OpenRaiser/Intern-Atlas huggingface dataset:
Enhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learning
Venue: Conference IJCAI 2025
Year: 2025

Chemical reaction and retrosynthesis prediction are fundamental tasks in drug discovery. Recently, large language models (LLMs) have shown potential in many domains. However, directly applying LLMs to these tasks faces two major challenges: (i) lacking a large-scale chemical synthesis-related instruction dataset; (ii) ignoring the close correlation between reaction and retrosynthesis prediction for the existing fine-tuning strategies. To address these challenges, we propose ChemDual, a novel LLM framework for accurate chemical synthesis. Specifically, considering the high cost of data acquisition for reaction and retrosynthesis, ChemDual regards the reaction-and-retrosynthesis of molecules as a related recombination-and-fragmentation process and constructs a large-scale of 4.4 million instruction dataset. Furthermore, ChemDual introduces an enhanced LLaMA, equipped with a multi-scale tokenizer and dual-task learning strategy, to jointly optimize the process of recombination and fragmentation as well as the tasks between reaction and retrosynthesis prediction. Extensive experiments on Mol-Instruction and USPTO-50K datasets demonstrate that ChemDual achieves state-of-the-art performance in both predictions of reaction and retrosynthesis, outperforming the existing conventional single-task approaches and the general open-source LLMs. Through molecular docking analysis, ChemDual generates compounds with diverse and strong protein binding affinity, further highlighting its strong potential in drug design.
FBQuant: FeedBack Quantization for Large Language Models
Venue: Conference IJCAI 2025
Year: 2025

Deploying Large Language Models (LLMs) on edge devices is increasingly important, as it eliminates reliance on network connections, reduces expensive API calls, and enhances user privacy. However, on-device deployment is challenging due to the limited computational resources of edge devices. In particular, the key bottleneck stems from memory bandwidth constraints related to weight loading. Weight-only quantization effectively reduces memory access, yet often induces significant accuracy degradation. Recent efforts to incorporate sub-branches have shown promise for mitigating quantization errors, but these methods either lack robust optimization strategies or rely on suboptimal objectives. To address these gaps, we propose FeedBack Quantization (FBQuant), a novel approach inspired by negative feedback mechanisms in automatic control. FBQuant inherently ensures that the reconstructed weights remain bounded by the quantization process, thereby reducing the risk of overfitting. To further offset the additional latency introduced by sub-branches, we develop an efficient CUDA kernel that decreases 60% of extra inference time. Comprehensive experiments demonstrate the efficiency and effectiveness of FBQuant across various LLMs. Notably, for 3-bit Llama2-7B, FBQuant improves zero-shot accuracy by 1.2%.
Enhancing Multimodal Protein Function Prediction Through Dual-Branch Dynamic Selection with Reconstructive Pre-Training
Venue: Conference IJCAI 2025
Year: 2025

Multimodal protein features play a crucial role in protein function prediction. However, these features encompass a wide range of information, ranging from structural data and sequence features to protein attributes and interaction networks, making it challenging to decipher their complex interconnections. In this work, we propose a multimodal protein function prediction method (DSRPGO) by utilizing dynamic selection and reconstructive pre-training mechanisms. To acquire complex protein information, we introduce reconstructive pre-training to mine more fine-grained information with low semantic levels. Moreover, we put forward the Bidirectional Interaction Module (BInM) to facilitate interactive learning among multimodal features. Additionally, to address the difficulty of hierarchical multi-label classification in this task, a Dynamic Selection Module (DSM) is designed to select the feature representation that is most conducive to current protein function prediction. Our proposed DSRPGO model improves significantly in BPO, MFO, and CCO on human datasets, thereby outperforming other benchmark models.
MMET: A Multi-Input and Multi-Scale Transformer for Efficient PDEs Solving
Venue: Conference IJCAI 2025
Year: 2025

Partial Differential Equations (PDEs) are fundamental for modeling physical systems, yet solving them in a generic and efficient manner using machine learning-based approaches remains challenging due to limited multi-input and multi-scale generalization capabilities, as well as high computational costs. This paper proposes the Multi-input and Multi-scale Efficient Transformer (MMET), a novel framework designed to address the above challenges. MMET decouples mesh and query points as two sequences and feeds them into the encoder and decoder, respectively, and uses a Gated Condition Embedding (GCE) layer to embed input variables or functions with varying dimensions, enabling effective solutions for multi-scale and multi-input problems. Additionally, a Hilbert curve-based reserialization and patch embedding mechanism decrease the input length. This significantly reduces the computational cost when dealing with large-scale geometric models. These innovations enable efficient representations and support multi-scale resolution queries for large-scale and multi-input PDE problems. Experimental evaluations on diverse benchmarks spanning different physical fields demonstrate that MMET outperforms SOTA methods in both accuracy and computational efficiency. This work highlights the potential of MMET as a robust and scalable solution for real-time PDE solving in engineering and physics-based applications, paving the way for future explorations into pre-trained large-scale models in specific domains. This work is open-sourced at https://github.com/YichenLuo-0/MMET.
InnateCoder: Learning Programmatic Options with Foundation Models
Venue: Conference IJCAI 2025
Year: 2025

Outside of transfer learning settings, reinforcement learning agents start their learning process from a clean slate. As a result, such agents have to go through a slow process to learn even the most obvious skills required to solve a problem. In this paper, we present InnateCoder, a system that leverages human knowledge encoded in foundation models to provide programmatic policies that encode "innate skills" in the form of temporally extended actions, or options. In contrast to existing approaches to learning options, InnateCoder learns them from the general human knowledge encoded in foundation models in a zero-shot setting, and not from the knowledge the agent gains by interacting with the environment. Then, InnateCoder searches for a programmatic policy by combining the programs encoding these options into larger and more complex programs. We hypothesized that InnateCoder's way of learning and using options could improve the sampling efficiency of current methods for learning programmatic policies. Empirical results in MicroRTS and Karel the Robot support our hypothesis, since they show that InnateCoder is more sample efficient than versions of the system that do not use options or learn them from experience.
Adaptive Wizard for Removing Cross-Tier Misconfigurations in Active Directory
Venue: Conference IJCAI 2025
Year: 2025

Security vulnerabilities in Windows Active Directory (AD) systems are typically modeled using an attack graph and hardening AD systems involves an iterative workflow: security teams propose an edge to remove, and IT operations teams manually review these fixes before implementing the removal. As verification requires significant manual effort, we formulate an Adaptive Path Removal Problem to minimize the number of steps in this iterative removal process. In our model, a wizard proposes an attack path in each step and presents it as a set of multiple-choice options to the IT admin. The IT admin then selects one edge from the proposed set to remove. This process continues until the target $t$ is disconnected from source $s$ or the number of proposed paths reaches $B$. The model aims to optimize the human effort by minimizing the expected number of interactions between the IT admin and the security wizard. We first prove that the problem is $\mathcal{\#P}$-hard. We then propose a set of solutions including an exact algorithm, an approximate algorithm, and several scalable heuristics. Our best heuristic, called DPR, can operate effectively on larger-scale graphs compared to the exact algorithm and consistently outperforms the approximate algorithm across all graphs. We verify the effectiveness of our algorithms on several synthetic AD graphs and an AD attack graph collected from a real organization.
Think Twice Before Adaptation: Improving Adaptability of DeepFake Detection via Online Test-Time Adaptation
Venue: Conference IJCAI 2025
Year: 2025

Deepfake (DF) detectors face significant challenges when deployed in real-world environments, particularly when encountering test samples deviated from training data through either postprocessing manipulations or distribution shifts. We demonstrate postprocessing techniques can completely obscure generation artifacts presented in DF samples, leading to performance degradation of DF detectors. To address these challenges, we propose Think Twice before Adaptation (\texttt{T$^2$A}), a novel online test-time adaptation method that enhances the adaptability of detectors during inference without requiring access to source training data or labels. Our key idea is to enable the model to explore alternative options through an Uncertainty-aware Negative Learning objective rather than solely relying on its initial predictions as commonly seen in entropy minimization (EM)-based approaches. We also introduce an Uncertain Sample Prioritization strategy and Gradients Masking technique to improve the adaptation by focusing on important samples and model parameters. Our theoretical analysis demonstrates that the proposed negative learning objective exhibits complementary behavior to EM, facilitating better adaptation capability. Empirically, our method achieves state-of-the-art results compared to existing test-time adaptation (TTA) approaches and significantly enhances the resilience and generalization of DF detectors during inference. Code is available \href{https://github.com/HongHanh2104/T2A-Think-Twice-Before-Adaptation}{here}.
Solving Copyright Infringement on Short Video Platforms: Novel Datasets and an Audio Restoration Deep Learning Pipeline
Venue: Conference IJCAI 2025
Year: 2025

Short video platforms like YouTube Shorts and TikTok face significant copyright compliance challenges, as infringers frequently embed arbitrary background music (BGM) to obscure original soundtracks (OST) and evade content originality detection. To tackle this issue, we propose a novel pipeline that integrates Music Source Separation (MSS) and cross-modal video-music retrieval (CMVMR). Our approach effectively separates arbitrary BGM from the original OST, enabling the restoration of authentic video audio tracks. To support this work, we introduce two domain-specific datasets: OASD-20K for audio separation and OSVAR-160 for pipeline evaluation. OASD-20K contains 20,000 audio clips featuring mixed BGM and OST pairs, while OSVAR-160 is a unique benchmark dataset comprising 1,121 video and mixed-audio pairs, specifically designed for short video restoration tasks. Experimental results demonstrate that our pipeline not only removes arbitrary BGM with high accuracy but also restores OSTs, ensuring content integrity. This approach provides an ethical and scalable solution to copyright challenges in user-generated content on short video platforms.
Diffusion-aware Censored Gaussian Processes for Demand Modelling
Venue: Conference IJCAI 2025
Year: 2025

Inferring the true demand for a product or a service from aggregate data is often challenging due to the limited available supply, thus resulting in observations that are censored and correspond to the realized demand, thereby not accounting for the unsatisfied demand. Censored regression models are able to account for the effect of censoring due to the limited supply, but they don't consider the effect of substitutions, which may cause the demand for similar alternative products or services to increase. This paper proposes Diffusion-aware Censored Demand Models, which combine a Tobit likelihood with a graph diffusion process in order to model the latent process of transfer of unsatisfied demand between similar products or services. We instantiate this new class of models under the framework of GPs and, based on both simulated and real-world data for modeling sales, bike-sharing demand, and EV charging demand, demonstrate its ability to better recover the true demand and produce more accurate out-of-sample predictions.
MTPNet: Multi-Grained Target Perception for Unified Activity Cliff Prediction
Venue: Conference IJCAI 2025
Year: 2025

Activity cliff prediction is a critical task in drug discovery and material design. Existing computational methods are limited to handling single binding targets, which restricts the applicability of these prediction models. In this paper, we present the Multi-Grained Target Perception network (MTPNet) to incorporate the prior knowledge of interactions between the molecules and their target proteins. Specifically, MTPNet is a unified framework for activity cliff prediction, which consists of two components: Macro-level Target Semantic (MTS) guidance and Micro-level Pocket Semantic (MPS) guidance. By this way, MTPNet dynamically optimizes molecular representations through multi-grained protein semantic conditions. To our knowledge, it is the first time to employ the receptor proteins as guiding information to effectively capture critical interaction details. Extensive experiments on 30 representative activity cliff datasets demonstrate that MTPNet significantly outperforms previous approaches, achieving an average RMSE improvement of 18.95% on top of several mainstream GNN architectures. Overall, MTPNet internalizes interaction patterns through conditional deep learning to achieve unified predictions of activity cliffs, helping to accelerate compound optimization and design. Codes are available at: https://github.com/ZishanShu/MTPNet.
LogiCase: Effective Test Case Generation from Logical Description in Competitive Programming
Venue: Conference IJCAI 2025
Year: 2025

Automated Test Case Generation (ATCG) is crucial for evaluating software reliability, particularly in competitive programming where robust algorithm assessments depend on diverse and accurate test cases. However, existing ATCG methods often fail to meet complex specifications or generate effective corner cases, limiting their utility. In this work, we introduce Context-Free Grammars with Counters (CCFGs), a formalism that captures both syntactic and semantic structures in input specifications. Using a fine-tuned CodeT5 model, we translate natural language input specifications into CCFGs, enabling the systematic generation of high-quality test cases. Experiments on the CodeContests dataset demonstrate that CCFG-based test cases outperform baseline methods in identifying incorrect algorithms, achieving significant gains in validity and effectiveness. Our approach provides a scalable and reliable grammar-driven framework for enhancing automated competitive programming evaluations.
PeSANet: Physics-encoded Spectral Attention Network for Simulating PDE-Governed Complex Systems
Venue: Conference IJCAI 2025
Year: 2025

Accurately modeling and forecasting complex systems governed by partial differential equations (PDEs) is crucial in various scientific and engineering domains. However, traditional numerical methods struggle in real-world scenarios due to incomplete or unknown physical laws. Meanwhile, machine learning approaches often fail to generalize effectively when faced with scarce observational data and the challenge of capturing local and global features. To this end, we propose the Physics-encoded Spectral Attention Network (PeSANet), which integrates local and global information to forecast complex systems with limited data and incomplete physical priors. The model consists of two key components: a physics-encoded block that uses hard constraints to approximate local differential operators from limited data, and a spectral-enhanced block that captures long-range global dependencies in the frequency domain. Specifically, we introduce a novel spectral attention mechanism to model inter-spectrum relationships and learn long-range spatial features. Experimental results demonstrate that PeSANet outperforms existing methods across all metrics, particularly in long-term forecasting accuracy, providing a promising solution for simulating complex systems with limited data and incomplete physics.
Robust Misinformation Detection by Visiting Potential Commonsense Conflict
Venue: Conference IJCAI 2025
Year: 2025

The development of Internet technology has led to an increased prevalence of misinformation, causing severe negative effects across diverse domains. To mitigate this challenge, Misinformation Detection (MD), aiming to detect online misinformation automatically, emerges as a rapidly growing research topic in the community. In this paper, we propose a novel plug-and-play augmentation method for the MD task, namely Misinformation Detection with Potential Commonsense Conflict (MD-PCC). We take inspiration from the prior studies indicating that fake articles are more likely to involve commonsense conflict. Accordingly, we construct commonsense expressions for articles, serving to express potential commonsense conflicts inferred by the difference between extracted commonsense triplet and golden ones inferred by the well-established commonsense reasoning tool COMET. These expressions are then specified for each article as augmentation. Any specific MD methods can be then trained on those commonsense-augmented articles. Besides, we also collect a novel commonsense-oriented dataset named CoMis, whose all fake articles are caused by commonsense conflict. We integrate MD-PCC with various existing MD backbones and compare them across both 4 public benchmark datasets and CoMis. Empirical results demonstrate that MD-PCC can consistently outperform the existing MD baselines.
Advancing Embodied Agent Security: From Safety Benchmarks to Input Moderation
Venue: Conference IJCAI 2025
Year: 2025

Embodied agents exhibit immense potential across a multitude of domains, making the assurance of their behavioral safety a fundamental prerequisite for their widespread deployment. However, existing research predominantly concentrates on the security of general large language models, lacking specialized methodologies for establishing safety benchmarks and input moderation tailored to embodied agents. To bridge this gap, this paper introduces a novel input moderation framework, meticulously designed to safeguard embodied agents. This framework encompasses the entire pipeline, including taxonomy definition, dataset curation, moderator architecture, model training, and rigorous evaluation. Notably, we introduce EAsafetyBench, a meticulously crafted safety benchmark engineered to facilitate both the training and stringent assessment of moderators specifically designed for embodied agents. Furthermore, we propose Pinpoint, an innovative prompt-decoupled input moderation scheme that harnesses a masked attention mechanism to effectively isolate and mitigate the influence of functional prompts on moderation tasks. Extensive experiments conducted on diverse benchmark datasets and models validate the feasibility and efficacy of the proposed approach. The results demonstrate that our methodologies achieve an impressive average detection accuracy of 94.58%, surpassing the performance of existing state-of-the-art techniques, alongside an exceptional moderation processing time of merely 0.002 seconds per instance.
Incorporating Legal Logic into Deep Learning: An Intelligent Approach to Probation Prediction
Venue: Conference IJCAI 2025
Year: 2025

Probation is a crucial institution in modern criminal law, embodying the principles of fairness and justice while contributing to the harmonious development of society. Despite its importance, the current Intelligent Judicial Assistant System (IJAS) lacks dedicated methods for probation prediction, and research on the underlying factors influencing probation eligibility remains limited. In addition, probation eligibility requires a comprehensive analysis of both criminal circumstances and remorse. Much of the existing research in IJAS relies primarily on data-driven methodologies, which often overlooks the legal logic underpinning judicial decision-making. To address this gap, we propose a novel approach that integrates legal logic into deep learning models for probation prediction, implemented in three distinct stages. First, we construct a specialized probation dataset that includes fact descriptions and probation legal elements (PLEs). Second, we design a distinct probation prediction model named the Multi-Task Dual-Theory Probation Prediction Model (MT-DT), which is grounded in the legal logic of probation and the \textit{Dual-Track Theory of Punishment}. Finally, our experiments on the probation dataset demonstrate that the MT-DT model outperforms baseline models, and an analysis of the underlying legal logic further validates the effectiveness of the proposed approach.
ARMR: Adaptively Responsive Network for Medication Recommendation
Venue: Conference IJCAI 2025
Year: 2025

Medication recommendation is a crucial task in healthcare, especially for patients with complex medical conditions. However, existing methods often struggle to effectively balance the reuse of historical medications with the introduction of new drugs in response to the changing patient conditions. In order to address this challenge, we propose an Adaptively Responsive network for Medication Recommendation (ARMR), a new method which incorporates 1) a piecewise temporal learning component that distinguishes between recent and distant patient history, enabling more nuanced temporal understanding, and 2) an adaptively responsive mechanism that dynamically adjusts attention to new and existing drugs based on the patient's current health state and medication history. Experiments on the MIMIC-III and MIMIC-IV datasets indicate that ARMR has better performance compared with the state-of-the-art baselines in different evaluation metrics, which contributes to more personalized and accurate medication recommendations. The source code is publicly avaiable at: https://github.com/seucoin/armr2.