Knowledge Graph-Guided Retrieval Augmented Generation

Retrieval-augmented generation (RAG) has emerged as a promising technology for addressing hallucination issues in the responses generated by large language models (LLMs). Existing studies on RAG primarily focus on applying semantic-based approaches to retrieve isolated relevant chunks, which ignore their intrinsic relationships. In this paper, we propose a novel Knowledge Graph-Guided Retrieval Augmented Generation (KG$^2$RAG) framework that utilizes knowledge graphs (KGs) to provide fact-level relationships between chunks, improving the diversity and coherence of the retrieved results. Specifically, after performing a semantic-based retrieval to provide seed chunks, KG$^2$RAG employs a KG-guided chunk expansion process and a KG-based chunk organization process to deliver relevant and important knowledge in well-organized paragraphs. Extensive experiments conducted on the HotpotQA dataset and its variants demonstrate the advantages of KG$^2$RAG compared to existing RAG-based approaches, in terms of both response quality and retrieval quality.

QMe14S, A Comprehensive and Efficient Spectral Dataset for Small Organic Molecules

Developing machine learning protocols for molecular simulations requires comprehensive and efficient datasets. Here we introduce the QMe14S dataset, comprising 186,102 small organic molecules featuring 14 elements (H, B, C, N, O, F, Al, Si, P, S, Cl, As, Se, Br) and 47 functional groups. Using density functional theory at the B3LYP/TZVP level, we optimized the geometries and calculated properties including energy, atomic charge, atomic force, dipole moment, quadrupole moment, polarizability, octupole moment, first hyperpolarizability, and Hessian. At the same level, we obtained the harmonic IR, Raman and NMR spectra. Furthermore, we conducted ab initio molecular dynamics simulations to generate dynamic configurations and extract nonequilibrium properties, including energy, forces, and Hessians. By leveraging our E(3)-equivariant message-passing neural network (DetaNet), we demonstrated that models trained on QMe14S outperform those trained on the previously developed QM9S dataset in simulating molecular spectra. The QMe14S dataset thus serves as a comprehensive benchmark for molecular simulations, offering valuable insights into structure-property relationships.

Controllable Protein Sequence Generation with LLM Preference Optimization

Designing proteins with specific attributes offers an important solution to address biomedical challenges. Pre-trained protein large language models (LLMs) have shown promising results on protein sequence generation. However, to control sequence generation for specific attributes, existing work still exhibits poor functionality and structural stability. In this paper, we propose a novel controllable protein design method called CtrlProt. We finetune a protein LLM with a new multi-listwise preference optimization strategy to improve generation quality and support multi-attribute controllable generation. Experiments demonstrate that CtrlProt can meet functionality and structural stability requirements effectively, achieving state-of-the-art performance in both single-attribute and multi-attribute protein sequence generation.

Deep Learning and Foundation Models for Weather Prediction: A Survey

Physics-based numerical models have been the bedrock of atmospheric sciences for decades, offering robust solutions but often at the cost of significant computational resources. Deep learning (DL) models have emerged as powerful tools in meteorology, capable of analyzing complex weather and climate data by learning intricate dependencies and providing rapid predictions once trained. While these models demonstrate promising performance in weather prediction, often surpassing traditional physics-based methods, they still face critical challenges. This paper presents a comprehensive survey of recent deep learning and foundation models for weather prediction. We propose a taxonomy to classify existing models based on their training paradigms: deterministic predictive learning, probabilistic generative learning, and pre-training and fine-tuning. For each paradigm, we delve into the underlying model architectures, address major challenges, offer key insights, and propose targeted directions for future research. Furthermore, we explore real-world applications of these methods and provide a curated summary of open-source code repositories and widely used datasets, aiming to bridge research advancements with practical implementations while fostering open and trustworthy scientific practices in adopting cutting-edge artificial intelligence for weather prediction. The related sources are available at https://github.com/JimengShi/ DL-Foundation-Models-Weather.

Multi-scale Latent Point Consistency Models for 3D Shape Generation

Consistency Models (CMs) have significantly accelerated the sampling process in diffusion models, yielding impressive results in synthesizing high-resolution images. To explore and extend these advancements to point-cloud-based 3D shape generation, we propose a novel Multi-scale Latent Point Consistency Model (MLPCM). Our MLPCM follows a latent diffusion framework and introduces hierarchical levels of latent representations, ranging from point-level to super-point levels, each corresponding to a different spatial resolution. We design a multi-scale latent integration module along with 3D spatial attention to effectively denoise the point-level latent representations conditioned on those from multiple super-point levels. Additionally, we propose a latent consistency model, learned through consistency distillation, that compresses the prior into a one-step generator. This significantly improves sampling efficiency while preserving the performance of the original teacher model. Extensive experiments on standard benchmarks ShapeNet and ShapeNet-Vol demonstrate that MLPCM achieves a 100x speedup in the generation process, while surpassing state-of-the-art diffusion models in terms of both shape quality and diversity.

Improving the Transferability of 3D Point Cloud Attack via Spectral-aware Admix and Optimization Designs

Deep learning models for point clouds have shown to be vulnerable to adversarial attacks, which have received increasing attention in various safety-critical applications such as autonomous driving, robotics, and surveillance. Existing 3D attackers generally design various attack strategies in the white-box setting, requiring the prior knowledge of 3D model details. However, real-world 3D applications are in the black-box setting, where we can only acquire the outputs of the target classifier. Although few recent works try to explore the black-box attack, they still achieve limited attack success rates (ASR). To alleviate this issue, this paper focuses on attacking the 3D models in a transfer-based black-box setting, where we first carefully design adversarial examples in a white-box surrogate model and then transfer them to attack other black-box victim models. Specifically, we propose a novel Spectral-aware Admix with Augmented Optimization method (SAAO) to improve the adversarial transferability. In particular, since traditional Admix strategy are deployed in the 2D domain that adds pixel-wise images for perturbing, we can not directly follow it to merge point clouds in coordinate domain as it will destroy the geometric shapes. Therefore, we design spectral-aware fusion that performs Graph Fourier Transform (GFT) to get spectral features of the point clouds and add them in the spectral domain. Afterward, we run a few steps with spectral-aware weighted Admix to select better optimization paths as well as to adjust corresponding learning weights. At last, we run more steps to generate adversarial spectral feature along the optimization path and perform Inverse-GFT on the adversarial spectral feature to obtain the adversarial example in the data domain. Experiments show that our SAAO achieves better transferability compared to existing 3D attack methods.

Hard-Label Black-Box Attacks on 3D Point Clouds

With the maturity of depth sensors in various 3D safety-critical applications, 3D point cloud models have been shown to be vulnerable to adversarial attacks. Almost all existing 3D attackers simply follow the white-box or black-box setting to iteratively update coordinate perturbations based on back-propagated or estimated gradients. However, these methods are hard to deploy in real-world scenarios (no model details are provided) as they severely rely on parameters or output logits of victim models. To this end, we propose point cloud attacks from a more practical setting, i.e., hard-label black-box attack, in which attackers can only access the prediction label of 3D input. We introduce a novel 3D attack method based on a new spectrum-aware decision boundary algorithm to generate high-quality adversarial samples. In particular, we first construct a class-aware model decision boundary, by developing a learnable spectrum-fusion strategy to adaptively fuse point clouds of different classes in the spectral domain, aiming to craft their intermediate samples without distorting the original geometry. Then, we devise an iterative coordinate-spectrum optimization method with curvature-aware boundary search to move the intermediate sample along the decision boundary for generating adversarial point clouds with trivial perturbations. Experiments demonstrate that our attack competitively outperforms existing white/black-box attackers in terms of attack performance and adversary quality.

Abrupt Learning in Transformers: A Case Study on Matrix Completion

Recent analysis on the training dynamics of Transformers has unveiled an interesting characteristic: the training loss plateaus for a significant number of training steps, and then suddenly (and sharply) drops to near--optimal values. To understand this phenomenon in depth, we formulate the low-rank matrix completion problem as a masked language modeling (MLM) task, and show that it is possible to train a BERT model to solve this task to low error. Furthermore, the loss curve shows a plateau early in training followed by a sudden drop to near-optimal values, despite no changes in the training procedure or hyper-parameters. To gain interpretability insights into this sudden drop, we examine the model's predictions, attention heads, and hidden states before and after this transition. Concretely, we observe that (a) the model transitions from simply copying the masked input to accurately predicting the masked entries; (b) the attention heads transition to interpretable patterns relevant to the task; and (c) the embeddings and hidden states encode information relevant to the problem. We also analyze the training dynamics of individual model components to understand the sudden drop in loss.

Joint Top-Down and Bottom-Up Frameworks for 3D Visual Grounding

This paper tackles the challenging task of 3D visual grounding-locating a specific object in a 3D point cloud scene based on text descriptions. Existing methods fall into two categories: top-down and bottom-up methods. Top-down methods rely on a pre-trained 3D detector to generate and select the best bounding box, resulting in time-consuming processes. Bottom-up methods directly regress object bounding boxes with coarse-grained features, producing worse results. To combine their strengths while addressing their limitations, we propose a joint top-down and bottom-up framework, aiming to enhance the performance while improving the efficiency. Specifically, in the first stage, we propose a bottom-up based proposal generation module, which utilizes lightweight neural layers to efficiently regress and cluster several coarse object proposals instead of using a complex 3D detector. Then, in the second stage, we introduce a top-down based proposal consolidation module, which utilizes graph design to effectively aggregate and propagate the query-related object contexts among the generated proposals for further refinement. By jointly training these two modules, we can avoid the inherent drawbacks of the complex proposals in the top-down framework and the coarse proposals in the bottom-up framework. Experimental results on the ScanRefer benchmark show that our framework is able to achieve the state-of-the-art performance.

A Prompt-Based Knowledge Graph Foundation Model for Universal In-Context Reasoning

Extensive knowledge graphs (KGs) have been constructed to facilitate knowledge-driven tasks across various scenarios. However, existing work usually develops separate reasoning models for different KGs, lacking the ability to generalize and transfer knowledge across diverse KGs and reasoning settings. In this paper, we propose a prompt-based KG foundation model via in-context learning, namely KG-ICL, to achieve a universal reasoning ability. Specifically, we introduce a prompt graph centered with a query-related example fact as context to understand the query relation. To encode prompt graphs with the generalization ability to unseen entities and relations in queries, we first propose a unified tokenizer that maps entities and relations in prompt graphs to predefined tokens. Then, we propose two message passing neural networks to perform prompt encoding and KG reasoning, respectively. We conduct evaluation on 43 different KGs in both transductive and inductive settings. Results indicate that the proposed KG-ICL outperforms baselines on most datasets, showcasing its outstanding generalization and universal reasoning capabilities. The source code is accessible on GitHub: https://github.com/nju-websoft/KG-ICL.