X. Rosalind Wang

Nikhel Gupta, Zeeshan Hayder, Ray P. Norris et al.

The present work discusses the use of a weakly-supervised deep learning algorithm that reduces the cost of labelling pixel-level masks for complex radio galaxies with multiple components. The algorithm is trained on weak class-level labels of radio galaxies to get class activation maps (CAMs). The CAMs are further refined using an inter-pixel relations network (IRNet) to get instance segmentation masks over radio galaxies and the positions of their infrared hosts. We use data from the Australian Square Kilometre Array Pathfinder (ASKAP) telescope, specifically the Evolutionary Map of the Universe (EMU) Pilot Survey, which covered a sky area of 270 square degrees with an RMS sensitivity of 25-35 $μ$Jy/beam. We demonstrate that weakly-supervised deep learning algorithms can achieve high accuracy in predicting pixel-level information, including masks for the extended radio emission encapsulating all galaxy components and the positions of the infrared host galaxies. We evaluate the performance of our method using mean Average Precision (mAP) across multiple classes at a standard intersection over union (IoU) threshold of 0.5. We show that the model achieves a mAP$_{50}$ of 67.5\% and 76.8\% for radio masks and infrared host positions, respectively. The network architecture can be found at the following link: https://github.com/Nikhel1/Gal-CAM

Nwe Ni Win, Jim Basilakis, Steven Thomas et al.

Extracting clinically relevant information from unstructured medical narratives such as admission notes, discharge summaries, and emergency case histories remains a challenge in clinical natural language processing (NLP). Medical Entity Recognition (MER) identifies meaningful concepts embedded in these records. Recent advancements in large language models (LLMs) have shown competitive MER performance; however, evaluations often focus on general entity types, offering limited utility for real-world clinical needs requiring finer-grained extraction. To address this gap, we rigorously evaluated the open-source LLaMA3 model for fine-grained medical entity recognition across 18 clinically detailed categories. To optimize performance, we employed three learning paradigms: zero-shot, few-shot, and fine-tuning with Low-Rank Adaptation (LoRA). To further enhance few-shot learning, we introduced two example selection methods based on token- and sentence-level embedding similarity, utilizing a pre-trained BioBERT model. Unlike prior work assessing zero-shot and few-shot performance on proprietary models (e.g., GPT-4) or fine-tuning different architectures, we ensured methodological consistency by applying all strategies to a unified LLaMA3 backbone, enabling fair comparison across learning settings. Our results showed that fine-tuned LLaMA3 surpasses zero-shot and few-shot approaches by 63.11% and 35.63%, respectivel respectively, achieving an F1 score of 81.24% in granular medical entity extraction.

Midhun Shyam, Jim Basilakis, Kieran Luken et al.

Triage notes, created at the start of a patient's hospital visit, contain a wealth of information that can help medical staff and researchers understand Emergency Department patient epidemiology and the degree of time-dependent illness or injury. Unfortunately, applying modern Natural Language Processing and Machine Learning techniques to analyse triage data faces some challenges: Firstly, hospital data contains highly sensitive information that is subject to privacy regulation thus need to be analysed on site; Secondly, most hospitals and medical facilities lack the necessary hardware to fine-tune a Large Language Model (LLM), much less training one from scratch; Lastly, to identify the records of interest, expert inputs are needed to manually label the datasets, which can be time-consuming and costly. We present in this paper a pipeline that enables the classification of triage data using LLM and limited compute resources. We first fine-tuned a pre-trained LLM with a classifier using a small (2k) open sourced dataset on a GPU; and then further fine-tuned the model with a hospital specific dataset of 1000 samples on a CPU. We demonstrated that by carefully curating the datasets and leveraging existing models and open sourced data, we can successfully classify triage data with limited compute resources.

Nikhel Gupta, Ray P. Norris, Zeeshan Hayder et al.

We present source detection and catalogue construction pipelines to build the first catalogue of radio galaxies from the 270 $\rm deg^2$ pilot survey of the Evolutionary Map of the Universe (EMU-PS) conducted with the Australian Square Kilometre Array Pathfinder (ASKAP) telescope. The detection pipeline uses Gal-DINO computer-vision networks (Gupta et al., 2024) to predict the categories of radio morphology and bounding boxes for radio sources, as well as their potential infrared host positions. The Gal-DINO network is trained and evaluated on approximately 5,000 visually inspected radio galaxies and their infrared hosts, encompassing both compact and extended radio morphologies. We find that the Intersection over Union (IoU) for the predicted and ground truth bounding boxes is larger than 0.5 for 99% of the radio sources, and 98% of predicted host positions are within $3^{\prime \prime}$ of the ground truth infrared host in the evaluation set. The catalogue construction pipeline uses the predictions of the trained network on the radio and infrared image cutouts based on the catalogue of radio components identified using the Selavy source finder algorithm. Confidence scores of the predictions are then used to prioritize Selavy components with higher scores and incorporate them first into the catalogue. This results in identifications for a total of 211,625 radio sources, with 201,211 classified as compact and unresolved. The remaining 10,414 are categorized as extended radio morphologies, including 582 FR-I, 5,602 FR-II, 1,494 FR-x (uncertain whether FR-I or FR-II), 2,375 R (single-peak resolved) radio galaxies, and 361 with peculiar and other rare morphologies. We cross-match the radio sources in the catalogue with the infrared and optical catalogues, finding infrared cross-matches for 73% and photometric redshifts for 36% of the radio galaxies.

Mike Li, X. Rosalind Wang

We present ChromAlignNet, a deep learning model for alignment of peaks in Gas Chromatography-Mass Spectrometry (GC-MS) data. In GC-MS data, a compound's retention time (RT) may not stay fixed across multiple chromatograms. To use GC-MS data for biomarker discovery requires alignment of identical analyte's RT from different samples. Current methods of alignment are all based on a set of formal, mathematical rules. We present a solution to GC-MS alignment using deep learning neural networks, which are more adept at complex, fuzzy data sets. We tested our model on several GC-MS data sets of various complexities and analysed the alignment results quantitatively. We show the model has very good performance (AUC $\sim 1$ for simple data sets and AUC $\sim 0.85$ for very complex data sets). Further, our model easily outperforms existing algorithms on complex data sets. Compared with existing methods, ChromAlignNet is very easy to use as it requires no user input of reference chromatograms and parameters. This method can easily be adapted to other similar data such as those from liquid chromatography. The source code is written in Python and available online.

Yu Sun, Louis F. Rossi, Chien-Chung Shen et al.

Swarm dynamics is the study of collections of agents that interact with one another without central control. In natural systems, insects, birds, fish and other large mammals function in larger units to increase the overall fitness of the individuals. Their behavior is coordinated through local interactions to enhance mate selection, predator detection, migratory route identification and so forth [Andersson and Wallander 2003; Buhl et al. 2006; Nagy et al. 2010; Partridge 1982; Sumpter et al. 2008]. In artificial systems, swarms of autonomous agents can augment human activities such as search and rescue, and environmental monitoring by covering large areas with multiple nodes [Alami et al. 2007; Caruso et al. 2008; Ogren et al. 2004; Paley et al. 2007; Sibley et al. 2002]. In this paper, we explore the interplay between swarm dynamics, covert leadership and theoretical information transfer. A leader is a member of the swarm that acts upon information in addition to what is provided by local interactions. Depending upon the leadership model, leaders can use their external information either all the time or in response to local conditions [Couzin et al. 2005; Sun et al. 2013]. A covert leader is a leader that is treated no differently than others in the swarm, so leaders and followers participate equally in whatever interaction model is used [Rossi et al. 2007]. In this study, we use theoretical information transfer as a means of analyzing swarm interactions to explore whether or not it is possible to distinguish between followers and leaders based on interactions within the swarm. We find that covert leaders can be distinguished from followers in a swarm because they receive less transfer entropy than followers.