Boyuan Wang

Zihao Tang, Boyuan Wang, Chuan Wen et al.

Conformal prediction is widely adopted in uncertainty quantification, due to its post-hoc, distribution-free, and model-agnostic properties. In the realm of modern deep learning, researchers have proposed Feature Conformal Prediction (FCP), which deploys conformal prediction in a feature space, yielding reduced band lengths. However, the practical utility of FCP is limited due to the time-consuming non-linear operations required to transform confidence bands from feature space to output space. In this paper, we introduce Fast Feature Conformal Prediction (FFCP), which features a novel non-conformity score and is convenient for practical applications. FFCP serves as a fast version of FCP, in that it equivalently employs a Taylor expansion to approximate the aforementioned non-linear operations in FCP. Empirical validations showcase that FFCP performs comparably with FCP (both outperforming the vanilla version) while achieving a significant reduction in computational time by approximately 50x. The code is available at https://github.com/ElvisWang1111/FastFeatureCP

Qin Wang, Jun Wei, Boyuan Wang et al.

Protein secondary structure prediction (PSSP) is essential for protein function analysis. However, for low homologous proteins, the PSSP suffers from insufficient input features. In this paper, we explicitly import external self-supervised knowledge for low homologous PSSP under the guidance of residue-wise profile fusion. In practice, we firstly demonstrate the superiority of profile over Position-Specific Scoring Matrix (PSSM) for low homologous PSSP. Based on this observation, we introduce the novel self-supervised BERT features as the pseudo profile, which implicitly involves the residue distribution in all native discovered sequences as the complementary features. Further-more, a novel residue-wise attention is specially designed to adaptively fuse different features (i.e.,original low-quality profile, BERT based pseudo profile), which not only takes full advantage of each feature but also avoids noise disturbance. Be-sides, the feature consistency loss is proposed to accelerate the model learning from multiple semantic levels. Extensive experiments confirm that our method outperforms state-of-the-arts (i.e.,4.7%forextremely low homologous cases on BC40 dataset).