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Taming large-scale genomic analyses via sparsified genomics.
Nat Commun
January 2025
Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland.
Searching for similar genomic sequences is an essential and fundamental step in biomedical research. State-of-the-art computational methods performing such comparisons fail to cope with the exponential growth of genomic sequencing data. We introduce the concept of sparsified genomics where we systematically exclude a large number of bases from genomic sequences and enable faster and memory-efficient processing of the sparsified, shorter genomic sequences, while providing comparable accuracy to processing non-sparsified sequences.
View Article and Find Full Text PDFTaming vision transformers for clinical laryngoscopy assessment.
J Biomed Inform
January 2025
Eye & ENT Hospital of Fudan University, Fenyang Road 83, Shanghai, 200000, China. Electronic address:
Objective: Laryngoscopy, essential for diagnosing laryngeal cancer (LCA), faces challenges due to high inter-observer variability and the reliance on endoscopist expertise. Distinguishing precancerous from early-stage cancerous lesions is particularly challenging, even for experienced practitioners, given their similar appearances. This study aims to enhance laryngoscopic image analysis to improve early screening/detection of cancer or precancerous conditions.
View Article and Find Full Text PDFTaming chimeras in coupled oscillators using soft actor-critic based reinforcement learning.
Chaos
January 2025
Complex Systems Group, Department of Mathematics and Statistics, The University of Western Australia, Crawley, Western Australia 6009, Australia.
We propose a universal method based on deep reinforcement learning (specifically, soft actor-critic) to control the chimera state in the coupled oscillators. The policy for control is learned by maximizing the expectation of the cumulative reward in the reinforcement learning framework. With the aid of the local order parameter, we design a class of reward functions for controlling the chimera state, specifically confining the spatial position of coherent and incoherent domains to any desired lateral position of oscillators.
View Article and Find Full Text PDFResistance risk and mechanism of Ustilaginoidea virens to pydiflumetofen.
Pestic Biochem Physiol
December 2024
College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China. Electronic address:
Rice false smut, caused by Ustilaginoidea virens, is a devastating fungal disease in rice that not only leads to yield reduction but also poses a serious threat to food safety and human health due to the production of numerous mycotoxins. Pydiflumetofen, one of the most promising SDHI fungicides widely used for controlling various plant diseases, lacks available information regarding its antifungal activity against U. virens and the potential risk of resistance development in this pathogen.
View Article and Find Full Text PDFSI-MIL: Taming Deep MIL for Self-Interpretability in Gigapixel Histopathology.
Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit
June 2024
Stony Brook University, USA.
Introducing interpretability and reasoning into Multiple Instance Learning (MIL) methods for Whole Slide Image (WSI) analysis is challenging, given the complexity of gigapixel slides. Traditionally, MIL interpretability is limited to identifying salient regions deemed pertinent for downstream tasks, offering little insight to the end-user (pathologist) regarding the rationale behind these selections. To address this, we propose Self-Interpretable MIL (SI-MIL), a method intrinsically designed for interpretability from the very outset.
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