Tan Yang

Yang Tan, Mingchen Li, Pan Tan et al.

Large protein language models are adept at capturing the underlying evolutionary information in primary structures, offering significant practical value for protein engineering. Compared to natural language models, protein amino acid sequences have a smaller data volume and a limited combinatorial space. Choosing an appropriate vocabulary size to optimize the pre-trained model is a pivotal issue. Moreover, despite the wealth of benchmarks and studies in the natural language community, there remains a lack of a comprehensive benchmark for systematically evaluating protein language model quality. Given these challenges, PETA trained language models with 14 different vocabulary sizes under three tokenization methods. It conducted thousands of tests on 33 diverse downstream datasets to assess the models' transfer learning capabilities, incorporating two classification heads and three random seeds to mitigate potential biases. Extensive experiments indicate that vocabulary sizes between 50 and 200 optimize the model, whereas sizes exceeding 800 detrimentally affect the model's representational performance. Our code, model weights and datasets are available at https://github.com/ginnm/ProteinPretraining.

Yang Tan, Chen Liu, Jingyuan Gao et al.

Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However, interdisciplinary adoption remains limited due to challenges in data collection, task benchmarking, and application. This work presents VenusFactory, a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular fine-tuning of PLMs. VenusFactory supports both computer science and biology communities with choices of both a command-line execution and a Gradio-based no-code interface, integrating $40+$ protein-related datasets and $40+$ popular PLMs. All implementations are open-sourced on https://github.com/tyang816/VenusFactory.

Yang Tan, Yang Li, Shao-Lun Huang

Transferability estimation is a fundamental problem in transfer learning to predict how good the performance is when transferring a source model (or source task) to a target task. With the guidance of transferability score, we can efficiently select the highly transferable source models without performing the real transfer in practice. Recent analytical transferability metrics are mainly designed for image classification problem, and currently there is no specific investigation for the transferability estimation of semantic segmentation task, which is an essential problem in autonomous driving, medical image analysis, etc. Consequently, we further extend the recent analytical transferability metric OTCE (Optimal Transport based Conditional Entropy) score to the semantic segmentation task. The challenge in applying the OTCE score is the high dimensional segmentation output, which is difficult to find the optimal coupling between so many pixels under an acceptable computation cost. Thus we propose to randomly sample N pixels for computing OTCE score and take the expectation over K repetitions as the final transferability score. Experimental evaluation on Cityscapes, BDD100K and GTA5 datasets demonstrates that the OTCE score highly correlates with the transfer performance.

Yang Tan, Yang Li, Shao-Lun Huang

Transferability estimation is an essential problem in transfer learning to predict how good the performance is when transferring a source model (or source task) to a target task. Recent analytical transferability metrics have been widely used for source model selection and multi-task learning. A major challenge is how to make transfereability estimation robust under the cross-domain cross-task settings. The recently proposed OTCE score solves this problem by considering both domain and task differences, with the help of transfer experiences on auxiliary tasks, which causes an efficiency overhead. In this work, we propose a practical transferability metric called JC-NCE score that dramatically improves the robustness of the task difference estimation in OTCE, thus removing the need for auxiliary tasks. Specifically, we build the joint correspondences between source and target data via solving an optimal transport problem with a ground cost considering both the sample distance and label distance, and then compute the transferability score as the negative conditional entropy of the matched labels. Extensive validations under the intra-dataset and inter-dataset transfer settings demonstrate that our JC-NCE score outperforms the auxiliary-task free version of OTCE for 7% and 12%, respectively, and is also more robust than other existing transferability metrics on average.

Yang Tan, Yang Li, Shao-Lun Huang

Transfer learning across heterogeneous data distributions (a.k.a. domains) and distinct tasks is a more general and challenging problem than conventional transfer learning, where either domains or tasks are assumed to be the same. While neural network based feature transfer is widely used in transfer learning applications, finding the optimal transfer strategy still requires time-consuming experiments and domain knowledge. We propose a transferability metric called Optimal Transport based Conditional Entropy (OTCE), to analytically predict the transfer performance for supervised classification tasks in such cross-domain and cross-task feature transfer settings. Our OTCE score characterizes transferability as a combination of domain difference and task difference, and explicitly evaluates them from data in a unified framework. Specifically, we use optimal transport to estimate domain difference and the optimal coupling between source and target distributions, which is then used to derive the conditional entropy of the target task (task difference). Experiments on the largest cross-domain dataset DomainNet and Office31 demonstrate that OTCE shows an average of 21% gain in the correlation with the ground truth transfer accuracy compared to state-of-the-art methods. We also investigate two applications of the OTCE score including source model selection and multi-source feature fusion.

Yang Tan, Hongxin Lin, Zelin Xiao et al.

Previous works have shown that face recognition with high accurate 3D data is more reliable and insensitive to pose and illumination variations. Recently, low-cost and portable 3D acquisition techniques like ToF(Time of Flight) and DoE based structured light systems enable us to access 3D data easily, e.g., via a mobile phone. However, such devices only provide sparse(limited speckles in structured light system) and noisy 3D data which can not support face recognition directly. In this paper, we aim at achieving high-performance face recognition for devices equipped with such modules which is very meaningful in practice as such devices will be very popular. We propose a framework to perform face recognition by fusing a sequence of low-quality 3D data. As 3D data are sparse and noisy which can not be well handled by conventional methods like the ICP algorithm, we design a PointNet-like Deep Registration Network(DRNet) which works with ordered 3D point coordinates while preserving the ability of mining local structures via convolution. Meanwhile we develop a novel loss function to optimize our DRNet based on the quaternion expression which obviously outperforms other widely used functions. For face recognition, we design a deep convolutional network which takes the fused 3D depth-map as input based on AMSoftmax model. Experiments show that our DRNet can achieve rotation error 0.95° and translation error 0.28mm for registration. The face recognition on fused data also achieves rank-1 accuracy 99.2% , FAR-0.001 97.5% on Bosphorus dataset which is comparable with state-of-the-art high-quality data based recognition performance.