GenAI4ELab/papercli-papers huggingface dataset:
MMPG: MoE-based Adaptive Multi-Perspective Graph Fusion for Protein Representation Learning
Authors: Yusong Wang; Jialun Shen; Zhihao Wu; Yicheng Xu; Shiyin Tan; Mingkun Xu; Changshuo Wang; Zixing Song; Prayag Tiwari
Venue: AAAI 2026 (main)

Abstract: Graph Neural Networks (GNNs) have been widely adopted for Protein Representation Learning (PRL), as residue interaction networks can be naturally represented as graphs. Current GNN-based PRL methods typically rely on single-perspective graph construction strategies, which capture partial properties of residue interactions, resulting in incomplete protein representations. To address this limitation, we propose MMPG, a framework that constructs protein graphs from multiple perspectives and adaptively fuses them via Mixture of Experts (MoE) for PRL. MMPG constructs graphs from physical, chemical, and geometric perspectives to characterize different properties of residue interactions. To capture both perspective-specific features and their synergies, we develop an MoE module, which dynamically routes perspectives to specialized experts, where experts learn intrinsic features and cross-perspective interactions. We quantitatively verify that MoE automatically specializes experts in modeling distinct levels of interaction—from individual representations, to pairwise inter-perspective synergies, and ultimately to a global consensus across all perspectives. Through integrating this multi-level information, MMPG produces superior protein representations and achieves advanced performance on four different downstream protein tasks.
Reasoning About the Unsaid: Misinformation Detection with Omission-Aware Graph Inference
Authors: Zhengjia Wang; Danding Wang; Qiang Sheng; Jiaying Wu; Juan Cao
Venue: AAAI 2026 (main)

Abstract: This paper investigates the detection of misinformation, which deceives readers by explicitly fabricating misleading content or implicitly omitting important information necessary for informed judgment. While the former has been extensively studied, omission-based deception remains largely overlooked, even though it can subtly guide readers toward false conclusions under the illusion of completeness. To pioneer in this direction, this paper presents OmiGraph, the first omission-aware framework for misinformation detection.  Specifically, OmiGraph constructs an omission-aware graph for the target news by utilizing a contextual environment that captures complementary perspectives of the same event, thereby surfacing potentially omitted contents. Based on this graph, omission-oriented relation modeling is then proposed to identify the internal contextual dependencies, as well as the dynamic omission intents, formulating a comprehensive omission relation representation. Finally, to extract omission patterns for detection, OmiGraph introduces omission-aware message-passing and aggregation that establishes holistic deception perception by integrating the omission contents and relations. Experiments show that, by considering the omission perspective, our approach attains remarkable performance, achieving average improvements of +5.4% F1 and +5.3% ACC on two large-scale benchmarks.
Dual-Channel Learning Framework for Zero-Shot CircRNA-miRNA Interaction Prediction via State Space Modeling
Authors: Mengmeng Wei; Lei Wang; Zhu-Hong You; Pengwei Hu; Bowei Zhao; Zhi-An Huang; Yu-An Huang; Haicheng Yi
Venue: AAAI 2026 (main)

Abstract: CircRNA-miRNA interaction (CMI) plays a pivotal role in disease therapeutics and drug discovery. However, existing methods face several challenges in modeling complex biological networks and zero-shot learning scenarios. Biological networks encapsulate rich biological information, yet current approaches often fail to fully exploit this depth. Moreover, zero-shot prediction requires models to identify new interactions without relying on previously observed samples, imposing stringent requirements on generalization capabilities. To address these limitations, we propose a dual-channel learning framework leveraging State space modeling for Zero-shot CMI prediction (ZeroStem). ZeroStem first enhances the biological relevance of node using prior knowledge, and employs a graph Transformer to extract macro-topological representations. Subsequently, it generates semantic subgraphs based on meta-paths to focus on specific biological relationships, utilizing the Mamba to extract micro-semantic representations via state space modeling. Finally, macro-topological and micro-semantic representations are seamlessly integrated through linear transformation and residual connections, enabling high-precision zero-shot CMI prediction. Extensive experiments on multiple benchmark datasets demonstrate that ZeroStem significantly outperforms existing methods, validating its efficiency and robust generalization in CMI prediction. Case studies further illustrate that ZeroStem offers novel insights into the molecular mechanisms underlying intricate disease-associated networks.
Synergizing Multigrid Algorithms with Vision Transformer: A Novel Approach to Enhance the Seismic Foundation Model
Authors: Huiwen Wu; Shuo Zhang; Yi Liu; Hongbin Ye
Venue: AAAI 2026 (main)

Abstract: Due to the rapid advancement and homogenization of Artificial Intelligence (AI) technology development, transformer-based foundation models have revolutionized scientific applications, such as drug discovery, materials research, and astronomy. However, seismic data presents unique characteristics that require specialized processing techniques for pretraining foundation models in seismic contexts with high- and low-frequency features playing crucial roles. Existing Vision Transformer (ViT) with sequential image tokenization fails to efficiently and effectively capture both high- and low-frequency seismic information  because they ignore the intrinsic structural patterns of seismograms.  This work introduces ADATG, a novel adaptive two-grid training strategy with Hilbert encoding, explicitly tailored for seismogram data and leveraging the hierarchical structures inherent in seismic data. Specifically, our approach employs spectrum decomposition to separate high- and low-frequency components, and hierarchical Hilbert encoding to represent the data effectively. Moreover, inspired by the frequency principle, we propose an adaptive training strategy that initially emphasizes coarse-level information and then progressively refines the model's focus on fine-level features. Extensive experiments demonstrate the effectiveness and efficiency of our method. This research highlights the importance of data encoding and training strategies informed by the distinct characteristics of high- and low-frequency features in seismic images, ultimately enhancing the pretraining of visual seismic foundation models.
Generalizable Drug–Target Interaction Prediction via ESM-2 Representations and Progressive Contrastive Curriculum Learning
Authors: Qianyang Wu; Jingwei Lv; Zilong Zhang; Feifei Cui
Venue: AAAI 2026 (main)

Abstract: Predicting drug–target interactions (DTIs) is a fundamental task in computational drug discovery, yet it remains challenging under distribution shifts and limited training data. Existing approaches often suffer from poor generalization, weak cross-modal alignment between molecular and protein representations, and vulnerability to noisy supervision.We propose ESP-DTI, a unified framework designed to enhance generalization by integrating large-scale protein language models with curriculum learning and cross-modal contrastive alignment. Specifically, we leverage ESM-2 to encode context-aware protein representations and adopt a CLIP-style contrastive objective to align drug and protein embeddings in a shared latent space. To further improve learning robustness, we introduce a progressive curriculum sampling strategy that dynamically schedules training instances based on model confidence, enabling a gradual shift from easy to hard examples.Experimental results on four benchmark datasets demonstrate that ESP-DTI consistently outperforms state-of-the-art baselines, achieving a +3.1% improvement in average accuracy. Ablation studies confirm the complementary benefits of each component, validating their collective contribution to robust and generalizable DTI prediction.Our work underscores the effectiveness of combining pretrained protein language models with structured training curricula and cross-modal contrastive learning for reliable DTI prediction under real-world, distribution-shifted conditions.
Exploring Selective Avoidance for Online User Behavior Analysis: A Forest of Thought Explanation
Authors: Xiaohua Wu; Lin Li; Kaize Shi; Xiaohui Tao; Jianwei Zhang; Yuefeng Li
Venue: AAAI 2026 (main)

Abstract: The response behaviors observed in online user-generated content (UGC) frequently demonstrate non-linear characteristics, such as conditional branching and selective avoidance. These patterns present additional challenges for ensuring the trustworthiness of Large Language Model (LLMs) reasoning, particularly as their unidirectional, left-to-right inference mechanisms may not adequately capture such complex reasoning dynamics. To address this, we propose a Forest of Thought Explanation (FoTE), a novel prompting that models the selective avoidance in UGC while ensuring explanation consensus through reasoning paths across all decision sub-trees. FoTE firstly generates various reasoning paths through an adaptive CoT prompting. Each generated thought is subsequently evaluated through cooperative game theory to quantify its fair influence. The thoughts with the top-k contribution scores are preserved and randomly sampled to emulate selective avoidance for the next reasoning iteration. Through extensive evaluations across three open-source LLMs and two established social science problems (spanning four benchmark datasets), FoTE demonstrates superior success rates compared to competing prompting strategies. Notably, its performance gains increase with the strength of selective avoidance in social problems. The trustworthiness of our FoTE is enhanced by the incorporation of (1) a solid theoretical foundation and (2) a transparent reasoning path that converges toward consensus.
Investigating Data Pruning for Pretraining Biological Foundation Models at Scale
Authors: Yifan Wu; Jiyue Jiang; Xichen Ye; Yiqi Wang; Chang Zhou; Yitao Xu; Jiayang Chen; He Hu; Weizhong Zhang; Cheng Jin; Jiao Yuan; Yu Li
Venue: AAAI 2026 (main)

Abstract: Biological foundation models (BioFMs), pretrained on large-scale biological sequences, have recently shown strong potential in providing meaningful representations for diverse downstream bioinformatics tasks. However, such models often rely on millions to billions of training sequences and billions of parameters, resulting in prohibitive computational costs and significant barriers to reproducibility and accessibility—particularly for academic labs. To address these challenges, we investigate the feasibility of data pruning for BioFM pretraining and propose a post-hoc influence-guided data pruning framework tailored to biological domains. Our approach first introduces a subset-based self-influence formulation that enables efficient estimation of sample importance at low computational cost. Built upon this, we propose two simple yet effective selection strategies: Top-k Influence (Top I) and Coverage-Centric Influence (CCI). Then, we empirically validate our method on two representative BioFMs: RNA-FM and ESM-C. For RNA, our framework consistently outperforms random selection baselines under an extreme pruning rate of over 99%, which displays our framework's effectiveness. Furthermore, we demonstrate the generalizability of our framework on protein-related tasks using ESM-C. Specifically, our coreset even outperforms random 10x subsets in both RNA and protein settings, revealing substantial redundancy in biological sequence datasets. These findings underscore the potential of influence-guided data pruning to substantially reduce the computational cost of BioFM pretraining, paving the way for more efficient, accessible, and sustainable biological AI research.
Sim-to-Real: An Unsupervised Noise Layer for Screen-Camera Watermarking Robustness
Authors: Yufeng Wu; Xin Liao; Baowei Wang; Han Fang; Xiaoshuai Wu; Mingyue Chen; Guiling Wang
Venue: AAAI 2026 (main)

Abstract: Unauthorized screen capturing and dissemination pose severe security threats such as data leakage and information theft. Several studies propose robust watermarking methods to track the copyright of Screen-Camera (SC) images, facilitating post-hoc certification against infringement. These techniques typically employ heuristic mathematical modeling or supervised neural network fitting as the noise layer, to enhance watermarking robustness against SC. However, both strategies cannot fundamentally achieve an effective approximation of SC noise. Mathematical simulation suffers from biased approximations due to the incomplete decomposition of the noise and the absence of interdependence among the noise components. Supervised networks require paired data to train the noise-fitting model, and it is difficult for the model to learn all the features of the noise. To address the above issues, we propose Simulation-to-Real (S2R). Specifically, an unsupervised noise layer employs unpaired data to learn the discrepancy between the modeled simulated noise distribution and the real-world SC noise distribution, rather than directly learning the mapping from sharp images to real-world images. Learning this transformation from simulation to reality is inherently simpler, as it primarily involves bridging the gap in noise distributions, instead of the complex task of reconstructing fine-grained image details. Extensive experimental results validate the efficacy of the proposed method, demonstrating superior watermark robustness and generalization compared to state-of-the-art methods.
GROVER: Graph-guided Representation of Omics and Vision with Expert Regulation for Adaptive Spatial Multi-omics Fusion
Authors: Yongjun Xiao; Dian Meng; Xinlei Huang; Yanran Liu; Shiwei Ruan; Ziyue Qiao; Xubin Zheng
Venue: AAAI 2026 (main)

Abstract: Effectively modeling multimodal spatial omics data is critical for understanding tissue complexity and underlying biological mechanisms. While spatial transcriptomics, proteomics, and epigenomics capture molecular features, they lack pathological morphological context. Integrating these omics with histopathological images is thus critical for comprehensive disease tissue analysis. However, substantial heterogeneity across omics, imaging, and spatial modalities poses significant challenges. Naive fusion of semantically distinct sources often leads to ambiguous representations. Additionally, the resolution mismatch between high-resolution histology images and lower-resolution sequencing spots complicates spatial alignment. Biological perturbations during sample preparation further distort modality-specific signals, hindering accurate integration. To address these challenges, we propose Graph-guided Representation of Omics and Vision with Expert Regulation for Adaptive Spatial Multi-omics Fusion (GROVER), a novel framework for adaptive integration of spatial multi-omics data. GROVER leverages a Graph Convolutional Network encoder based on Kolmogorov–Arnold Networks to capture the nonlinear dependencies between each modality and its associated spatial structure, thereby producing expressive, modality-specific embeddings. To align these representations, we introduce a spot-feature-pair contrastive learning strategy that explicitly optimizes the correspondence across modalities at each spot. Furthermore, we design a dynamic expert routing mechanism that adaptively selects informative modalities for each spot while suppressing noisy or low-quality inputs. Experiments on real-world spatial omics datasets demonstrate that GROVER outperforms state-of-the-art baselines, providing a robust and reliable solution for multimodal integration.
Informative Subgraph Extraction with Deep Reinforcement Learning for Drug-Drug Interaction Prediction
Authors: Jiancong Xie; Wentao Wei; Chi Zhang; Jiahua Rao; Yuedong Yang
Venue: AAAI 2026 (main)

Abstract: Drug-drug interaction (DDI) prediction is pivotal for drug safety and clinical decision-making. Recently, subgraph-based methods utilizing knowledge graphs (KGs) and domain information have achieved promising results by extracting informative subgraphs for DDI prediction. However, existing subgraph extraction methods are typically coarse-grained and nonspecific, facing two key limitations: First, they are constrained by the vast and noisy nature of real-world KGs, making it challenging to identify the most informative substructures from the massive space of candidate subgraphs. Second, current methods often fail to exploit the molecular structural specificity of drugs to selectively extract relevant subgraphs, lacking effective integration of molecular structure information with knowledge graph context. To address these challenges, we propose RISE-DDI, a novel framework for Reinforced-based Informative Subgraph Extraction approach for drug-drug interaction prediction. Specifically, RISE-DDI formulates the subgraph extraction as a Markov Decision Process (MDP) and leverages a deep reinforcement learning (RL) agent to dynamically and adaptively extract the most informative and context-specific subgraphs for each drug pair. The agent is guided by a learnable structure-aware reward model that considers both the topological context from the knowledge graph and the molecular features of the drug pairs, thereby encouraging the selection of subgraphs that are both structurally relevant and biologically informative. Extensive experiments on DDI benchmark datasets demonstrate that our method outperforms state-of-the-art baselines in both transductive and inductive scenarios, achieving improvements of up to 20%. Furthermore, visualization analyses of the extracted subgraphs highlight the interpretability of our model, providing insights into the underlying mechanisms of drug interactions.
Where to Start Alignment? Diffusion Large Language Model May Demand a Distinct Position
Authors: Zhixin Xie; Xurui Song; Jun Luo
Venue: AAAI 2026 (main)

Abstract: Diffusion Large Language Models (dLLMs) have recently emerged as a competitive non-autoregressive paradigm due to their unique training and inference approach. However, there is currently a lack of safety study on this novel architecture. In this paper, we present the first analysis of dLLMs' safety performance and propose a novel safety alignment method tailored to their unique generation characteristics. Specifically, we identify a critical asymmetry between the defender and attacker in terms of security. For the defender, we reveal that the middle tokens of the response, rather than the initial ones, are more critical to the overall safety of dLLM outputs; this seems to suggest that aligning middle tokens can be more beneficial to the defender. The attacker, on the contrary, may have limited power to manipulate middle tokens, as we find dLLMs have a strong tendency towards a sequential generation order in practice, forcing the attack to meet this distribution and diverting it from influencing the critical middle tokens. Building on this asymmetry, we introduce Middle-tOken Safety Alignment (MOSA), a novel method that directly aligns the model's middle generation with safe refusals exploiting reinforcement learning. We implement MOSA and compare its security performance against eight attack methods on two benchmarks. We also test the utility of MOSA-aligned dLLM on coding, math, and general reasoning. The results strongly prove the superiority of MOSA.
ChipMind: Retrieval-Augmented Reasoning for Long-Context Circuit Design Specifications
Authors: Changwen Xing; SamZaak Wong; Xinlai Wan; Yanfeng Lu; Mengli Zhang; Zebin Ma; Lei Qi; Zhengxiong Li; Nan Guan; Zhe Jiang; Xi Wang; Jun Yang
Venue: AAAI 2026 (main)

Abstract: While Large Language Models (LLMs) demonstrate immense potential for automating integrated circuit (IC) development, their practical deployment is fundamentally limited by restricted context windows. Existing context-extension methods struggle to achieve effective semantic modeling and thorough multi-hop reasoning over extensive, intricate circuit specifications. To address this, we introduce ChipMind, a novel knowledge graph-augmented reasoning framework specifically designed for lengthy IC specifications. ChipMind first transforms circuit specifications into a domain-specific knowledge graph (ChipKG) through the Circuit Semantic-Aware Knowledge Graph Construction methodology. It then leverages the ChipKG-Augmented Reasoning mechanism, combining information-theoretic adaptive retrieval to dynamically trace logical dependencies with intent-aware semantic filtering to prune irrelevant noise, effectively balancing retrieval completeness and precision. Evaluated on an industrial-scale specification reasoning benchmark, ChipMind significantly outperforms state-of-the-art baselines, achieving an average improvement of 34.59% (up to 72.73%). Our framework bridges a critical gap between academic research and practical industrial deployment of LLM-aided Hardware Design (LAD).
SynWeather: Weather Observation Data Synthesis Across Multiple Regions and Variables via a General Diffusion Transformer
Authors: Kaiyi Xu; Junchao Gong; Zhiwang Zhou; Zhangrui Li; Yuandong Pu; Yihao Liu; Ben Fei; Fenghua Ling; Wenlong Zhang; Lei Bai
Venue: AAAI 2026 (main)

Abstract: With the advancement of meteorological instruments, abundant data has become available. 
However, due to instruments’ intrinsic limitations such as environmental sensitivity and orbital constraints, raw data often suffer from temporal or spatial gaps, making it urgent to leverage data synthesis techniques to fill in missing information. 
Current approaches are typically focus on single-variable, single-region tasks and primarily rely on deterministic modeling. 
This limits unified synthesis across variables and regions, overlooks cross-variable complementarity and often leads to over-smoothed results. 
To address above challenges, we introduce SynWeather, the first dataset designed for Unified Multi-region and Multi-variable Weather Observation Data Synthesis. 
SynWeather covers four representative regions: the Continental United States, Europe, East Asia, and Tropical Cyclone regions, as well as provides high-resolution observations of key weather variables, including Composite Radar Reflectivity, Hourly Precipitation, Visible Light, and Microwave Brightness Temperature. 
In addition, we introduce SynWeatherDiff, a general and probabilistic weather synthesis model built upon the Diffusion Transformer framework to address the over-smoothed problem. 
Experiments on the SynWeather dataset demonstrate the effectiveness of our network compared with both task-specific and general models. 
Moreover, SynWeatherDiff is able to generate results that are both fine-grained and accurate in high-value regions.
Through the dataset and baseline model, we aim to advance meteorological downstream tasks and promote the development of general models for weather variable synthesis.