Evolutionary design of explainable algorithms for biomedical image segmentation

Adaptive Evolutionary Optimization of Deep Learning Architectures for Focused Liver Ultrasound Image Segmentation

Background: Liver ultrasound segmentation is challenging due to low image quality and variability. While deep learning (DL) models have been widely applied for medical segmentation, generic pre-configured models may not meet the specific requirements for targeted areas in liver ultrasound. Quantitative ultrasound (QUS) is emerging as a promising tool for liver fat measurement; however, accurately segmenting regions of interest within liver ultrasound images remains a challenge. Methods: We introduce a generalizable framework using an adaptive evolutionary genetic algorithm to optimize deep learning models, specifically U-Net, for focused liver segmentation. The algorithm simultaneously adjusts the depth (number of layers) and width (neurons per layer) of the network, dropout, and skip connections. Various architecture configurations are evaluated based on segmentation performance to find the optimal model for liver ultrasound images. Results: The model with a depth of 4 and filter sizes of [16, 64, 128, 256] achieved the highest mean adjusted Dice score of 0.921, outperforming the other configurations, using three-fold cross-validation with early stoppage. Conclusions: Adaptive evolutionary optimization enhances the deep learning architecture for liver ultrasound segmentation. Future work may extend this optimization to other imaging modalities and deep learning architectures.

Rapid and accurate bacteria identification through deep-learning-based two-dimensional Raman spectroscopy

Surface-enhanced Raman spectroscopy (SERS) offers a distinctive vibrational fingerprint of the molecules and has led to widespread applications in medical diagnosis, biochemistry, and virology. With the rapid development of artificial intelligence (AI) technology, AI-enabled Raman spectroscopic techniques, as a promising avenue for biosensing applications, have significantly boosted bacteria identification. By converting spectra into images, the dataset is enriched with more detailed information, allowing AI to identify bacterial isolates with enhanced precision. However, previous studies usually suffer from a trade-off between high-resolution spectrograms for high-accuracy identification and short training time for data processing. Here, we present an efficient bacteria identification strategy that combines deep learning models with a spectrogram encoding algorithm based on wavelet packet transform and Gramian angular field techniques. In contrast to the direct analysis of raw Raman spectra, our approach utilizes wavelet packet transform techniques to compress the spectra by a factor of 1/15, while concurrently maintaining state-of-the-art accuracy by amplifying the subtle differences via Gramian angular field techniques. The results demonstrate that our approach can achieve a 99.64 % and a 90.55 % identification accuracy for two types of bacterial isolates and thirty types of bacterial isolates, respectively, while a 90 % reduction in training time compared to the conventional methods. To verify the model's stability, Gaussian noises were superimposed on the testing dataset, showing a specific generalization ability and superior performance. This algorithm has the potential for integration into on-site testing protocols and is readily updatable with new bacterial isolates. This study provides profound insights and contributes to the current understanding of spectroscopy, paving the way for accurate and rapid bacteria identification in diverse applications of environment monitoring, food safety, microbiology, and public health.

Defining the boundaries: challenges and advances in identifying cells in microscopy images

Segmentation, or the outlining of objects within images, is a critical step in the measurement and analysis of cells within microscopy images. While improvements continue to be made in tools that rely on classical methods for segmentation, deep learning-based tools increasingly dominate advances in the technology. Specialist models such as Cellpose continue to improve in accuracy and user-friendliness, and segmentation challenges such as the Multi-Modality Cell Segmentation Challenge continue to push innovation in accuracy across widely varying test data as well as efficiency and usability. Increased attention on documentation, sharing, and evaluation standards is leading to increased user-friendliness and acceleration toward the goal of a truly universal method.