Lei Tong

Lei Tong, Adam Corrigan, Navin Rathna Kumar et al.

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.

Cheng Kang, Jindich Prokop, Lei Tong et al.

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.

Zheheng Jiang, Zhihua Liu, Long Chen et al.

The study of mouse social behaviours has been increasingly undertaken in neuroscience research. However, automated quantification of mouse behaviours from the videos of interacting mice is still a challenging problem, where object tracking plays a key role in locating mice in their living spaces. Artificial markers are often applied for multiple mice tracking, which are intrusive and consequently interfere with the movements of mice in a dynamic environment. In this paper, we propose a novel method to continuously track several mice and individual parts without requiring any specific tagging. Firstly, we propose an efficient and robust deep learning based mouse part detection scheme to generate part candidates. Subsequently, we propose a novel Bayesian Integer Linear Programming Model that jointly assigns the part candidates to individual targets with necessary geometric constraints whilst establishing pair-wise association between the detected parts. There is no publicly available dataset in the research community that provides a quantitative test-bed for the part detection and tracking of multiple mice, and we here introduce a new challenging Multi-Mice PartsTrack dataset that is made of complex behaviours and actions. Finally, we evaluate our proposed approach against several baselines on our new datasets, where the results show that our method outperforms the other state-of-the-art approaches in terms of accuracy.