CSGDN: Contrastive Signed Graph Diffusion Network for Predicting Crop Gene-Trait Associations

Positive and negative association preidiction between gene and trait help studies for crops to perform complex physiological functions. The transcription and regulation activity of specific genes will be adjusted accordingly in different cell types, developmental stages, and physiological states to meet the needs of organisms. Determing gene-trait associations can resolve the mechanism of trait formation and benefit the improvement of crop yield and quality. There are the following two problems in obtaining the positive/negative associations between gene and trait: 1) High-throughput DNA/RNA sequencing and trait data collection are expensive and time-consuming due to the need to process large sample sizes; 2) experiments introduce both random and systematic errors, and, at the same time, calculations or predictions using software or models may produce noise. To address these two issues, we propose a Contrastive Signed Graph Diffusion Network, CSGDN, to learn robust node representations with fewer training samples to achieve higher link prediction accuracy. CSGDN employs a signed graph diffusion method to uncover the underlying regulatory associations between genes and traits. Then, stochastic perterbation strategies are used to create two views for both original and diffusive graphs. At last, a multi-view contrastive learning paradigm loss is designed to unify the node presentations learned from the two views to resist interference and reduce noise. We conduct experiments to validate the performance of CSGDN on three crop datasets: Gossypium hirsutum, Brassica napus, and Triticum turgidum. The results demonstrate that the proposed model outperforms state-of-the-art methods by up to 9.28% AUC for link sign prediction in G. hirsutum dataset.

Verbalized Graph Representation Learning: A Fully Interpretable Graph Model Based on Large Language Models Throughout the Entire Process

Representation learning on text-attributed graphs (TAGs) has attracted significant interest due to its wide-ranging real-world applications, particularly through Graph Neural Networks (GNNs). Traditional GNN methods focus on encoding the structural information of graphs, often using shallow text embeddings for node or edge attributes. This limits the model to understand the rich semantic information in the data and its reasoning ability for complex downstream tasks, while also lacking interpretability. With the rise of large language models (LLMs), an increasing number of studies are combining them with GNNs for graph representation learning and downstream tasks. While these approaches effectively leverage the rich semantic information in TAGs datasets, their main drawback is that they are only partially interpretable, which limits their application in critical fields. In this paper, we propose a verbalized graph representation learning (VGRL) method which is fully interpretable. In contrast to traditional graph machine learning models, which are usually optimized within a continuous parameter space, VGRL constrains this parameter space to be text description which ensures complete interpretability throughout the entire process, making it easier for users to understand and trust the decisions of the model. We conduct several studies to empirically evaluate the effectiveness of VGRL and we believe these method can serve as a stepping stone in graph representation learning.

DropEdge not Foolproof: Effective Augmentation Method for Signed Graph Neural Networks

The paper discusses signed graphs, which model friendly or antagonistic relationships using edges marked with positive or negative signs, focusing on the task of link sign prediction. While Signed Graph Neural Networks (SGNNs) have advanced, they face challenges like graph sparsity and unbalanced triangles. The authors propose using data augmentation (DA) techniques to address these issues, although many existing methods are not suitable for signed graphs due to a lack of side information. They highlight that the random DropEdge method, a rare DA approach applicable to signed graphs, does not enhance link sign prediction performance. In response, they introduce the Signed Graph Augmentation (SGA) framework, which includes a structure augmentation module to identify candidate edges and a strategy for selecting beneficial candidates, ultimately improving SGNN training. Experimental results show that SGA significantly boosts the performance of SGNN models, with a notable 32.3% improvement in F1-micro for SGCN on the Slashdot dataset.

SE-SGformer: A Self-Explainable Signed Graph Transformer for Link Sign Prediction

Signed Graph Neural Networks (SGNNs) have been shown to be effective in analyzing complex patterns in real-world situations where positive and negative links coexist. However, SGNN models suffer from poor explainability, which limit their adoptions in critical scenarios that require understanding the rationale behind predictions. To the best of our knowledge, there is currently no research work on the explainability of the SGNN models. Our goal is to address the explainability of decision-making for the downstream task of link sign prediction specific to signed graph neural networks. Since post-hoc explanations are not derived directly from the models, they may be biased and misrepresent the true explanations. Therefore, in this paper we introduce a Self-Explainable Signed Graph transformer (SE-SGformer) framework, which can not only outputs explainable information while ensuring high prediction accuracy. Specifically, We propose a new Transformer architecture for signed graphs and theoretically demonstrate that using positional encoding based on signed random walks has greater expressive power than current SGNN methods and other positional encoding graph Transformer-based approaches. We constructs a novel explainable decision process by discovering the $K$-nearest (farthest) positive (negative) neighbors of a node to replace the neural network-based decoder for predicting edge signs. These $K$ positive (negative) neighbors represent crucial information about the formation of positive (negative) edges between nodes and thus can serve as important explanatory information in the decision-making process. We conducted experiments on several real-world datasets to validate the effectiveness of SE-SGformer, which outperforms the state-of-the-art methods by improving 2.2\% prediction accuracy and 73.1\% explainablity accuracy in the best-case scenario.

Semantic-CC: Boosting Remote Sensing Image Change Captioning via Foundational Knowledge and Semantic Guidance

Remote sensing image change captioning (RSICC) aims to articulate the changes in objects of interest within bi-temporal remote sensing images using natural language. Given the limitations of current RSICC methods in expressing general features across multi-temporal and spatial scenarios, and their deficiency in providing granular, robust, and precise change descriptions, we introduce a novel change captioning (CC) method based on the foundational knowledge and semantic guidance, which we term Semantic-CC. Semantic-CC alleviates the dependency of high-generalization algorithms on extensive annotations by harnessing the latent knowledge of foundation models, and it generates more comprehensive and accurate change descriptions guided by pixel-level semantics from change detection (CD). Specifically, we propose a bi-temporal SAM-based encoder for dual-image feature extraction; a multi-task semantic aggregation neck for facilitating information interaction between heterogeneous tasks; a straightforward multi-scale change detection decoder to provide pixel-level semantic guidance; and a change caption decoder based on the large language model (LLM) to generate change description sentences. Moreover, to ensure the stability of the joint training of CD and CC, we propose a three-stage training strategy that supervises different tasks at various stages. We validate the proposed method on the LEVIR-CC and LEVIR-CD datasets. The experimental results corroborate the complementarity of CD and CC, demonstrating that Semantic-CC can generate more accurate change descriptions and achieve optimal performance across both tasks.

Applications of Explainable artificial intelligence in Earth system science

In recent years, artificial intelligence (AI) rapidly accelerated its influence and is expected to promote the development of Earth system science (ESS) if properly harnessed. In application of AI to ESS, a significant hurdle lies in the interpretability conundrum, an inherent problem of black-box nature arising from the complexity of AI algorithms. To address this, explainable AI (XAI) offers a set of powerful tools that make the models more transparent. The purpose of this review is twofold: First, to provide ESS scholars, especially newcomers, with a foundational understanding of XAI, serving as a primer to inspire future research advances; second, to encourage ESS professionals to embrace the benefits of AI, free from preconceived biases due to its lack of interpretability. We begin with elucidating the concept of XAI, along with typical methods. We then delve into a review of XAI applications in the ESS literature, highlighting the important role that XAI has played in facilitating communication with AI model decisions, improving model diagnosis, and uncovering scientific insights. We identify four significant challenges that XAI faces within the ESS, and propose solutions. Furthermore, we provide a comprehensive illustration of multifaceted perspectives. Given the unique challenges in ESS, an interpretable hybrid approach that seamlessly integrates AI with domain-specific knowledge appears to be a promising way to enhance the utility of AI in ESS. A visionary outlook for ESS envisions a harmonious blend where process-based models govern the known, AI models explore the unknown, and XAI bridges the gap by providing explanations.

MAP: Low-compute Model Merging with Amortized Pareto Fronts via Quadratic Approximation

Model merging has emerged as an effective approach to combine multiple single-task models, fine-tuned from the same pre-trained model, into a multitask model. This process typically involves computing a weighted average of the model parameters without any additional training. Existing model-merging methods focus on enhancing average task accuracy. However, interference and conflicts between the objectives of different tasks can lead to trade-offs during model merging. In real-world applications, a set of solutions with various trade-offs can be more informative, helping practitioners make decisions based on diverse preferences. In this paper, we introduce a novel low-compute algorithm, Model Merging with Amortized Pareto Front (MAP). MAP identifies a Pareto set of scaling coefficients for merging multiple models to reflect the trade-offs. The core component of MAP is approximating the evaluation metrics of the various tasks using a quadratic approximation surrogate model derived from a pre-selected set of scaling coefficients, enabling amortized inference. Experimental results on vision and natural language processing tasks show that MAP can accurately identify the Pareto front. To further reduce the required computation of MAP, we propose (1) a Bayesian adaptive sampling algorithm and (2) a nested merging scheme with multiple stages.

VCR: Visual Caption Restoration

We introduce Visual Caption Restoration (VCR), a novel vision-language task that challenges models to accurately restore partially obscured texts using pixel-level hints within images. This task stems from the observation that text embedded in images is intrinsically different from common visual elements and natural language due to the need to align the modalities of vision, text, and text embedded in images. While numerous works have integrated text embedded in images into visual question-answering tasks, approaches to these tasks generally rely on optical character recognition or masked language modeling, thus reducing the task to mainly text-based processing. However, text-based processing becomes ineffective in VCR as accurate text restoration depends on the combined information from provided images, context, and subtle cues from the tiny exposed areas of masked texts. We develop a pipeline to generate synthetic images for the VCR task using image-caption pairs, with adjustable caption visibility to control the task difficulty. With this pipeline, we construct a dataset for VCR called VCR-Wiki using images with captions from Wikipedia, comprising 2.11M English and 346K Chinese entities in both easy and hard split variants. Our results reveal that current vision language models significantly lag behind human performance in the VCR task, and merely fine-tuning the models on our dataset does not lead to notable improvements. We release VCR-Wiki and the data construction code to facilitate future research.

MarsSeg: Mars Surface Semantic Segmentation with Multi-level Extractor and Connector

The segmentation and interpretation of the Martian surface play a pivotal role in Mars exploration, providing essential data for the trajectory planning and obstacle avoidance of rovers. However, the complex topography, similar surface features, and the lack of extensive annotated data pose significant challenges to the high-precision semantic segmentation of the Martian surface. To address these challenges, we propose a novel encoder-decoder based Mars segmentation network, termed MarsSeg. Specifically, we employ an encoder-decoder structure with a minimized number of down-sampling layers to preserve local details. To facilitate a high-level semantic understanding across the shadow multi-level feature maps, we introduce a feature enhancement connection layer situated between the encoder and decoder. This layer incorporates Mini Atrous Spatial Pyramid Pooling (Mini-ASPP), Polarized Self-Attention (PSA), and Strip Pyramid Pooling Module (SPPM). The Mini-ASPP and PSA are specifically designed for shadow feature enhancement, thereby enabling the expression of local details and small objects. Conversely, the SPPM is employed for deep feature enhancement, facilitating the extraction of high-level semantic category-related information. Experimental results derived from the Mars-Seg and AI4Mars datasets substantiate that the proposed MarsSeg outperforms other state-of-the-art methods in segmentation performance, validating the efficacy of each proposed component.

Gemini 1.5: Unlocking multimodal understanding across millions of tokens of context

In this report, we present the latest model of the Gemini family, Gemini 1.5 Pro, a highly compute-efficient multimodal mixture-of-experts model capable of recalling and reasoning over fine-grained information from millions of tokens of context, including multiple long documents and hours of video and audio. Gemini 1.5 Pro achieves near-perfect recall on long-context retrieval tasks across modalities, improves the state-of-the-art in long-document QA, long-video QA and long-context ASR, and matches or surpasses Gemini 1.0 Ultra's state-of-the-art performance across a broad set of benchmarks. Studying the limits of Gemini 1.5 Pro's long-context ability, we find continued improvement in next-token prediction and near-perfect retrieval (>99%) up to at least 10M tokens, a generational leap over existing models such as Claude 2.1 (200k) and GPT-4 Turbo (128k). Finally, we highlight surprising new capabilities of large language models at the frontier; when given a grammar manual for Kalamang, a language with fewer than 200 speakers worldwide, the model learns to translate English to Kalamang at a similar level to a person who learned from the same content.