READRetro: natural product biosynthesis predicting with retrieval-augmented dual-view retrosynthesis.

Plants, as a sessile organism, produce various secondary metabolites to interact with the environment. These chemicals have fascinated the plant science community because of their ecological significance and notable biological activity. However, predicting the complete biosynthetic pathways from target molecules to metabolic building blocks remains a challenge. Here, we propose retrieval-augmented dual-view retrosynthesis (READRetro) as a practical bio-retrosynthesis tool to predict the biosynthetic pathways of plant natural products. Conventional bio-retrosynthesis models have been limited in their ability to predict biosynthetic pathways for natural products. READRetro was optimized for the prediction of complex metabolic pathways by incorporating cutting-edge deep learning architectures, an ensemble approach, and two retrievers. Evaluation of single- and multi-step retrosynthesis showed that each component of READRetro significantly improved its ability to predict biosynthetic pathways. READRetro was also able to propose the known pathways of secondary metabolites such as monoterpene indole alkaloids and the unknown pathway of menisdaurilide, demonstrating its applicability to real-world bio-retrosynthesis of plant natural products. For researchers interested in the biosynthesis and production of secondary metabolites, a user-friendly website (https://readretro.net) and the open-source code of READRetro have been made available.

Reading between the lines: object localization using implicit cues from image tags.

Current uses of tagged images typically exploit only the most explicit information: the link between the nouns named and the objects present somewhere in the image. We propose to leverage "unspoken" cues that rest within an ordered list of image tags so as to improve object localization. We define three novel implicit features from an image's tags-the relative prominence of each object as signified by its order of mention, the scale constraints implied by unnamed objects, and the loose spatial links hinted at by the proximity of names on the list. By learning a conditional density over the localization parameters (position and scale) given these cues, we show how to improve both accuracy and efficiency when detecting the tagged objects. Furthermore, we show how the localization density can be learned in a semantic space shared by the visual and tag-based features, which makes the technique applicable for detection in untagged input images. We validate our approach on the PASCAL VOC, LabelMe, and Flickr image data sets, and demonstrate its effectiveness relative to both traditional sliding windows as well as a visual context baseline. Our algorithm improves state-of-the-art methods, successfully translating insights about human viewing behavior (such as attention, perceived importance, or gaze) into enhanced object detection.