Daily Papers

Recent researches attempt to improve the detection performance by adopting the idea of cascade for single-stage detectors. In this paper, we analyze and discover that inconsistency is the major factor limiting the performance. The refined anchors are associated with the feature extracted from the previous location and the classifier is confused by misaligned classification and localization. Further, we point out two main designing rules for the cascade manner: improving consistency between classification confidence and localization performance, and maintaining feature consistency between different stages. A multistage object detector named Cas-RetinaNet, is then proposed for reducing the misalignments. It consists of sequential stages trained with increasing IoU thresholds for improving the correlation, and a novel Feature Consistency Module for mitigating the feature inconsistency. Experiments show that our proposed Cas-RetinaNet achieves stable performance gains across different models and input scales. Specifically, our method improves RetinaNet from 39.1 AP to 41.1 AP on the challenging MS COCO dataset without any bells or whistles.

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

We introduce ReFinED, an efficient end-to-end entity linking model which uses fine-grained entity types and entity descriptions to perform linking. The model performs mention detection, fine-grained entity typing, and entity disambiguation for all mentions within a document in a single forward pass, making it more than 60 times faster than competitive existing approaches. ReFinED also surpasses state-of-the-art performance on standard entity linking datasets by an average of 3.7 F1. The model is capable of generalising to large-scale knowledge bases such as Wikidata (which has 15 times more entities than Wikipedia) and of zero-shot entity linking. The combination of speed, accuracy and scale makes ReFinED an effective and cost-efficient system for extracting entities from web-scale datasets, for which the model has been successfully deployed. Our code and pre-trained models are available at https://github.com/alexa/ReFinED