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.

Lei Tong, Xujing Yao, Adam Corrigan et al.

High-Content Screening routinely generates massive volumes of cell painting images for phenotypic profiling. However, technical variations across experimental executions inevitably induce biological batch (bio-batch) effects. These cause covariate shifts and degrade the generalization of deep learning models on unseen data. Existing batch correction methods typically rely on additional prior knowledge (e.g., treatment or cell culture information) or struggle to generalize to unseen bio-batches. In this work, we frame bio-batch mitigation as a Domain Generalization (DG) problem and propose Adversarial Batch Representation Augmentation (ABRA). ABRA explicitly models batch-wise statistical fluctuations by parameterizing feature statistics as structured uncertainties. Through a min-max optimization framework, it actively synthesizes worst-case bio-batch perturbations in the representation space, guided by a strict angular geometric margin to preserve fine-grained class discriminability. To prevent representation collapse during this adversarial exploration, we introduce a synergistic distribution alignment objective. Extensive evaluations on the large-scale RxRx1 and RxRx1-WILDS benchmarks demonstrate that ABRA establishes a new state-of-the-art for siRNA perturbation classification.

Zhihua Liu, Amrutha Saseendran, Lei Tong et al.

Open-set image segmentation poses a significant challenge because existing methods often demand extensive training or fine-tuning and generally struggle to segment unified objects consistently across diverse text reference expressions. Motivated by this, we propose Segment Anyword, a novel training-free visual concept prompt learning approach for open-set language grounded segmentation that relies on token-level cross-attention maps from a frozen diffusion model to produce segmentation surrogates or mask prompts, which are then refined into targeted object masks. Initial prompts typically lack coherence and consistency as the complexity of the image-text increases, resulting in suboptimal mask fragments. To tackle this issue, we further introduce a novel linguistic-guided visual prompt regularization that binds and clusters visual prompts based on sentence dependency and syntactic structural information, enabling the extraction of robust, noise-tolerant mask prompts, and significant improvements in segmentation accuracy. The proposed approach is effective, generalizes across different open-set segmentation tasks, and achieves state-of-the-art results of 52.5 (+6.8 relative) mIoU on Pascal Context 59, 67.73 (+25.73 relative) cIoU on gRefCOCO, and 67.4 (+1.1 relative to fine-tuned methods) mIoU on GranDf, which is the most complex open-set grounded segmentation task in the field.

Lei Tong, Zhihua Liu, Chaochao Lu et al.

We present Causal-Adapter, a modular framework that adapts frozen text-to-image diffusion backbones for counterfactual image generation. Our method enables causal interventions on target attributes, consistently propagating their effects to causal dependents without altering the core identity of the image. In contrast to prior approaches that rely on prompt engineering without explicit causal structure, Causal-Adapter leverages structural causal modeling augmented with two attribute regularization strategies: prompt-aligned injection, which aligns causal attributes with textual embeddings for precise semantic control, and a conditioned token contrastive loss to disentangle attribute factors and reduce spurious correlations. Causal-Adapter achieves state-of-the-art performance on both synthetic and real-world datasets, with up to 91% MAE reduction on Pendulum for accurate attribute control and 87% FID reduction on ADNI for high-fidelity MRI image generation. These results show that our approach enables robust, generalizable counterfactual editing with faithful attribute modification and strong identity preservation.

Zhihua Liu, Lei Tong, Xilin He et al.

Existed echocardiography segmentation methods often suffer from anatomical inconsistency challenge caused by shape variation, partial observation and region ambiguity with similar intensity across 2D echocardiographic sequences, resulting in false positive segmentation with anatomical defeated structures in challenging low signal-to-noise ratio conditions. To provide a strong anatomical guarantee across different echocardiographic frames, we propose a novel segmentation framework named BOTM (Bi-directional Optimal Token Matching) that performs echocardiography segmentation and optimal anatomy transportation simultaneously. Given paired echocardiographic images, BOTM learns to match two sets of discrete image tokens by finding optimal correspondences from a novel anatomical transportation perspective. We further extend the token matching into a bi-directional cross-transport attention proxy to regulate the preserved anatomical consistency within the cardiac cyclic deformation in temporal domain. Extensive experimental results show that BOTM can generate stable and accurate segmentation outcomes (e.g. -1.917 HD on CAMUS2H LV, +1.9% Dice on TED), and provide a better matching interpretation with anatomical consistency guarantee.

Kailong Liu, Xiaosong Hu, Huiyu Zhou et al.

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.

Pan Xiong, Lei Tong, Kun Zhang et al.

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.

Feixiang Zhou, Zheheng Jiang, Zhihua Liu et al.

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 human pose estimation, they cannot be directly applied to pose estimation of mice due to different physiological natures. Particularly, since mouse body is highly deformable, it is a 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 (CMLS) are subsequently implemented. SCM can adaptively learn and enhance the proposed structured context information of each mouse part by a novel graphical model that takes into account the motion 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, increasing the robustness of the whole network.Using the multi-level prediction information from SCM and CMLS, we develop an inference method to ensure the accuracy of the localisation results. Finally, we evaluate our proposed approach against several baselines...

Long Chen, Zheheng Jiang, Lei Tong et al.

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.

Zhihua Liu, Lei Tong, Zheheng Jiang et al.

Brain tumor segmentation is one of the most challenging problems in medical image analysis. The goal of brain tumor segmentation is to generate accurate delineation of brain tumor regions. In recent years, deep learning methods have shown 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 promising results. Considering the remarkable breakthroughs made by state-of-the-art technologies, we use this survey to provide a comprehensive study of recently developed deep learning based brain tumor segmentation techniques. More than 100 scientific papers are selected and discussed in this survey, extensively covering technical aspects such as network architecture design, segmentation under imbalanced conditions, and multi-modality processes. We also provide insightful discussions for future development directions.

Zhihua Liu, Lei Tong, Long Chen et al.

Automated segmentation of brain glioma plays an active role in diagnosis decision, progression monitoring and surgery planning. Based on deep neural networks, previous studies have shown promising technologies for brain glioma segmentation. However, these approaches lack powerful strategies to incorporate contextual information of tumor cells and their surrounding, which has been proven as a fundamental cue to deal with local ambiguity. In this work, we propose a novel approach named Context-Aware Network (CANet) for brain glioma segmentation. CANet captures high dimensional and discriminative features with contexts from both the convolutional space and feature interaction graphs. We further propose context guided attentive conditional random fields which can selectively aggregate features. We evaluate our method using publicly accessible brain glioma segmentation datasets BRATS2017, BRATS2018 and BRATS2019. The experimental results show that the proposed algorithm has better or competitive performance against several State-of-The-Art approaches under different segmentation metrics on the training and validation sets.

Long Chen, Lei Tong, Feixiang Zhou et al.

Underwater image enhancement is such an important vision task due to its significance in marine engineering and aquatic robot. It is usually work as a pre-processing step to improve the performance of high level vision tasks such as underwater object detection. Even though many previous works show the underwater image enhancement algorithms can boost the detection accuracy of the detectors, no work specially focus on investigating the relationship between these two tasks. This is mainly because existing underwater datasets lack either bounding box annotations or high quality reference images, based on which detection accuracy or image quality assessment metrics are calculated. To investigate how the underwater image enhancement methods influence the following underwater object detection tasks, in this paper, we provide a large-scale underwater object detection dataset with both bounding box annotations and high quality reference images, namely OUC dataset. The OUC dataset provides a platform for researchers to comprehensive study the influence of underwater image enhancement algorithms on the underwater object detection task.

Long Chen, Zhihua Liu, Lei Tong et al.

In recent years, deep learning based methods have achieved promising performance in standard object detection. However, these methods lack sufficient capabilities to handle underwater object detection due to these challenges: (1) Objects in real applications are usually small and their images are blurry, and (2) images in the underwater datasets and real applications accompany heterogeneous noise. To address these two problems, we first propose a novel neural network architecture, namely Sample-WeIghted hyPEr Network (SWIPENet), for small object detection. SWIPENet consists of high resolution and semantic rich Hyper Feature Maps which can significantly improve small object detection accuracy. In addition, we propose a novel sample-weighted loss function which can model sample weights for SWIPENet, which uses a novel sample re-weighting algorithm, namely Invert Multi-Class Adaboost (IMA), to reduce the influence of noise on the proposed SWIPENet. Experiments on two underwater robot picking contest datasets URPC2017 and URPC2018 show that the proposed SWIPENet+IMA framework achieves better performance in detection accuracy against several state-of-the-art object detection approaches.

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.

Lei Tong, Zhihua Liu, Zheheng Jiang et al.

Depression is one of the most common mental health disorders, and a large number of depressed people commit suicide each year. Potential depression sufferers usually 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, Cost-sensitive Boosting Pruning Trees (CBPT), which demonstrates a strong classification ability on two publicly accessible Twitter depression detection datasets. To comprehensively evaluate the classification capability of the CBPT, we use additional three datasets from the UCI machine learning repository and the CBPT obtains appealing classification results against several state of the arts boosting algorithms. Finally, we comprehensively explore the influence factors of model prediction, and the results manifest that our proposed framework is promising for identifying Twitter users with depression.