CLANet: A Comprehensive Framework for Cross-Batch Cell Line Identification Using Brightfield Images

Cell line authentication plays a crucial role in the biomedical field, ensuring researchers work with accurately identified cells. Supervised deep learning has made remarkable strides in cell line identification by studying cell morphological features through cell imaging. However, batch effects, a significant issue stemming from the different times at which data is generated, lead to substantial shifts in the underlying data distribution, thus complicating reliable differentiation between cell lines from distinct batch cultures. To address this challenge, we introduce CLANet, a pioneering framework for cross-batch cell line identification using brightfield images, specifically designed to tackle three distinct batch effects. We propose a cell cluster-level selection method to efficiently capture cell density variations, and a self-supervised learning strategy to manage image quality variations, thus producing reliable patch representations. Additionally, we adopt multiple instance learning(MIL) for effective aggregation of instance-level features for cell line identification. Our innovative time-series segment sampling module further enhances MIL's feature-learning capabilities, mitigating biases from varying incubation times across batches. We validate CLANet using data from 32 cell lines across 93 experimental batches from the AstraZeneca Global Cell Bank. Our results show that CLANet outperforms related approaches (e.g. domain adaptation, MIL), demonstrating its effectiveness in addressing batch effects in cell line identification.

giMLPs: Gate with Inhibition Mechanism in MLPs

This paper presents a new model architecture, gate with inhibition MLP (giMLP).The gate with inhibition on CycleMLP (gi-CycleMLP) can produce equal performance on the ImageNet classification task, and it also improves the BERT, Roberta, and DeBERTaV3 models depending on two novel techniques. The first is the gating MLP, where matrix multiplications between the MLP and the trunk Attention input in further adjust models' adaptation. The second is inhibition which inhibits or enhances the branch adjustment, and with the inhibition levels increasing, it offers models more muscular features restriction. We show that the giCycleMLP with a lower inhibition level can be competitive with the original CycleMLP in terms of ImageNet classification accuracy. In addition, we also show through a comprehensive empirical study that these techniques significantly improve the performance of fine-tuning NLU downstream tasks. As for the gate with inhibition MLPs on DeBERTa (giDeBERTa) fine-tuning, we find it can achieve appealing results on most parts of NLU tasks without any extra pretraining again. We also find that with the use of Gate With Inhibition, the activation function should have a short and smooth negative tail, with which the unimportant features or the features that hurt models can be moderately inhibited. The experiments on ImageNet and twelve language downstream tasks demonstrate the effectiveness of Gate With Inhibition, both for image classification and for enhancing the capacity of nature language fine-tuning without any extra pretraining.

Feature Analyses and Modelling of Lithium-ion Batteries Manufacturing based on Random Forest Classification

Lithium-ion battery manufacturing is a highly complicated process with strongly coupled feature interdependencies, a feasible solution that can analyse feature variables within manufacturing chain and achieve reliable classification is thus urgently needed. This article proposes a random forest (RF)-based classification framework, through using the out of bag (OOB) predictions, Gini changes as well as predictive measure of association (PMOA), for effectively quantifying the importance and correlations of battery manufacturing features and their effects on the classification of electrode properties. Battery manufacturing data containing three intermediate product features from the mixing stage and one product parameter from the coating stage are analysed by the designed RF framework to investigate their effects on both the battery electrode active material mass load and porosity. Illustrative results demonstrate that the proposed RF framework not only achieves the reliable classification of electrode properties but also leads to the effective quantification of both manufacturing feature importance and correlations. This is the first time to design a systematic RF framework for simultaneously quantifying battery production feature importance and correlations by three various quantitative indicators including the unbiased feature importance (FI), gain improvement FI and PMOA, paving a promising solution to reduce model dimension and conduct efficient sensitivity analysis of battery manufacturing.

Towards advancing the earthquake forecasting by machine learning of satellite data

Amongst the available technologies for earthquake research, remote sensing has been commonly used due to its unique features such as fast imaging and wide image-acquisition range. Nevertheless, early studies on pre-earthquake and remote-sensing anomalies are mostly oriented towards anomaly identification and analysis of a single physical parameter. Many analyses are based on singular events, which provide a lack of understanding of this complex natural phenomenon because usually, the earthquake signals are hidden in the environmental noise. The universality of such analysis still is not being demonstrated on a worldwide scale. In this paper, we investigate physical and dynamic changes of seismic data and thereby develop a novel machine learning method, namely Inverse Boosting Pruning Trees (IBPT), to issue short-term forecast based on the satellite data of 1,371 earthquakes of magnitude six or above due to their impact on the environment. We have analyzed and compared our proposed framework against several states of the art machine learning methods using ten different infrared and hyperspectral measurements collected between 2006 and 2013. Our proposed method outperforms all the six selected baselines and shows a strong capability in improving the likelihood of earthquake forecasting across different earthquake databases.

Structured Context Enhancement Network for Mouse Pose Estimation

Automated analysis of mouse behaviours is crucial for many applications in neuroscience. However, quantifying mouse behaviours from videos or images remains a challenging problem, where pose estimation plays an important role in describing mouse behaviours. Although deep learning based methods have made promising advances in mouse or other animal pose estimation, they cannot properly handle complicated scenarios (e.g., occlusions, invisible keypoints, and abnormal poses). Particularly, since mouse body is highly deformable, it is a big challenge to accurately locate different keypoints on the mouse body. In this paper, we propose a novel hourglass network based model, namely Graphical Model based Structured Context Enhancement Network (GM-SCENet) where two effective modules, i.e., Structured Context Mixer (SCM) and Cascaded Multi-Level Supervision module (CMLS) are designed. The SCM can adaptively learn and enhance the proposed structured context information of each mouse part by a novel graphical model with close consideration on the difference between body parts. Then, the CMLS module is designed to jointly train the proposed SCM and the hourglass network by generating multi-level information, which increases the robustness of the whole network. Based on the multi-level predictions from the SCM and the CMLS module, we also propose an inference method to enhance the localization results. Finally, we evaluate our proposed approach against several baselines...

Perceptual underwater image enhancement with deep learning and physical priors

Underwater image enhancement, as a pre-processing step to improve the accuracy of the following object detection task, has drawn considerable attention in the field of underwater navigation and ocean exploration. However, most of the existing underwater image enhancement strategies tend to consider enhancement and detection as two independent modules with no interaction, and the practice of separate optimization does not always help the underwater object detection task. In this paper, we propose two perceptual enhancement models, each of which uses a deep enhancement model with a detection perceptor. The detection perceptor provides coherent information in the form of gradients to the enhancement model, guiding the enhancement model to generate patch level visually pleasing images or detection favourable images. In addition, due to the lack of training data, a hybrid underwater image synthesis model, which fuses physical priors and data-driven cues, is proposed to synthesize training data and generalise our enhancement model for real-world underwater images. Experimental results show the superiority of our proposed method over several state-of-the-art methods on both real-world and synthetic underwater datasets.

Detection perceptual underwater image enhancement with deep learning and physical priors

Underwater image enhancement, as a pre-processing step to improve the accuracy of the following object detection task, has drawn considerable attention in the field of underwater navigation and ocean exploration. However, most of the existing underwater image enhancement strategies tend to consider enhancement and detection as two independent modules with no interaction, and the practice of separate optimization does not always help the underwater object detection task. In this paper, we propose two perceptual enhancement models, each of which uses a deep enhancement model with a detection perceptor. The detection perceptor provides coherent information in the form of gradients to the enhancement model, guiding the enhancement model to generate patch level visually pleasing images or detection favourable images. In addition, due to the lack of training data, a hybrid underwater image synthesis model, which fuses physical priors and data-driven cues, is proposed to synthesize training data and generalise our enhancement model for real-world underwater images. Experimental results show the superiority of our proposed method over several state-of-the-art methods on both real-world and synthetic underwater datasets.

Deep Learning Based Brain Tumor Segmentation: A Survey

Brain tumor segmentation is a challenging problem in medical image analysis. The goal of brain tumor segmentation is to generate accurate delineation of brain tumor regions with correctly located masks. In recent years, deep learning methods have shown very promising performance in solving various computer vision problems, such as image classification, object detection and semantic segmentation. A number of deep learning based methods have been applied to brain tumor segmentation and achieved impressive system performance. Considering state-of-the-art technologies and their performance, the purpose of this paper is to provide a comprehensive survey of recently developed deep learning based brain tumor segmentation techniques. The established works included in this survey extensively cover technical aspects such as the strengths and weaknesses of different approaches, pre- and post-processing frameworks, datasets and evaluation metrics. Finally, we conclude this survey by discussing the potential development in future research work.

CANet: Context Aware Network for 3D Brain Tumor Segmentation

Automated segmentation of brain tumors in 3D magnetic resonance imaging plays an active role in tumor diagnosis, progression monitoring and surgery planning. Based on convolutional neural networks, especially fully convolutional networks, previous studies have shown some promising technologies for brain tumor segmentation. However, these approaches lack suitable strategies to incorporate contextual information to deal with local ambiguities, leading to unsatisfactory segmentation outcomes in challenging circumstances. In this work, we propose a novel Context-Aware Network (CANet) with a Hybrid Context Aware Feature Extractor (HCA-FE) and a Context Guided Attentive Conditional Random Field (CG-ACRF) for feature fusion. HCA-FE captures high dimensional and discriminative features with the contexts from both the convolutional space and feature interaction graphs. We adopt the powerful inference ability of probabilistic graphical models to learn hidden feature maps, and then use CG-ACRF to fuse the features of different contexts. We evaluate our proposed method on publicly accessible brain tumor segmentation datasets BRATS2017 and BRATS2018 against several state-of-the-art approaches using different segmentation metrics. The experimental results show that the proposed algorithm has better or competitive performance, compared to the standard approaches.