OpenRaiser/Intern-Atlas huggingface dataset:
Leveraging Wastewater Monitoring for COVID-19 Forecasting in the US: a Deep Learning study
Venue: arXiv cs.LG 2022
Year: 2022

The outburst of COVID-19 in late 2019 was the start of a health crisis that shook the world and took millions of lives in the ensuing years. Many governments and health officials failed to arrest the rapid circulation of infection in their communities. The long incubation period and the large proportion of asymptomatic cases made COVID-19 particularly elusive to track. However, wastewater monitoring soon became a promising data source in addition to conventional indicators such as confirmed daily cases, hospitalizations, and deaths. Despite the consensus on the effectiveness of wastewater viral load data, there is a lack of methodological approaches that leverage viral load to improve COVID-19 forecasting. This paper proposes using deep learning to automatically discover the relationship between daily confirmed cases and viral load data. We trained one Deep Temporal Convolutional Networks (DeepTCN) and one Temporal Fusion Transformer (TFT) model to build a global forecasting model. We supplement the daily confirmed cases with viral loads and other socio-economic factors as covariates to the models. Our results suggest that TFT outperforms DeepTCN and learns a better association between viral load and daily cases. We demonstrated that equipping the models with the viral load improves their forecasting performance significantly. Moreover, viral load is shown to be the second most predictive input, following the containment and health index. Our results reveal the feasibility of training a location-agnostic deep-learning model to capture the dynamics of infection diffusion when wastewater viral load data is provided.
Towards Robust Handwritten Text Recognition with On-the-fly User Participation
Venue: arXiv cs.CV 2022
Year: 2022

Long-term OCR services aim to provide high-quality output to their users at competitive costs. It is essential to upgrade the models because of the complex data loaded by the users. The service providers encourage the users who provide data where the OCR model fails by rewarding them based on data complexity, readability, and available budget. Hitherto, the OCR works include preparing the models on standard datasets without considering the end-users. We propose a strategy of consistently upgrading an existing Handwritten Hindi OCR model three times on the dataset of 15 users. We fix the budget of 4 users for each iteration. For the first iteration, the model directly trains on the dataset from the first four users. For the rest iteration, all remaining users write a page each, which service providers later analyze to select the 4 (new) best users based on the quality of predictions on the human-readable words. Selected users write 23 more pages for upgrading the model. We upgrade the model with Curriculum Learning (CL) on the data available in the current iteration and compare the subset from previous iterations. The upgraded model is tested on a held-out set of one page each from all 23 users. We provide insights into our investigations on the effect of CL, user selection, and especially the data from unseen writing styles. Our work can be used for long-term OCR services in crowd-sourcing scenarios for the service providers and end users.
'If you build they will come': Automatic Identification of News-Stakeholders to detect Party Preference in News Coverage
Venue: arXiv cs.CL 2022
Year: 2022

The coverage of different stakeholders mentioned in the news articles significantly impacts the slant or polarity detection of the concerned news publishers. For instance, the pro-government media outlets would give more coverage to the government stakeholders to increase their accessibility to the news audiences. In contrast, the anti-government news agencies would focus more on the views of the opponent stakeholders to inform the readers about the shortcomings of government policies. In this paper, we address the problem of stakeholder extraction from news articles and thereby determine the inherent bias present in news reporting. Identifying potential stakeholders in multi-topic news scenarios is challenging because each news topic has different stakeholders. The research presented in this paper utilizes both contextual information and external knowledge to identify the topic-specific stakeholders from news articles. We also apply a sequential incremental clustering algorithm to group the entities with similar stakeholder types. We carried out all our experiments on news articles on four Indian government policies published by numerous national and international news agencies. We also further generalize our system, and the experimental results show that the proposed model can be extended to other news topics.
Exploiting Rich Textual User-Product Context for Improving Sentiment Analysis
Venue: arXiv cs.CL 2022
Year: 2022

User and product information associated with a review is useful for sentiment polarity prediction. Typical approaches incorporating such information focus on modeling users and products as implicitly learned representation vectors. Most do not exploit the potential of historical reviews, or those that currently do require unnecessary modifications to model architecture or do not make full use of user/product associations. The contribution of this work is twofold: i) a method to explicitly employ historical reviews belonging to the same user/product to initialize representations, and ii) efficient incorporation of textual associations between users and products via a user-product cross-context module. Experiments on IMDb, Yelp-2013 and Yelp-2014 benchmarks show that our approach substantially outperforms previous state-of-the-art. Since we employ BERT-base as the encoder, we additionally provide experiments in which our approach performs well with Span-BERT and Longformer. Furthermore, experiments where the reviews of each user/product in the training data are downsampled demonstrate the effectiveness of our approach under a low-resource setting.
Neural-Network-Augmented Projection-Based Model Order Reduction for Mitigating the Kolmogorov Barrier to Reducibility of CFD Models
Venue: arXiv cs.CE 2022
Year: 2022

Inspired by our previous work on mitigating the Kolmogorov barrier using a quadratic approximation manifold, we propose in this paper a computationally tractable approach for combining a projection-based reduced-order model (PROM) and an artificial neural network (ANN) for mitigating the Kolmogorov barrier to reducibility of convection-dominated flow problems. The main objective the PROM-ANN concept that we propose is to reduce the dimensionality of the online approximation of the solution beyond what is possible using affine and quadratic approximation manifolds. In contrast to previous approaches for constructing arbitrarily nonlinear manifold approximations for nonlinear model reduction that exploited one form or another of ANN, the training of the PROM-ANN we propose in this paper does not involve data whose dimension scales with that of the high-dimensional model; and this PROM-ANN is hyperreducible using any well-established hyperreduction method. Hence, unlike many other ANN-based approaches, the PROM-ANN concept we propose in this paper is practical for large-scale and industry-relevant CFD problems. Its potential is demonstrated here for a parametric, shock-dominated, benchmark problem.
Toward Data Heterogeneity of Federated Learning
Venue: arXiv cs.LG 2022
Year: 2022

Federated learning is a popular paradigm for machine learning. Ideally, federated learning works best when all clients share a similar data distribution. However, it is not always the case in the real world. Therefore, the topic of federated learning on heterogeneous data has gained more and more effort from both academia and industry. In this project, we first do extensive experiments to show how data skew and quantity skew will affect the performance of state-of-art federated learning algorithms. Then we propose a new algorithm FedMix which adjusts existing federated learning algorithms and we show its performance. We find that existing state-of-art algorithms such as FedProx and FedNova do not have a significant improvement in all testing cases. But by testing the existing and new algorithms, it seems that tweaking the client side is more effective than tweaking the server side.
Beyond the C: Retargetable Decompilation using Neural Machine Translation
Venue: arXiv cs.CR 2022
Year: 2022

The problem of reversing the compilation process, decompilation, is an important tool in reverse engineering of computer software. Recently, researchers have proposed using techniques from neural machine translation to automate the process in decompilation. Although such techniques hold the promise of targeting a wider range of source and assembly languages, to date they have primarily targeted C code. In this paper we argue that existing neural decompilers have achieved higher accuracy at the cost of requiring language-specific domain knowledge such as tokenizers and parsers to build an abstract syntax tree (AST) for the source language, which increases the overhead of supporting new languages. We explore a different tradeoff that, to the extent possible, treats the assembly and source languages as plain text, and show that this allows us to build a decompiler that is easily retargetable to new languages. We evaluate our prototype decompiler, Beyond The C (BTC), on Go, Fortran, OCaml, and C, and examine the impact of parameters such as tokenization and training data selection on the quality of decompilation, finding that it achieves comparable decompilation results to prior work in neural decompilation with significantly less domain knowledge. We will release our training data, trained decompilation models, and code to help encourage future research into language-agnostic decompilation.
Training Robots to Evaluate Robots: Example-Based Interactive Reward Functions for Policy Learning
Venue: arXiv cs.LG 2022
Year: 2022

Physical interactions can often help reveal information that is not readily apparent. For example, we may tug at a table leg to evaluate whether it is built well, or turn a water bottle upside down to check that it is watertight. We propose to train robots to acquire such interactive behaviors automatically, for the purpose of evaluating the result of an attempted robotic skill execution. These evaluations in turn serve as "interactive reward functions" (IRFs) for training reinforcement learning policies to perform the target skill, such as screwing the table leg tightly. In addition, even after task policies are fully trained, IRFs can serve as verification mechanisms that improve online task execution. For any given task, our IRFs can be conveniently trained using only examples of successful outcomes, and no further specification is needed to train the task policy thereafter. In our evaluations on door locking and weighted block stacking in simulation, and screw tightening on a real robot, IRFs enable large performance improvements, even outperforming baselines with access to demonstrations or carefully engineered rewards. Project website: https://sites.google.com/view/lirf-corl-2022/
GPU Load Balancing
Venue: arXiv cs.DC 2022
Year: 2022

Fine-grained workload and resource balancing is the key to high performance for regular and irregular computations on the GPUs. In this dissertation, we conduct an extensive survey of existing load-balancing techniques to build an abstraction that addresses the difficulty of scheduling computations on the GPU. We propose a GPU fine-grained load-balancing abstraction that decouples load balancing from work processing and aims to support both static and dynamic schedules with a programmable interface to implement new load-balancing schedules. Prior to our work, the only way to unleash the GPU's potential on irregular problems has been to workload-balance through application-specific, tightly coupled load-balancing techniques. With our open-source framework for load-balancing, we hope to improve programmers' productivity when developing irregular-parallel algorithms on the GPU, and also improve the overall performance characteristics for such applications by allowing a quick path to experimentation with a variety of existing load-balancing techniques. Using our insights from load-balancing irregular workloads, we build Stream-K, a work-centric parallelization of matrix multiplication (GEMM) and related computations in dense linear algebra. Whereas contemporary decompositions are primarily tile-based, our method operates by partitioning an even share of the aggregate inner loop iterations among physical processing elements. This provides a near-perfect utilization of computing resources, regardless of how efficiently the output tiling for any given problem quantizes across the underlying processing elements. On GPU processors, our Stream-K parallelization of GEMM produces a peak speedup of up to 14x and 6.7x, and an average performance response that is both higher and more consistent across 32K GEMM problem geometries than state-of-the-art math libraries such as CUTLASS and cuBLAS.
Clinical Deterioration Prediction in Brazilian Hospitals Based on Artificial Neural Networks and Tree Decision Models
Venue: arXiv cs.LG 2022
Year: 2022

Early recognition of clinical deterioration (CD) has vital importance in patients' survival from exacerbation or death. Electronic health records (EHRs) data have been widely employed in Early Warning Scores (EWS) to measure CD risk in hospitalized patients. Recently, EHRs data have been utilized in Machine Learning (ML) models to predict mortality and CD. The ML models have shown superior performance in CD prediction compared to EWS. Since EHRs data are structured and tabular, conventional ML models are generally applied to them, and less effort is put into evaluating the artificial neural network's performance on EHRs data. Thus, in this article, an extremely boosted neural network (XBNet) is used to predict CD, and its performance is compared to eXtreme Gradient Boosting (XGBoost) and random forest (RF) models. For this purpose, 103,105 samples from thirteen Brazilian hospitals are used to generate the models. Moreover, the principal component analysis (PCA) is employed to verify whether it can improve the adopted models' performance. The performance of ML models and Modified Early Warning Score (MEWS), an EWS candidate, are evaluated in CD prediction regarding the accuracy, precision, recall, F1-score, and geometric mean (G-mean) metrics in a 10-fold cross-validation approach. According to the experiments, the XGBoost model obtained the best results in predicting CD among Brazilian hospitals' data.
Plankton-FL: Exploration of Federated Learning for Privacy-Preserving Training of Deep Neural Networks for Phytoplankton Classification
Venue: arXiv cs.LG 2022
Year: 2022

Creating high-performance generalizable deep neural networks for phytoplankton monitoring requires utilizing large-scale data coming from diverse global water sources. A major challenge to training such networks lies in data privacy, where data collected at different facilities are often restricted from being transferred to a centralized location. A promising approach to overcome this challenge is federated learning, where training is done at site level on local data, and only the model parameters are exchanged over the network to generate a global model. In this study, we explore the feasibility of leveraging federated learning for privacy-preserving training of deep neural networks for phytoplankton classification. More specifically, we simulate two different federated learning frameworks, federated learning (FL) and mutually exclusive FL (ME-FL), and compare their performance to a traditional centralized learning (CL) framework. Experimental results from this study demonstrate the feasibility and potential of federated learning for phytoplankton monitoring.
Rare-Seed Generation for Fuzzing
Venue: arXiv cs.SE 2022
Year: 2022

Starting with a random initial seed, fuzzers search for inputs that trigger bugs or vulnerabilities. However, fuzzers often fail to generate inputs for program paths guarded by restrictive branch conditions. In this paper, we show that by first identifying rare-paths in programs (i.e., program paths with path constraints that are unlikely to be satisfied by random input generation), and then, generating inputs/seeds that trigger rare-paths, one can improve the coverage of fuzzing tools. In particular, we present techniques 1) that identify rare paths using quantitative symbolic analysis, and 2) generate inputs that can explore these rare paths using path-guided concolic execution. We provide these inputs as initial seed sets to three state of the art fuzzers. Our experimental evaluation on a set of programs (that contain a lot of restrictive branch conditions) shows that the fuzzers achieve better coverage with the rare-path based seed set compared to a random initial seed.
MeSH Suggester: A Library and System for MeSH Term Suggestion for Systematic Review Boolean Query Construction
Venue: arXiv cs.IR 2022
Year: 2022

Boolean query construction is often critical for medical systematic review literature search. To create an effective Boolean query, systematic review researchers typically spend weeks coming up with effective query terms and combinations. One challenge to creating an effective systematic review Boolean query is the selection of effective MeSH Terms to include in the query. In our previous work, we created neural MeSH term suggestion methods and compared them to state-of-the-art MeSH term suggestion methods. We found neural MeSH term suggestion methods to be highly effective. In this demonstration, we build upon our previous work by creating (1) a Web-based MeSH term suggestion prototype system that allows users to obtain suggestions from a number of underlying methods and (2) a Python library that implements ours and others' MeSH term suggestion methods and that is aimed at researchers who want to further investigate, create or deploy such type of methods. We describe the architecture of the web-based system and how to use it for the MeSH term suggestion task. For the Python library, we describe how the library can be used for advancing further research and experimentation, and we validate the results of the methods contained in the library on standard datasets. Our web-based prototype system is available at http://ielab-mesh-suggest.uqcloud.net, while our Python library is at https://github.com/ielab/meshsuggestlib.
Marginal-Certainty-aware Fair Ranking Algorithm
Venue: arXiv cs.IR 2022
Year: 2022

Ranking systems are ubiquitous in modern Internet services, including online marketplaces, social media, and search engines. Traditionally, ranking systems only focus on how to get better relevance estimation. When relevance estimation is available, they usually adopt a user-centric optimization strategy where ranked lists are generated by sorting items according to their estimated relevance. However, such user-centric optimization ignores the fact that item providers also draw utility from ranking systems. It has been shown in existing research that such user-centric optimization will cause much unfairness to item providers, followed by unfair opportunities and unfair economic gains for item providers. To address ranking fairness, many fair ranking methods have been proposed. However, as we show in this paper, these methods could be suboptimal as they directly rely on the relevance estimation without being aware of the uncertainty (i.e., the variance of the estimated relevance). To address this uncertainty, we propose a novel Marginal-Certainty-aware Fair algorithm named MCFair. MCFair jointly optimizes fairness and user utility, while relevance estimation is constantly updated in an online manner. In MCFair, we first develop a ranking objective that includes uncertainty, fairness, and user utility. Then we directly use the gradient of the ranking objective as the ranking score. We theoretically prove that MCFair based on gradients is optimal for the aforementioned ranking objective. Empirically, we find that on semi-synthesized datasets, MCFair is effective and practical and can deliver superior performance compared to state-of-the-art fair ranking methods. To facilitate reproducibility, we release our code https://github.com/Taosheng-ty/WSDM22-MCFair.
Answer-Set Programming for Lexicographical Makespan Optimisation in Parallel Machine Scheduling
Venue: arXiv cs.AI 2022
Year: 2022

We deal with a challenging scheduling problem on parallel machines with sequence-dependent setup times and release dates from a real-world application of semiconductor work-shop production. There, jobs can only be processed by dedicated machines, thus few machines can determine the makespan almost regardless of how jobs are scheduled on the remaining ones. This causes problems when machines fail and jobs need to be rescheduled. Instead of optimising only the makespan, we put the individual machine spans in non-ascending order and lexicographically minimise the resulting tuples. This achieves that all machines complete as early as possible and increases the robustness of the schedule. We study the application of Answer-Set Programming (ASP) to solve this problem. While ASP eases modelling, the combination of timing constraints and the considered objective function challenges current solving technology. The former issue is addressed by using an extension of ASP by difference logic. For the latter, we devise different algorithms that use multi-shot solving. To tackle industrial-sized instances, we study different approximations and heuristics. Our experimental results show that ASP is indeed a promising KRR paradigm for this problem and is competitive with state-of-the-art CP and MIP solvers. Under consideration in Theory and Practice of Logic Programming (TPLP).
JEMMA: An Extensible Java Dataset for ML4Code Applications
Venue: arXiv cs.SE 2022
Year: 2022

Machine Learning for Source Code (ML4Code) is an active research field in which extensive experimentation is needed to discover how to best use source code's richly structured information. With this in mind, we introduce JEMMA, an Extensible Java Dataset for ML4Code Applications, which is a large-scale, diverse, and high-quality dataset targeted at ML4Code. Our goal with JEMMA is to lower the barrier to entry in ML4Code by providing the building blocks to experiment with source code models and tasks. JEMMA comes with a considerable amount of pre-processed information such as metadata, representations (e.g., code tokens, ASTs, graphs), and several properties (e.g., metrics, static analysis results) for 50,000 Java projects from the 50KC dataset, with over 1.2 million classes and over 8 million methods. JEMMA is also extensible allowing users to add new properties and representations to the dataset, and evaluate tasks on them. Thus, JEMMA becomes a workbench that researchers can use to experiment with novel representations and tasks operating on source code. To demonstrate the utility of the dataset, we also report results from two empirical studies on our data, ultimately showing that significant work lies ahead in the design of context-aware source code models that can reason over a broader network of source code entities in a software project, the very task that JEMMA is designed to help with.
Predicting Citi Bike Demand Evolution Using Dynamic Graphs
Venue: arXiv cs.LG 2022
Year: 2022

Bike sharing systems often suffer from poor capacity management as a result of variable demand. These bike sharing systems would benefit from models to predict demand in order to moderate the number of bikes stored at each station. In this paper, we attempt to apply a graph neural network model to predict bike demand in the New York City, Citi Bike dataset.