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We propose InstructDET, a data-centric method for referring object detection (ROD) that localizes target objects based on user instructions. While deriving from referring expressions (REC), the instructions we leverage are greatly diversified to encompass common user intentions related to object detection. For one image, we produce tremendous instructions that refer to every single object and different combinations of multiple objects. Each instruction and its corresponding object bounding boxes (bbxs) constitute one training data pair. In order to encompass common detection expressions, we involve emerging vision-language model (VLM) and large language model (LLM) to generate instructions guided by text prompts and object bbxs, as the generalizations of foundation models are effective to produce human-like expressions (e.g., describing object property, category, and relationship). We name our constructed dataset as InDET. It contains images, bbxs and generalized instructions that are from foundation models. Our InDET is developed from existing REC datasets and object detection datasets, with the expanding potential that any image with object bbxs can be incorporated through using our InstructDET method. By using our InDET dataset, we show that a conventional ROD model surpasses existing methods on standard REC datasets and our InDET test set. Our data-centric method InstructDET, with automatic data expansion by leveraging foundation models, directs a promising field that ROD can be greatly diversified to execute common object detection instructions., Comment: 29 pages (include Appendix) Published in ICLR

Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements., Comment: 64 pages, 11 figures

Markov State Models (MSMs) are a powerful framework to reproduce the long-time conformational dynamics of biomolecules using a set of short Molecular Dynamics (MD) simulations. However, precise kinetics predictions of MSMs heavily rely on the features selected to describe the system. Despite the importance of feature selection for large system, determining an optimal set of features remains a difficult unsolved problem. Here, we introduce an automatic approach to optimize feature selection based on genetic algorithms (GA), which adaptively evolves the most fitted solution according to natural selection laws. The power of the GA-based method is illustrated on long atomistic folding simulations of four proteins, varying in length from 28 to 80 residues. Due to the diversity of tested proteins, we expect that our method will be extensible to other proteins and drive MSM building to a more objective protocol., Comment: 9 Pages, 5 figures