An Evaluation of Non-Contrastive Self-Supervised Learning for Federated Medical Image Analysis

Privacy and annotation bottlenecks are two major issues that profoundly affect the practicality of machine learning-based medical image analysis. Although significant progress has been made in these areas, these issues are not yet fully resolved. In this paper, we seek to tackle these concerns head-on and systematically explore the applicability of non-contrastive self-supervised learning (SSL) algorithms under federated learning (FL) simulations for medical image analysis. We conduct thorough experimentation of recently proposed state-of-the-art non-contrastive frameworks under standard FL setups. With the SoTA Contrastive Learning algorithm, SimCLR as our comparative baseline, we benchmark the performances of our 4 chosen non-contrastive algorithms under non-i.i.d. data conditions and with a varying number of clients. We present a holistic evaluation of these techniques on 6 standardized medical imaging datasets. We further analyse different trends inferred from the findings of our research, with the aim to find directions for further research based on ours. To the best of our knowledge, ours is the first to perform such a thorough analysis of federated self-supervised learning for medical imaging. All of our source code will be made public upon acceptance of the paper

Segmenting Scientific Abstracts into Discourse Categories: A Deep Learning-Based Approach for Sparse Labeled Data

The abstract of a scientific paper distills the contents of the paper into a short paragraph. In the biomedical literature, it is customary to structure an abstract into discourse categories like BACKGROUND, OBJECTIVE, METHOD, RESULT, and CONCLUSION, but this segmentation is uncommon in other fields like computer science. Explicit categories could be helpful for more granular, that is, discourse-level search and recommendation. The sparsity of labeled data makes it challenging to construct supervised machine learning solutions for automatic discourse-level segmentation of abstracts in non-bio domains. In this paper, we address this problem using transfer learning. In particular, we define three discourse categories BACKGROUND, TECHNIQUE, OBSERVATION-for an abstract because these three categories are the most common. We train a deep neural network on structured abstracts from PubMed, then fine-tune it on a small hand-labeled corpus of computer science papers. We observe an accuracy of 75% on the test corpus. We perform an ablation study to highlight the roles of the different parts of the model. Our method appears to be a promising solution to the automatic segmentation of abstracts, where the labeled data is sparse.Comment: to appear in the proceedings of JCDL'202

A lightweight QRS detector for single lead ECG signals using a max-min difference algorithm

Background and objectives - Detection of the R-peak pertaining to the QRS complex of an ECG signal plays an important role for the diagnosis of a patient's heart condition. To accurately identify the QRS locations from the acquired raw ECG signals, we need to handle a number of challenges, which include noise, baseline wander, varying peak amplitudes, and signal abnormality. This research aims to address these challenges by developing an efficient lightweight algorithm for QRS (i.e., R-peak) detection from raw ECG signals. Methods - A lightweight real-time sliding window-based Max-Min Difference (MMD) algorithm for QRS detection from Lead II ECG signals is proposed. Targeting to achieve the best trade-off between computational efficiency and detection accuracy, the proposed algorithm consists of five key steps for QRS detection, namely, baseline correction, MMD curve generation, dynamic threshold computation, R-peak detection, and error correction. Five annotated databases from Physionet are used for evaluating the proposed algorithm in R-peak detection. Integrated with a feature extraction technique and a neural network classifier, the proposed ORS detection algorithm has also been extended to undertake normal and abnormal heartbeat detection from ECG signals. Results - The proposed algorithm exhibits a high degree of robustness in QRS detection and achieves an average sensitivity of 99.62% and an average positive predictivity of 99.67%. Its performance compares favorably with those from the existing state-of-the-art models reported in the literature. In regards to normal and abnormal heartbeat detection, the proposed QRS detection algorithm in combination with the feature extraction technique and neural network classifier achieves an overall accuracy rate of 93.44% based on an empirical evaluation using the MIT-BIH Arrhythmia data set with 10-fold cross validation. Conclusions - In comparison with other related studies, the proposed algorithm offers a lightweight adaptive alternative for R-peak detection with good computational efficiency. The empirical results indicate that it not only yields a high accuracy rate in QRS detection, but also exhibits efficient computational complexity at the order of O(n), where n is the length of an ECG signal

Generation of Highlights from Research Papers Using Pointer-Generator Networks and SciBERT Embeddings

Nowadays many research articles are prefaced with research highlights to summarize the main findings of the paper. Highlights not only help researchers precisely and quickly identify the contributions of a paper, they also enhance the discoverability of the article via search engines. We aim to automatically construct research highlights given certain segments of the research paper. We use a pointer-generator network with coverage mechanism and a contextual embedding layer at the input that encodes the input tokens into SciBERT embeddings. We test our model on a benchmark dataset, CSPubSum and also present MixSub, a new multi-disciplinary corpus of papers for automatic research highlight generation. For both CSPubSum and MixSub, we have observed that the proposed model achieves the best performance compared to related variants and other models proposed in the literature. On the CSPubSum data set, our model achieves the best performance when the input is only the abstract of a paper as opposed to other segments of the paper. It produces ROUGE-1, ROUGE-2 and ROUGE-L F1-scores of 38.26, 14.26 and 35.51, respectively, METEOR F1-score of 32.62, and BERTScore F1 of 86.65 which outperform all other baselines. On the new MixSub data set, where only the abstract is the input, our proposed model (when trained on the whole training corpus without distinguishing between the subject categories) achieves ROUGE-1, ROUGE-2 and ROUGE-L F1-scores of 31.78, 9.76 and 29.3, respectively, METEOR F1-score of 24.00, and BERTScore F1 of 85.25, outperforming other models.Comment: 18 pages, 7 figures, 7 table

A scattering and repulsive swarm intelligence algorithm for solving global optimization problems

The firefly algorithm (FA), as a metaheuristic search method, is useful for solving diverse optimization problems. However, it is challenging to use FA in tackling high dimensional optimization problems, and the random movement of FA has a high likelihood to be trapped in local optima. In this research, we propose three improved algorithms, i.e., Repulsive Firefly Algorithm (RFA), Scattering Repulsive Firefly Algorithm (SRFA), and Enhanced SRFA (ESRFA), to mitigate the premature convergence problem of the original FA model. RFA adopts a repulsive force strategy to accelerate fireflies (i.e. solutions) to move away from unpromising search regions, in order to reach global optimality in fewer iterations. SRFA employs a scattering mechanism along with the repulsive force strategy to divert weak neighbouring solutions to new search regions, in order to increase global exploration. Motivated by the survival tactics of hawk-moths, ESRFA incorporates a hovering-driven attractiveness operation, an exploration-driven evading mechanism, and a learning scheme based on the historical best experience in the neighbourhood to further enhance SRFA. Standard and CEC2014 benchmark optimization functions are used for evaluation of the proposed FA-based models. The empirical results indicate that ESRFA, SRFA and RFA significantly outperform the original FA model, a number of state-of-the-art FA variants, and other swarm-based algorithms, which include Simulated Annealing, Cuckoo Search, Particle Swarm, Bat Swarm, Dragonfly, and Ant-Lion Optimization, in diverse challenging benchmark functions