Backdiff: a diffusion model for generalized transferable protein backmapping

Coarse-grained (CG) models play a crucial role in the study of protein structures, protein thermodynamic properties, and protein conformation dynamics. Due to the information loss in the coarse-graining process, backmapping from CG to all-atom configurations is essential in many protein design and drug discovery applications when detailed atomic representations are needed for in-depth studies. Despite recent progress in data-driven backmapping approaches, devising a backmapping method that can be universally applied across various CG models and proteins remains unresolved. In this work, we propose BackDiff, a new generative model designed to achieve generalization and reliability in the protein backmapping problem. BackDiff leverages the conditional score-based diffusion model with geometric representations. Since different CG models can contain different coarse-grained sites which include selected atoms (CG atoms) and simple CG auxiliary functions of atomistic coordinates (CG auxiliary variables), we design a self-supervised training framework to adapt to different CG atoms, and constrain the diffusion sampling paths with arbitrary CG auxiliary variables as conditions. Our method facilitates end-to-end training and allows efficient sampling across different proteins and diverse CG models without the need for retraining. Comprehensive experiments over multiple popular CG models demonstrate BackDiff's superior performance to existing state-of-the-art approaches, and generalization and flexibility that these approaches cannot achieve. A pretrained BackDiff model can offer a convenient yet reliable plug-and-play solution for protein researchers, enabling them to investigate further from their own CG models.Comment: 22 pages, 5 figure

ONE-TOUCH SPEED DIAL CONFIGURATION USING NFC TECHNOLOGY

Internet Protocol (IP) phones contain line keys that can be used to configure speed dialing for one or more contacts. Currently, to configure a line key, a user manually enters a contact’s information to configure a speed dial by using the keypad on the IP phone, which can be a time-consuming and arduous task. Moreover, manual entry increases the likelihood of inaccurate information being input by the user. In order to address such issues, proposed herein are techniques for leveraging near-field communication (NFC) technology on IP phones and mobile devices to efficiently and securely transmit contact information data from a mobile application to an IP phone. With one touch of a button on the mobile application’s graphical user interface (GUI), the user can activate the mobile device’s NFC capability to transmit contact information data that can be used to configure a speed dial line key on the IP phone

Unbiasing Enhanced Sampling on a High-dimensional Free Energy Surface with Deep Generative Model

Biased enhanced sampling methods utilizing collective variables (CVs) are powerful tools for sampling conformational ensembles. Due to high intrinsic dimensions, efficiently generating conformational ensembles for complex systems requires enhanced sampling on high-dimensional free energy surfaces. While methods like temperature-accelerated molecular dynamics (TAMD) can adopt many CVs in a simulation, unbiasing the simulation requires accurate modeling of a high-dimensional CV probability distribution, which is challenging for traditional density estimation techniques. Here we propose an unbiasing method based on the score-based diffusion model, a deep generative learning method that excels in density estimation across complex data landscapes. We test the score-based diffusion unbiasing method on TAMD simulations. The results demonstrate that this unbiasing approach significantly outperforms traditional unbiasing methods, and can generate accurate unbiased conformational ensembles for simulations with a number of CVs higher than usual ranges

Fault line selection in cooperation with multi-mode grounding control for the floating nuclear power plant grid

The Floating nuclear power plant grid is composed of power generation, in-station power supply and external power delivery. To ensure the safety of the nuclear island, the in-station system adopts a special power supply mode, while the external power supply needs to be adapted to different types of external systems. Because of frequent single phase-ground faults and various fault forms, the fault line selection protection should be accurate, sensitive and adaptive. This paper presents a fault line selection method in cooperation with multi-mode grounding control. Based on the maximum united energy entropy ratio (MUEER), the optimal wavelet basis function and decomposition scale are adaptively chosen, while the fault line is selected by wavelet transform modulus maxima (WTMM). For high-impedance faults (HIFs), to enlarge the fault feature, the system grounding mode can be switched by the multi-mode grounding control. Based on the characteristic of HIFs, the fault line can be selected by comparing phase differences of zero-sequence current mutation and fault phase voltage mutation before and after the fault. Simulation results using MATLAB/Simulink show the effectiveness of the proposed method in solving the protection problems

NQE: N-ary Query Embedding for Complex Query Answering over Hyper-relational Knowledge Graphs

Complex query answering (CQA) is an essential task for multi-hop and logical reasoning on knowledge graphs (KGs). Currently, most approaches are limited to queries among binary relational facts and pay less attention to n-ary facts (n>=2) containing more than two entities, which are more prevalent in the real world. Moreover, previous CQA methods can only make predictions for a few given types of queries and cannot be flexibly extended to more complex logical queries, which significantly limits their applications. To overcome these challenges, in this work, we propose a novel N-ary Query Embedding (NQE) model for CQA over hyper-relational knowledge graphs (HKGs), which include massive n-ary facts. The NQE utilizes a dual-heterogeneous Transformer encoder and fuzzy logic theory to satisfy all n-ary FOL queries, including existential quantifiers, conjunction, disjunction, and negation. We also propose a parallel processing algorithm that can train or predict arbitrary n-ary FOL queries in a single batch, regardless of the kind of each query, with good flexibility and extensibility. In addition, we generate a new CQA dataset WD50K-NFOL, including diverse n-ary FOL queries over WD50K. Experimental results on WD50K-NFOL and other standard CQA datasets show that NQE is the state-of-the-art CQA method over HKGs with good generalization capability. Our code and dataset are publicly available.Comment: Accepted by the 37th AAAI Conference on Artificial Intelligence (AAAI-2023

ChatKBQA: A Generate-then-Retrieve Framework for Knowledge Base Question Answering with Fine-tuned Large Language Models

Knowledge Base Question Answering (KBQA) aims to derive answers to natural language questions over large-scale knowledge bases (KBs), which are generally divided into two research components: knowledge retrieval and semantic parsing. However, three core challenges remain, including inefficient knowledge retrieval, retrieval errors adversely affecting semantic parsing, and the complexity of previous KBQA methods. In the era of large language models (LLMs), we introduce ChatKBQA, a novel generate-then-retrieve KBQA framework built on fine-tuning open-source LLMs such as Llama-2, ChatGLM2 and Baichuan2. ChatKBQA proposes generating the logical form with fine-tuned LLMs first, then retrieving and replacing entities and relations through an unsupervised retrieval method, which improves both generation and retrieval more straightforwardly. Experimental results reveal that ChatKBQA achieves new state-of-the-art performance on standard KBQA datasets, WebQSP, and ComplexWebQuestions (CWQ). This work also provides a new paradigm for combining LLMs with knowledge graphs (KGs) for interpretable and knowledge-required question answering. Our code is publicly available.Comment: Preprin

GaussianEditor: Swift and Controllable 3D Editing with Gaussian Splatting

3D editing plays a crucial role in many areas such as gaming and virtual reality. Traditional 3D editing methods, which rely on representations like meshes and point clouds, often fall short in realistically depicting complex scenes. On the other hand, methods based on implicit 3D representations, like Neural Radiance Field (NeRF), render complex scenes effectively but suffer from slow processing speeds and limited control over specific scene areas. In response to these challenges, our paper presents GaussianEditor, an innovative and efficient 3D editing algorithm based on Gaussian Splatting (GS), a novel 3D representation. GaussianEditor enhances precision and control in editing through our proposed Gaussian semantic tracing, which traces the editing target throughout the training process. Additionally, we propose Hierarchical Gaussian splatting (HGS) to achieve stabilized and fine results under stochastic generative guidance from 2D diffusion models. We also develop editing strategies for efficient object removal and integration, a challenging task for existing methods. Our comprehensive experiments demonstrate GaussianEditor's superior control, efficacy, and rapid performance, marking a significant advancement in 3D editing. Project Page: https://buaacyw.github.io/gaussian-editor/Comment: Project Page: https://buaacyw.github.io/gaussian-editor/ Code: https://github.com/buaacyw/GaussianEdito

Text2NKG: Fine-Grained N-ary Relation Extraction for N-ary relational Knowledge Graph Construction

Beyond traditional binary relational facts, n-ary relational knowledge graphs (NKGs) are comprised of n-ary relational facts containing more than two entities, which are closer to real-world facts with broader applications. However, the construction of NKGs still significantly relies on manual labor, and n-ary relation extraction still remains at a course-grained level, which is always in a single schema and fixed arity of entities. To address these restrictions, we propose Text2NKG, a novel fine-grained n-ary relation extraction framework for n-ary relational knowledge graph construction. We introduce a span-tuple classification approach with hetero-ordered merging to accomplish fine-grained n-ary relation extraction in different arity. Furthermore, Text2NKG supports four typical NKG schemas: hyper-relational schema, event-based schema, role-based schema, and hypergraph-based schema, with high flexibility and practicality. Experimental results demonstrate that Text2NKG outperforms the previous state-of-the-art model by nearly 20\% points in the $F_1$ scores on the fine-grained n-ary relation extraction benchmark in the hyper-relational schema. Our code and datasets are publicly available.Comment: Preprin

Beyond the Obvious: Evaluating the Reasoning Ability In Real-life Scenarios of Language Models on Life Scapes Reasoning Benchmark~(LSR-Benchmark)

This paper introduces the Life Scapes Reasoning Benchmark (LSR-Benchmark), a novel dataset targeting real-life scenario reasoning, aiming to close the gap in artificial neural networks' ability to reason in everyday contexts. In contrast to domain knowledge reasoning datasets, LSR-Benchmark comprises free-text formatted questions with rich information on real-life scenarios, human behaviors, and character roles. The dataset consists of 2,162 questions collected from open-source online sources and is manually annotated to improve its quality. Experiments are conducted using state-of-the-art language models, such as gpt3.5-turbo and instruction fine-tuned llama models, to test the performance in LSR-Benchmark. The results reveal that humans outperform these models significantly, indicating a persisting challenge for machine learning models in comprehending daily human life

Assessing the ability of ChatGPT 4.0 in generating check-up reports

BackgroundChatGPT (Chat Generative Pre-trained Transformer), a generative language model, has been applied across various clinical domains. Health check-ups, a widely adopted method for comprehensively assessing personal health, are now chosen by an increasing number of individuals. This study aimed to evaluate ChatGPT 4.0’s ability to efficiently provide patients with accurate and personalized health reports.MethodsA total of 89 check-up reports generated by ChatGPT 4.0 were assessed. The reports were derived from the Check-up Center of the First Affiliated Hospital of Shantou University Medical College. Each report was translated into English by ChatGPT 4.0 and graded independently by three qualified doctors in both English and Chinese. The grading criteria encompassed six aspects: adherence to current treatment guidelines (Guide), diagnostic accuracy (Diagnosis), logical flow of information (Order), systematic presentation (System), internal consistency (Consistency), and appropriateness of recommendations (Suggestion), each scored on a 4-point scale. The complexity of the cases was categorized into three levels (LOW, MEDIUM, HIGH). Wilcoxon rank sum test and Kruskal-Wallis test were selected to examine differences in grading across languages and complexity levels.ResultsChatGPT 4.0 demonstrated strong performance in adhering to clinical guidelines, providing accurate diagnoses, systematic presentation, and maintaining consistency. However, it struggled with prioritizing high-risk items and providing comprehensive suggestions. In the “Order” category, a significant proportion of reports contained mixed data, several reports being completely incorrect. In the “Suggestion” category, most reports were deemed correct but inadequate. No significant language advantage was observed, with performance varying across complexity levels. English reports showed significant differences in grading across complexity levels, while Chinese reports exhibited distinct performance across all categories.ConclusionIn conclusion, ChatGPT 4.0 is currently well-suited as an assistant to the chief examiner, particularly for handling simpler tasks and contributing to specific sections of check-up reports. It holds the potential to enhance medical efficiency, improve the quality of clinical check-up work, and deliver patient-centered services