OpenRaiser/Intern-Atlas huggingface dataset:
Evaluating Biomedical BERT Models for Vocabulary Alignment at Scale in the UMLS Metathesaurus
Venue: arXiv cs.CL 2021
Year: 2021

The current UMLS (Unified Medical Language System) Metathesaurus construction process for integrating over 200 biomedical source vocabularies is expensive and error-prone as it relies on the lexical algorithms and human editors for deciding if the two biomedical terms are synonymous. Recent advances in Natural Language Processing such as Transformer models like BERT and its biomedical variants with contextualized word embeddings have achieved state-of-the-art (SOTA) performance on downstream tasks. We aim to validate if these approaches using the BERT models can actually outperform the existing approaches for predicting synonymy in the UMLS Metathesaurus. In the existing Siamese Networks with LSTM and BioWordVec embeddings, we replace the BioWordVec embeddings with the biomedical BERT embeddings extracted from each BERT model using different ways of extraction. In the Transformer architecture, we evaluate the use of the different biomedical BERT models that have been pre-trained using different datasets and tasks. Given the SOTA performance of these BERT models for other downstream tasks, our experiments yield surprisingly interesting results: (1) in both model architectures, the approaches employing these biomedical BERT-based models do not outperform the existing approaches using Siamese Network with BioWordVec embeddings for the UMLS synonymy prediction task, (2) the original BioBERT large model that has not been pre-trained with the UMLS outperforms the SapBERT models that have been pre-trained with the UMLS, and (3) using the Siamese Networks yields better performance for synonymy prediction when compared to using the biomedical BERT models.
A taxonomy of strategic human interactions in traffic conflicts
Venue: arXiv cs.AI 2021
Year: 2021

In order to enable autonomous vehicles (AV) to navigate busy traffic situations, in recent years there has been a focus on game-theoretic models for strategic behavior planning in AVs. However, a lack of common taxonomy impedes a broader understanding of the strategies the models generate as well as the development of safety specification to identity what strategies are safe for an AV to execute. Based on common patterns of interaction in traffic conflicts, we develop a taxonomy for strategic interactions along the dimensions of agents' initial response to right-of-way rules and subsequent response to other agents' behavior. Furthermore, we demonstrate a process of automatic mapping of strategies generated by a strategic planner to the categories in the taxonomy, and based on vehicle-vehicle and vehicle-pedestrian interaction simulation, we evaluate two popular solution concepts used in strategic planning in AVs, QLk and Subgame perfect $ε$-Nash Equilibrium, with respect to those categories.
Automated Estimation of Construction Equipment Emission using Inertial Sensors and Machine Learning Models
Venue: arXiv cs.LG 2021
Year: 2021

The construction industry is one of the main producers of greenhouse gasses (GHG). Quantifying the amount of air pollutants including GHG emissions during a construction project has become an additional project objective to traditional metrics such as time, cost, and safety in many parts of the world. A major contributor to air pollution during construction is the use of heavy equipment and thus their efficient operation and management can substantially reduce the harm to the environment. Although the on-road vehicle emission prediction is a widely researched topic, construction equipment emission measurement and reduction have received very little attention. This paper describes the development and deployment of a novel framework that uses machine learning (ML) methods to predict the level of emissions from heavy construction equipment monitored via an Internet of Things (IoT) system comprised of accelerometer and gyroscope sensors. The developed framework was validated using an excavator performing real-world construction work. A portable emission measurement system (PEMS) was employed along with the inertial sensors to record data including the amount of CO, NOX, CO2, SO2, and CH4 pollutions emitted by the equipment. Different ML algorithms were developed and compared to identify the best model to predict emission levels from inertial sensors data. The results showed that Random Forest with the coefficient of determination (R2) of 0.94, 0.91 and 0.94 for CO, NOX, CO2, respectively was the best algorithm among different models evaluated in this study.
Discriminative Attribution from Counterfactuals
Venue: arXiv cs.LG 2021
Year: 2021

We present a method for neural network interpretability by combining feature attribution with counterfactual explanations to generate attribution maps that highlight the most discriminative features between pairs of classes. We show that this method can be used to quantitatively evaluate the performance of feature attribution methods in an objective manner, thus preventing potential observer bias. We evaluate the proposed method on three diverse datasets, including a challenging artificial dataset and real-world biological data. We show quantitatively and qualitatively that the highlighted features are substantially more discriminative than those extracted using conventional attribution methods and argue that this type of explanation is better suited for understanding fine grained class differences as learned by a deep neural network.
Extended Irreducible Binary Sextic Goppa codes
Venue: arXiv cs.IT 2021
Year: 2021

Let $n (>3)$ be a prime number and $\Bbb F_{2^n}$ a finite field of $2^n$ elements. Let $L =\Bbb F_{2^n}\cup \{\infty\}$ be the support set and $g(x)$ an irreducible polynomial of degree $6$ over $\Bbb F_{2^n}$. In this paper, we obtain an upper bound on the number of extended irreducible binary Goppa codes $Γ(L, g)$ of degree $6$ and length $2^n+1$.
Evaluation of Deep Neural Network Domain Adaptation Techniques for Image Recognition
Venue: arXiv cs.CV 2021
Year: 2021

It has been well proved that deep networks are efficient at extracting features from a given (source) labeled dataset. However, it is not always the case that they can generalize well to other (target) datasets which very often have a different underlying distribution. In this report, we evaluate four different domain adaptation techniques for image classification tasks: DeepCORAL, DeepDomainConfusion, CDAN and CDAN+E. These techniques are unsupervised given that the target dataset dopes not carry any labels during training phase. We evaluate model performance on the office-31 dataset. A link to the github repository of this report can be found here: https://github.com/agrija9/Deep-Unsupervised-Domain-Adaptation.
An Adaptive Deep Learning Framework for Day-ahead Forecasting of Photovoltaic Power Generation
Venue: arXiv cs.LG 2021
Year: 2021

Accurate forecasts of photovoltaic power generation (PVPG) are essential to optimize operations between energy supply and demand. Recently, the propagation of sensors and smart meters has produced an enormous volume of data, which supports the development of data based PVPG forecasting. Although emerging deep learning (DL) models, such as the long short-term memory (LSTM) model, based on historical data, have provided effective solutions for PVPG forecasting with great successes, these models utilize offline learning. As a result, DL models cannot take advantage of the opportunity to learn from newly-arrived data, and are unable to handle concept drift caused by installing extra PV units and unforeseen PV unit failures. Consequently, to improve day-ahead PVPG forecasting accuracy, as well as eliminate the impacts of concept drift, this paper proposes an adaptive LSTM (AD-LSTM) model, which is a DL framework that can not only acquire general knowledge from historical data, but also dynamically learn specific knowledge from newly-arrived data. A two-phase adaptive learning strategy (TP-ALS) is integrated into AD-LSTM, and a sliding window (SDWIN) algorithm is proposed, to detect concept drift in PV systems. Multiple datasets from PV systems are utilized to assess the feasibility and effectiveness of the proposed approaches. The developed AD-LSTM model demonstrates greater forecasting capability than the offline LSTM model, particularly in the presence of concept drift. Additionally, the proposed AD-LSTM model also achieves superior performance in terms of day-ahead PVPG forecasting compared to other traditional machine learning models and statistical models in the literature.
CateCom: a practical data-centric approach to categorization of computational models
Venue: arXiv cs.DB 2021
Year: 2021

The advent of data-driven science in the 21st century brought about the need for well-organized structured data and associated infrastructure able to facilitate the applications of Artificial Intelligence and Machine Learning. We present an effort aimed at organizing the diverse landscape of physics-based and data-driven computational models in order to facilitate the storage of associated information as structured data. We apply object-oriented design concepts and outline the foundations of an open-source collaborative framework that is: (1) capable of uniquely describing the approaches in structured data, (2) flexible enough to cover the majority of widely used models, and (3) utilizes collective intelligence through community contributions. We present example database schemas and corresponding data structures and explain how these are deployed in software at the time of this writing.
Deep Reinforcement Learning with Adjustments
Venue: arXiv cs.LG 2021
Year: 2021

Deep reinforcement learning (RL) algorithms can learn complex policies to optimize agent operation over time. RL algorithms have shown promising results in solving complicated problems in recent years. However, their application on real-world physical systems remains limited. Despite the advancements in RL algorithms, the industries often prefer traditional control strategies. Traditional methods are simple, computationally efficient and easy to adjust. In this paper, we first propose a new Q-learning algorithm for continuous action space, which can bridge the control and RL algorithms and bring us the best of both worlds. Our method can learn complex policies to achieve long-term goals and at the same time it can be easily adjusted to address short-term requirements without retraining. Next, we present an approximation of our algorithm which can be applied to address short-term requirements of any pre-trained RL algorithm. The case studies demonstrate that both our proposed method as well as its practical approximation can achieve short-term and long-term goals without complex reward functions.
Dynamics in Coded Edge Computing for IoT: A Fractional Evolutionary Game Approach
Venue: arXiv cs.DC 2021
Year: 2021

Recently, coded distributed computing (CDC), with advantages in intensive computation and reduced latency, has attracted a lot of research interest for edge computing, in particular, IoT applications, including IoT data pre-processing and data analytics. Nevertheless, it can be challenging for edge infrastructure providers (EIPs) with limited edge resources to support IoT applications performed in a CDC approach in edge networks, given the additional computational resources required by CDC. In this paper, we propose coded edge federation, in which different EIPs collaboratively provide edge resources for CDC tasks. To study the Nash equilibrium, when no EIP has an incentive to unilaterally alter its decision on edge resource allocation, we model the coded edge federation based on evolutionary game theory. Since the replicator dynamics of the classical evolutionary game are unable to model economic-aware EIPs which memorize past decisions and utilities, we propose fractional replicator dynamics with a power-law fading memory via Caputo fractional derivatives. The proposed dynamics allow us to study a broad spectrum of EIP dynamic behaviors, such as EIP sensitivity and aggressiveness in strategy adaptation, which classical replicator dynamics cannot capture. Theoretical analysis and extensive numerical results justify the existence, uniqueness, and stability of the equilibrium in the fractional evolutionary game. The influence of the content and the length of the memory on the rate of convergence is also investigated.
Learning Ideological Embeddings from Information Cascades
Venue: arXiv cs.SI 2021
Year: 2021

Modeling information cascades in a social network through the lenses of the ideological leaning of its users can help understanding phenomena such as misinformation propagation and confirmation bias, and devising techniques for mitigating their toxic effects. In this paper we propose a stochastic model to learn the ideological leaning of each user in a multidimensional ideological space, by analyzing the way politically salient content propagates. In particular, our model assumes that information propagates from one user to another if both users are interested in the topic and ideologically aligned with each other. To infer the parameters of our model, we devise a gradient-based optimization procedure maximizing the likelihood of an observed set of information cascades. Our experiments on real-world political discussions on Twitter and Reddit confirm that our model is able to learn the political stance of the social media users in a multidimensional ideological space.
Efficient Global-Local Memory for Real-time Instrument Segmentation of Robotic Surgical Video
Venue: arXiv cs.CV 2021
Year: 2021

Performing a real-time and accurate instrument segmentation from videos is of great significance for improving the performance of robotic-assisted surgery. We identify two important clues for surgical instrument perception, including local temporal dependency from adjacent frames and global semantic correlation in long-range duration. However, most existing works perform segmentation purely using visual cues in a single frame. Optical flow is just used to model the motion between only two frames and brings heavy computational cost. We propose a novel dual-memory network (DMNet) to wisely relate both global and local spatio-temporal knowledge to augment the current features, boosting the segmentation performance and retaining the real-time prediction capability. We propose, on the one hand, an efficient local memory by taking the complementary advantages of convolutional LSTM and non-local mechanisms towards the relating reception field. On the other hand, we develop an active global memory to gather the global semantic correlation in long temporal range to current one, in which we gather the most informative frames derived from model uncertainty and frame similarity. We have extensively validated our method on two public benchmark surgical video datasets. Experimental results demonstrate that our method largely outperforms the state-of-the-art works on segmentation accuracy while maintaining a real-time speed.
Understanding Working from Home Practical Changes and Adaptations During the COVID-19 Pandemic
Venue: arXiv cs.CY 2021
Year: 2021

While much work focuses on the impacts of the pandemic on people's psychological and physical health, it is still unclear about the practical changes and adaptations. In this work, we interviewed 46 participants who were forced to work from home. Results show that there is an increased reliance on asynchronous communication, which slowed communication efficiency and decreased initiative to communicate. The home environment causes distraction from households and lacked facilities but is embraced by a group of people. Many people had to passively adapt to the communication and environmental changes and accept the limitations of technology, a situation that is not sustainable in the long run. We pointed out how technology can potentially play a larger role in supporting communication and coping with environmental changes in the future.
Clustering to the Fewest Clusters Under Intra-Cluster Dissimilarity Constraints
Venue: arXiv cs.LG 2021
Year: 2021

This paper introduces the equiwide clustering problem, where valid partitions must satisfy intra-cluster dissimilarity constraints. Unlike most existing clustering algorithms, equiwide clustering relies neither on density nor on a predefined number of expected classes, but on a dissimilarity threshold. Its main goal is to ensure an upper bound on the error induced by ultimately replacing any object with its cluster representative. Under this constraint, we then primarily focus on minimizing the number of clusters, along with potential sub-objectives. We argue that equiwide clustering is a sound clustering problem, and discuss its relationship with other optimization problems, existing and novel implementations as well as approximation strategies. We review and evaluate suitable clustering algorithms to identify trade-offs between the various practical solutions for this clustering problem.
Fail-Safe Human Detection for Drones Using a Multi-Modal Curriculum Learning Approach
Venue: arXiv cs.CV 2021
Year: 2021

Drones are currently being explored for safety-critical applications where human agents are expected to evolve in their vicinity. In such applications, robust people avoidance must be provided by fusing a number of sensing modalities in order to avoid collisions. Currently however, people detection systems used on drones are solely based on standard cameras besides an emerging number of works discussing the fusion of imaging and event-based cameras. On the other hand, radar-based systems provide up-most robustness towards environmental conditions but do not provide complete information on their own and have mainly been investigated in automotive contexts, not for drones. In order to enable the fusion of radars with both event-based and standard cameras, we present KUL-UAVSAFE, a first-of-its-kind dataset for the study of safety-critical people detection by drones. In addition, we propose a baseline CNN architecture with cross-fusion highways and introduce a curriculum learning strategy for multi-modal data termed SAUL, which greatly enhances the robustness of the system towards hard RGB failures and provides a significant gain of 15% in peak F1 score compared to the use of BlackIn, previously proposed for cross-fusion networks. We demonstrate the real-time performance and feasibility of the approach by implementing the system in an edge-computing unit. We release our dataset and additional material in the project home page.
Three New Infinite Families of Optimal Locally Repairable Codes from Matrix-Product Codes
Venue: arXiv cs.IT 2021
Year: 2021

Locally repairable codes have become a key instrument in large-scale distributed storage systems. This paper focuses on the construction of locally repairable codes with $(r,δ)$-locality that achieve the equality in the Singleton-type bound. We use matrix-product codes to propose two infinite families of $q$-ary optimal $(r,δ)$ locally repairable codes of lengths up to $q^2+q$. The ingredients in the matrix-product codes are either linear maximum distance separable codes or optimal locally repairable codes of small lengths. Further analysis and refinement yield a construction of another infinite family of optimal $(r,δ)$ locally repairable codes. The codes in this third family have unbounded lengths not divisible by $(r+δ-1)$. The three families of optimal $(r,δ)$ locally repairable codes constructed here are new. Previously constructed codes in the literature have not covered the same sets of parameters. Our construction proposals are flexible since one can easily vary $r$ and $δ$ to come up with particular parameters that can suit numerous scenarios.
Common Artifacts in Volume Rendering
Venue: arXiv cs.GR 2021
Year: 2021

Direct Volume Rendering is a popular and powerful visualization method for voxel data and other volumetric scalar data sets. Particularly, in medical applications volume rendering is very commonly used, and has become one of the state of the art methods for 3D visualization of medical data. In this article, some of the most common artifacts encountered will be discussed, and their possible remedies.
Deep Generative Modeling for Protein Design
Venue: arXiv cs.LG 2021
Year: 2021

Deep learning approaches have produced substantial breakthroughs in fields such as image classification and natural language processing and are making rapid inroads in the area of protein design. Many generative models of proteins have been developed that encompass all known protein sequences, model specific protein families, or extrapolate the dynamics of individual proteins. Those generative models can learn protein representations that are often more informative of protein structure and function than hand-engineered features. Furthermore, they can be used to quickly propose millions of novel proteins that resemble the native counterparts in terms of expression level, stability, or other attributes. The protein design process can further be guided by discriminative oracles to select candidates with the highest probability of having the desired properties. In this review, we discuss five classes of generative models that have been most successful at modeling proteins and provide a framework for model guided protein design.
To VR or not to VR: Is virtual reality suitable to understand software development metrics?
Venue: arXiv cs.SE 2021
Year: 2021

Background/Context: Currently, the usual interface for visualizing data is based on 2-D screens. Recently, devices capable of visualizing data while immersed in VR scenes are becoming common. However, it has not been studied in detail to which extent these devices are suitable for interacting with data visualizations in the specific case of data about software development. Objective/Aim: In this registered report, we propose to answer the following question: "Is comprehension of software development processes, via the visualization of their metrics, better when presented in VR scenes than in 2D screens?" In particular, we will study if answers obtained after interacting with visualizations presented as VR scenes are more or less correct than those obtained from traditional screens, and if it takes more or less time to produce those answers. Method: We will run an experiment with volunteer subjects from several backgrounds. We will have two setups: an on-screen application, and a VR scene. Both will be designed to be as much equivalent as possible in terms of the information they provide. For the former, we use a commercial-grade set of \kibana-based interactive dashboards that stakeholders currently use to get insights. For the latter, we use a set of visualizations similar to those in the on-screen case, prepared to provide the same set of data using the museum metaphor in a VR room. The field of analysis will be related to modern code review, in particular pull request activity. The subjects will try to answer some questions in both setups (some will work first in VR, some on-screen), which will be presented to them in random order. To draw results, we will compare and statistically analyze both the correctness of their answers, and the time spent until they are produced.