave imaging
Authors: Dingding Liang, Lizhong Jiang, Yang Chen
Date: 2021-05-27 00:00:00

A photonic-assisted multi-functional radar system for simultaneous distance and velocity measurement and high-resolution microwave imaging is proposed and experimentally demonstrated by using a composite transmitted microwave signal of a single-chirped linearly frequency-modulated (LFM) signal and a single-tone microwave signal. In the system, the transmitted signal is generated via photonic frequency up-conversion based on a single integrated dual-polarization dual-parallel Mach-Zehnder modulator (DPol-DPMZM), whereas the echo signals scattered from the target are de-chirped to two low-frequency signals using a microwave photonic frequency mixer. By using the two low-frequency de-chirped signals, the real-time distance and radial velocity of the moving target can be measured accurately according to the round-trip time of the echo signal and its Doppler frequency shift. Compared with the previous reported distance and velocity measurement methods, where two LFM signals with opposite chirps are used, these parameters can be obtained using only a single-chirped LFM signal and a single-tone microwave signal. Meanwhile, high-resolution inverse synthetic aperture radar (ISAR) imaging can also be realized using ISAR imaging algorithms. An experiment is performed to verify the proposed multi-functional microwave photonic radar system. An up-chirped LFM signal from 8.5 to 12.5 GHz and an 8.0 GHz single-tone microwave signal are used as the transmitted signal. The results show that the absolute measurement errors of distance and radial velocity are less than 5.9 cm and 2.8 cm/s, respectively. ISAR imaging results are also demonstrated, which proves the high-resolution and real-time ISAR imaging ability of the proposed system.
Structure-Preserving Deraining with Residue Channel Prior Guidance
Authors: Qiaosi Yi, Juncheng Li, Qinyan Dai, Faming Fang, Guixu Zhang, Tieyong Zeng
Date: 2021-08-20 00:00:00
Proceeding: ICCV 2021 10
Tasks: Rain Removal, Single Image Deraining

Single image deraining is important for many high-level computer vision tasks since the rain streaks can severely degrade the visibility of images, thereby affecting the recognition and analysis of the image. Recently, many CNN-based methods have been proposed for rain removal. Although these methods can remove part of the rain streaks, it is difficult for them to adapt to real-world scenarios and restore high-quality rain-free images with clear and accurate structures. To solve this problem, we propose a Structure-Preserving Deraining Network (SPDNet) with RCP guidance. SPDNet directly generates high-quality rain-free images with clear and accurate structures under the guidance of RCP but does not rely on any rain-generating assumptions. Specifically, we found that the RCP of images contains more accurate structural information than rainy images. Therefore, we introduced it to our deraining network to protect structure information of the rain-free image. Meanwhile, a Wavelet-based Multi-Level Module (WMLM) is proposed as the backbone for learning the background information of rainy images and an Interactive Fusion Module (IFM) is designed to make full use of RCP information. In addition, an iterative guidance strategy is proposed to gradually improve the accuracy of RCP, refining the result in a progressive path. Extensive experimental results on both synthetic and real-world datasets demonstrate that the proposed model achieves new state-of-the-art results. Code: https://github.com/Joyies/SPDNet
Asleep at the Keyboard? Assessing the Security of GitHub Copilot's Code Contributions
Authors: Hammond Pearce, Baleegh Ahmad, Benjamin Tan, Brendan Dolan-Gavitt, Ramesh Karri
Date: 2021-08-20 00:00:00
Tasks: Code Generation, Diversity, Language Modeling, Language Modelling

There is burgeoning interest in designing AI-based systems to assist humans in designing computing systems, including tools that automatically generate computer code. The most notable of these comes in the form of the first self-described `AI pair programmer', GitHub Copilot, a language model trained over open-source GitHub code. However, code often contains bugs - and so, given the vast quantity of unvetted code that Copilot has processed, it is certain that the language model will have learned from exploitable, buggy code. This raises concerns on the security of Copilot's code contributions. In this work, we systematically investigate the prevalence and conditions that can cause GitHub Copilot to recommend insecure code. To perform this analysis we prompt Copilot to generate code in scenarios relevant to high-risk CWEs (e.g. those from MITRE's "Top 25" list). We explore Copilot's performance on three distinct code generation axes -- examining how it performs given diversity of weaknesses, diversity of prompts, and diversity of domains. In total, we produce 89 different scenarios for Copilot to complete, producing 1,689 programs. Of these, we found approximately 40% to be vulnerable.
Open Relation Modeling: Learning to Define Relations between Entities
Authors: Jie Huang, Kevin Chen-Chuan Chang, JinJun Xiong, Wen-mei Hwu
Date: 2021-08-20 00:00:00
Proceeding: Findings (ACL) 2022 5
Tasks: Open Relation Modeling, Relation, Sentence

Relations between entities can be represented by different instances, e.g., a sentence containing both entities or a fact in a Knowledge Graph (KG). However, these instances may not well capture the general relations between entities, may be difficult to understand by humans, even may not be found due to the incompleteness of the knowledge source. In this paper, we introduce the Open Relation Modeling problem - given two entities, generate a coherent sentence describing the relation between them. To solve this problem, we propose to teach machines to generate definition-like relation descriptions by letting them learn from defining entities. Specifically, we fine-tune Pre-trained Language Models (PLMs) to produce definitions conditioned on extracted entity pairs. To help PLMs reason between entities and provide additional relational knowledge to PLMs for open relation modeling, we incorporate reasoning paths in KGs and include a reasoning path selection mechanism. Experimental results show that our model can generate concise but informative relation descriptions that capture the representative characteristics of entities.