Deep learning with self-supervision and uncertainty regularization to count fish in underwater images

Effective conservation actions require effective population monitoring. However, accurately counting animals in the wild to inform conservation decision-making is difficult. Monitoring populations through image sampling has made data collection cheaper, wide-reaching and less intrusive but created a need to process and analyse this data efficiently. Counting animals from such data is challenging, particularly when densely packed in noisy images. Attempting this manually is slow and expensive, while traditional computer vision methods are limited in their generalisability. Deep learning is the state-of-the-art method for many computer vision tasks, but it has yet to be properly explored to count animals. To this end, we employ deep learning, with a density-based regression approach, to count fish in low-resolution sonar images. We introduce a large dataset of sonar videos, deployed to record wild Lebranche mullet schools (Mugil liza), with a subset of 500 labelled images. We utilise abundant unlabelled data in a self-supervised task to improve the supervised counting task. For the first time in this context, by introducing uncertainty quantification, we improve model training and provide an accompanying measure of prediction uncertainty for more informed biological decision-making. Finally, we demonstrate the generalisability of our proposed counting framework through testing it on a recent benchmark dataset of high-resolution annotated underwater images from varying habitats (DeepFish). From experiments on both contrasting datasets, we demonstrate our network outperforms the few other deep learning models implemented for solving this task. By providing an open-source framework along with training data, our study puts forth an efficient deep learning template for crowd counting aquatic animals thereby contributing effective methods to assess natural populations from the ever-increasing visual data

Finding Answers from the Word of God: Domain Adaptation for Neural Networks in Biblical Question Answering

Question answering (QA) has significantly benefitted from deep learning techniques in recent years. However, domain-specific QA remains a challenge due to the significant amount of data required to train a neural network. This paper studies the answer sentence selection task in the Bible domain and answer questions by selecting relevant verses from the Bible. For this purpose, we create a new dataset BibleQA based on bible trivia questions and propose three neural network models for our task. We pre-train our models on a large-scale QA dataset, SQuAD, and investigate the effect of transferring weights on model accuracy. Furthermore, we also measure the model accuracies with different answer context lengths and different Bible translations. We affirm that transfer learning has a noticeable improvement in the model accuracy. We achieve relatively good results with shorter context lengths, whereas longer context lengths decreased model accuracy. We also find that using a more modern Bible translation in the dataset has a positive effect on the task.Comment: The paper has been accepted at IJCNN 201

Learning The Game: Implementations Of Convolutional Networks In Automated Strategy Identification

Games can be used to represent a wide variety of real world problems, giving rise to many applications of game theory. Various computational methods have been proposed for identifying game strategies, including optimized tree search algorithms, game-specific heuristics, and artificial intelligence. In the last decade, systems like AlphaGo and AlphaZero have significantly exceeded the performance of the best human players in Chess, Go, and other games. The most effective game engines to date employ convolutional neural networks (CNNs) to evaluate game boards, extract features, and predict the optimal next move. These engines are trained on billions of simulated games, wherein the strategies become increasingly refined as more games are played. To explore the trade-offs inherent in developing CNNs, we will train them to play the game Connect-4, which is relatively small and has known optimal strategies. In this setting, we experiment with a variety of neural structures and other related factors with only a few hundred thousand simulated games. The results will allow us to compare how different aspects of the neural network impact performance. We propose a framework for this training process which generalizes to any two-player board games meeting some necessary criteria

Process Mining Workshops

This open access book constitutes revised selected papers from the International Workshops held at the Third International Conference on Process Mining, ICPM 2021, which took place in Eindhoven, The Netherlands, during October 31–November 4, 2021. The conference focuses on the area of process mining research and practice, including theory, algorithmic challenges, and applications. The co-located workshops provided a forum for novel research ideas. The 28 papers included in this volume were carefully reviewed and selected from 65 submissions. They stem from the following workshops: 2nd International Workshop on Event Data and Behavioral Analytics (EDBA) 2nd International Workshop on Leveraging Machine Learning in Process Mining (ML4PM) 2nd International Workshop on Streaming Analytics for Process Mining (SA4PM) 6th International Workshop on Process Querying, Manipulation, and Intelligence (PQMI) 4th International Workshop on Process-Oriented Data Science for Healthcare (PODS4H) 2nd International Workshop on Trust, Privacy, and Security in Process Analytics (TPSA) One survey paper on the results of the XES 2.0 Workshop is included

Deep domain adaptation enhances Amplification Curve Analysis for single-channel multiplexing in real-time PCR

Data-driven approaches for molecular diagnostics are emerging as an alternative to perform an accurate and inexpensive multi-pathogen detection. A novel technique called Amplification Curve Analysis (ACA) has been recently developed by coupling machine learning and real-time Polymerase Chain Reaction (qPCR) to enable the simultaneous detection of multiple targets in a single reaction well. However, target classification purely relying on the amplification curve shapes currently faces several challenges, such as distribution discrepancies between different data sources of synthetic DNA and clinical samples (i.e., training vs testing). Optimisation of computational models is required to achieve higher performance of ACA classification in multiplex qPCR through the reduction of those discrepancies. Here, we proposed a novel transformer-based conditional domain adversarial network (T-CDAN) to eliminate data distribution differences between the source domain (synthetic DNA data) and the target domain (clinical isolate data). The labelled training data from the source domain and unlabelled testing data from the target domain are fed into the T-CDAN, which learns both domains' information simultaneously. After mapping the inputs into a domain-irrelevant space, T-CDAN removes the feature distribution differences and provides a clearer decision boundary for the classifier, resulting in a more accurate pathogen identification. Evaluation of 198 clinical isolates containing three types of carbapenem-resistant genes ( bla NDM , bla IMP and bla OXA-48 ) illustrates a curve-level accuracy of 93.1% and a sample-level accuracy of 97.0% using T-CDAN, showing an accuracy improvement of 20.9% and 4.9% respectively, compared with previous methods. This research emphasises the importance of deep domain adaptation to enable high-level multiplexing in a single qPCR reaction, providing a solid approach to extend qPCR instruments' capabilities without hardware modification in real-world clinical applications