March in Chat: Interactive Prompting for Remote Embodied Referring Expression

Many Vision-and-Language Navigation (VLN) tasks have been proposed in recent years, from room-based to object-based and indoor to outdoor. The REVERIE (Remote Embodied Referring Expression) is interesting since it only provides high-level instructions to the agent, which are closer to human commands in practice. Nevertheless, this poses more challenges than other VLN tasks since it requires agents to infer a navigation plan only based on a short instruction. Large Language Models (LLMs) show great potential in robot action planning by providing proper prompts. Still, this strategy has not been explored under the REVERIE settings. There are several new challenges. For example, the LLM should be environment-aware so that the navigation plan can be adjusted based on the current visual observation. Moreover, the LLM planned actions should be adaptable to the much larger and more complex REVERIE environment. This paper proposes a March-in-Chat (MiC) model that can talk to the LLM on the fly and plan dynamically based on a newly proposed Room-and-Object Aware Scene Perceiver (ROASP). Our MiC model outperforms the previous state-of-the-art by large margins by SPL and RGSPL metrics on the REVERIE benchmark.Comment: Accepted by ICCV 202

MOfinder: A Novel Algorithm for Detecting Overlapping Modules from Protein-Protein Interaction Network

Since organism development and many critical cell biology processes are organized in modular patterns, many algorithms have been proposed to detect modules. In this study, a new method, MOfinder, was developed to detect overlapping modules in a protein-protein interaction (PPI) network. We demonstrate that our method is more accurate than other 5 methods. Then, we applied MOfinder to yeast and human PPI network and explored the overlapping information. Using the overlapping modules of human PPI network, we constructed the module-module communication network. Functional annotation showed that the immune-related and cancer-related proteins were always together and present in the same modules, which offer some clues for immune therapy for cancer. Our study around overlapping modules suggests a new perspective on the analysis of PPI network and improves our understanding of disease

Functional Evolution of BRCT Domains from Binding DNA to Protein

The BRCT domain (BRCA1 C-terminal domain) is an important signaling and protein targeting motif in the DNA damage response system. The BRCT domain, which mainly occurs as a singleton (single BRCT) or tandem pair (double BRCT), contains a phosphate-binding pocket that can bind the phosphate from either the DNA end or a phosphopeptide. In this work, we performed a database search, phylogeny reconstruction, and phosphate-binding pocket comparison to analyze the functional evolution of the BRCT domain. We identified new BRCT-containing proteins in bacteria and eukaryotes, and found that the number of BRCT-containing proteins per genome is correlated with genome complexity. Phylogeny analyses revealed that there are two groups of single BRCT domains (sGroup I and sGroup II) and double BRCT domains (dGroup I and dGroup II). These four BRCT groups differ in their phosphate-binding pockets. In eukaryotes, the evolution of the BRCT domain can be divided into three phases. In the first phase, the sGroup I BRCT domain with the phosphate-binding pocket that can bind the phosphate of nicked DNA invaded eukaryotic genome. In the second phase, the phosphate-binding pocket changed from a DNA-binding type to a protein-binding type in sGroup II. The tandem duplication of sGroup II BRCT domain gave birth to double BRCT domain, from which two structurally and functionally distinct groups were evolved. The third phase is after the divergence between animals and plants. Both sGroup I and sGroup II BRCT domains originating in this phase lost the phosphate-binding pocket and many evolved protein-binding sites. Many dGroup I members were evolved in this stage but few dGroup II members were observed. The results further suggested that the BRCT domain expansion and functional change in eukaryote may be driven by the evolution of the DNA damage response system

The linear and nonlinear Jaynes-Cummings model for the multiphoton transition

With the Jaynes-Cummings model, we have studied the atom and light field quantum entanglement of multiphoton transition, and researched the effect of initial state superposition coefficient $C_{1}$, the transition photon number $N$, the quantum discord $\delta$ and the nonlinear coefficient $\chi$ on the quantum entanglement degrees. We have given the quantum entanglement degrees curves with time evolution, and obtained some results, which should have been used in quantum computing and quantum information.Comment: arXiv admin note: text overlap with arXiv:1404.0821, arXiv:1205.0979 by other author