Tong, Lei
CLANet: A Comprehensive Framework for Cross-Batch Cell Line Identification Using Brightfield Images
Tong, Lei, Corrigan, Adam, Kumar, Navin Rathna, Hallbrook, Kerry, Orme, Jonathan, Wang, Yinhai, Zhou, Huiyu
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
Kang, Cheng, Prokop, Jindich, Tong, Lei, Zhou, Huiyu, Hu, Yong, Novak, Daneil
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.
Inverse boosting pruning trees for depression detection on Twitter
Tong, Lei, Xiangrong, null, Zhang, Qianni, Sadka, Abdul, Li, Ling, Zhou, Huiyu
Depression is one of the most common mental health disorders, and a large number of depression people commit suicide each year. Potential depression sufferers do not consult psychological doctors because they feel ashamed or are unaware of any depression, which may result in severe delay of diagnosis and treatment. In the meantime, evidence shows that social media data provides valuable clues about physical and mental health conditions. In this paper, we argue that it is feasible to identify depression at an early stage by mining online social behaviours. Our approach, which is innovative to the practice of depression detection, does not rely on the extraction of numerous or complicated features to achieve accurate depression detection. Instead, we propose a novel classifier, namely, Inverse Boosting Pruning Trees (IBPT), which demonstrates a strong classification ability on a publicly accessible dataset with 7862 Twitter users. To comprehensively evaluate the classification capability of the IBPT, we use three real datasets from the UCI machine learning repository and the IBPT still obtains the best classification results against several state of the arts techniques. The results manifest that our proposed framework is promising for identifying social networks' users with depression.