Tong Lin

Yee-Yang Tee, Deruo Cheng, Chye-Soon Chee et al.

Deep learning has achieved great success in the challenging circuit annotation task by employing Convolutional Neural Networks (CNN) for the segmentation of circuit structures. The deep learning approaches require a large amount of manually annotated training data to achieve a good performance, which could cause a degradation in performance if a deep learning model trained on a given dataset is applied to a different dataset. This is commonly known as the domain shift problem for circuit annotation, which stems from the possibly large variations in distribution across different image datasets. The different image datasets could be obtained from different devices or different layers within a single device. To address the domain shift problem, we propose Histogram-gated Image Translation (HGIT), an unsupervised domain adaptation framework which transforms images from a given source dataset to the domain of a target dataset, and utilize the transformed images for training a segmentation network. Specifically, our HGIT performs generative adversarial network (GAN)-based image translation and utilizes histogram statistics for data curation. Experiments were conducted on a single labeled source dataset adapted to three different target datasets (without labels for training) and the segmentation performance was evaluated for each target dataset. We have demonstrated that our method achieves the best performance compared to the reported domain adaptation techniques, and is also reasonably close to the fully supervised benchmark.

Yucong Liu, Shixing Yu, Tong Lin

In this paper, we develop a novel regularization method for deep neural networks by penalizing the trace of Hessian. This regularizer is motivated by a recent guarantee bound of the generalization error. We explain its benefits in finding flat minima and avoiding Lyapunov stability in dynamical systems. We adopt the Hutchinson method as a classical unbiased estimator for the trace of a matrix and further accelerate its calculation using a dropout scheme. Experiments demonstrate that our method outperforms existing regularizers and data augmentation methods, such as Jacobian, Confidence Penalty, Label Smoothing, Cutout, and Mixup.

Dian Chen, Yunkai Chen, Tong Lin et al.

Multimodal approaches that integrate protein structure and sequence have achieved remarkable success in protein-protein interface prediction. However, extending these methods to protein-peptide interactions remains challenging due to the inherent conformational flexibility of peptides and the limited availability of structural data that hinder direct training of structure-aware models. To address these limitations, we introduce GeoPep, a novel framework for peptide binding site prediction that leverages transfer learning from ESM3, a multimodal protein foundation model. GeoPep fine-tunes ESM3's rich pre-learned representations from protein-protein binding to address the limited availability of protein-peptide binding data. The fine-tuned model is further integrated with a parameter-efficient neural network architecture capable of learning complex patterns from sparse data. Furthermore, the model is trained using distance-based loss functions that exploit 3D structural information to enhance binding site prediction. Comprehensive evaluations demonstrate that GeoPep significantly outperforms existing methods in protein-peptide binding site prediction by effectively capturing sparse and heterogeneous binding patterns.

Zhenguo Nie, Tong Lin, Haoliang Jiang et al.

In topology optimization using deep learning, load and boundary conditions represented as vectors or sparse matrices often miss the opportunity to encode a rich view of the design problem, leading to less than ideal generalization results. We propose a new data-driven topology optimization model called TopologyGAN that takes advantage of various physical fields computed on the original, unoptimized material domain, as inputs to the generator of a conditional generative adversarial network (cGAN). Compared to a baseline cGAN, TopologyGAN achieves a nearly $3\times$ reduction in the mean squared error and a $2.5\times$ reduction in the mean absolute error on test problems involving previously unseen boundary conditions. Built on several existing network models, we also introduce a hybrid network called U-SE(Squeeze-and-Excitation)-ResNet for the generator that further increases the overall accuracy. We publicly share our full implementation and trained network.