Lei Chen

Sirui Liu, Jun Zhang, Haotian Chu et al.

Proteins are essential component of human life and their structures are important for function and mechanism analysis. Recent work has shown the potential of AI-driven methods for protein structure prediction. However, the development of new models is restricted by the lack of dataset and benchmark training procedure. To the best of our knowledge, the existing open source datasets are far less to satisfy the needs of modern protein sequence-structure related research. To solve this problem, we present the first million-level protein structure prediction dataset with high coverage and diversity, named as PSP. This dataset consists of 570k true structure sequences (10TB) and 745k complementary distillation sequences (15TB). We provide in addition the benchmark training procedure for SOTA protein structure prediction model on this dataset. We validate the utility of this dataset for training by participating CAMEO contest in which our model won the first place. We hope our PSP dataset together with the training benchmark can enable a broader community of AI/biology researchers for AI-driven protein related research.

Zhenghong Zhou, Huangxuan Zhao, Jiemin Fang et al.

Four-dimensional Digital Subtraction Angiography (4D DSA) plays a critical role in the diagnosis of many medical diseases, such as Arteriovenous Malformations (AVM) and Arteriovenous Fistulas (AVF). Despite its significant application value, the reconstruction of 4D DSA demands numerous views to effectively model the intricate vessels and radiocontrast flow, thereby implying a significant radiation dose. To address this high radiation issue, we propose a Time-aware Attenuation Voxel (TiAVox) approach for sparse-view 4D DSA reconstruction, which paves the way for high-quality 4D imaging. Additionally, 2D and 3D DSA imaging results can be generated from the reconstructed 4D DSA images. TiAVox introduces 4D attenuation voxel grids, which reflect attenuation properties from both spatial and temporal dimensions. It is optimized by minimizing discrepancies between the rendered images and sparse 2D DSA images. Without any neural network involved, TiAVox enjoys specific physical interpretability. The parameters of each learnable voxel represent the attenuation coefficients. We validated the TiAVox approach on both clinical and simulated datasets, achieving a 31.23 Peak Signal-to-Noise Ratio (PSNR) for novel view synthesis using only 30 views on the clinically sourced dataset, whereas traditional Feldkamp-Davis-Kress methods required 133 views. Similarly, with merely 10 views from the synthetic dataset, TiAVox yielded a PSNR of 34.32 for novel view synthesis and 41.40 for 3D reconstruction. We also executed ablation studies to corroborate the essential components of TiAVox. The code will be publically available.

Tongtao Ling, Lei Chen, Huangxu Sheng et al.

The traditional way of sentence-level event detection involves two important subtasks: trigger identification and trigger classifications, where the identified event trigger words are used to classify event types from sentences. However, trigger classification highly depends on abundant annotated trigger words and the accuracy of trigger identification. In a real scenario, annotating trigger words is time-consuming and laborious. For this reason, we propose a trigger-free event detection model, which transforms event detection into a two-tower model based on machine reading comprehension and prompt learning. Compared to existing trigger-based and trigger-free methods, experimental studies on two event detection benchmark datasets (ACE2005 and MAVEN) have shown that the proposed approach can achieve competitive performance.

Meituan LongCat Team, Bairui Wang, Bayan et al.

We introduce LongCat-Flash-Omni, a state-of-the-art open-source omni-modal model with 560 billion parameters, excelling at real-time audio-visual interaction. By adopting a curriculum-inspired progressive training strategy that transitions from simpler to increasingly complex modality sequence modeling tasks, LongCat-Flash-Omni attains comprehensive multimodal capabilities while maintaining strong unimodal capability. Building upon LongCat-Flash, which adopts a high-performance Shortcut-connected Mixture-of-Experts (MoE) architecture with zero-computation experts, LongCat-Flash-Omni integrates efficient multimodal perception and speech reconstruction modules. Despite its immense size of 560B parameters (with 27B activated), LongCat-Flash-Omni achieves low-latency real-time audio-visual interaction. For training infrastructure, we developed a modality-decoupled parallelism scheme specifically designed to manage the data and model heterogeneity inherent in large-scale multimodal training. This innovative approach demonstrates exceptional efficiency by sustaining over 90% of the throughput achieved by text-only training. Extensive evaluations show that LongCat-Flash-Omni achieves state-of-the-art performance on omni-modal benchmarks among open-source models. Furthermore, it delivers highly competitive results across a wide range of modality-specific tasks, including text, image, and video understanding, as well as audio understanding and generation. We provide a comprehensive overview of the model architecture design, training procedures, and data strategies, and open-source the model to foster future research and development in the community.

Fangqi Zhu, Yongqi Zhang, Lei Chen et al.

Adverse drug-drug interactions~(DDIs) can compromise the effectiveness of concurrent drug administration, posing a significant challenge in healthcare. As the development of new drugs continues, the potential for unknown adverse effects resulting from DDIs becomes a growing concern. Traditional computational methods for DDI prediction may fail to capture interactions for new drugs due to the lack of knowledge. In this paper, we introduce a new problem setup as zero-shot DDI prediction that deals with the case of new drugs. Leveraging textual information from online databases like DrugBank and PubChem, we propose an innovative approach TextDDI with a language model-based DDI predictor and a reinforcement learning~(RL)-based information selector, enabling the selection of concise and pertinent text for accurate DDI prediction on new drugs. Empirical results show the benefits of the proposed approach on several settings including zero-shot and few-shot DDI prediction, and the selected texts are semantically relevant. Our code and data are available at \url{https://github.com/zhufq00/DDIs-Prediction}.

Xiangyu Dong, Xingyi Zhang, Lei Chen et al.

Node Anomaly Detection (NAD) has gained significant attention in the deep learning community due to its diverse applications in real-world scenarios. Existing NAD methods primarily embed graphs within a single Euclidean space, while overlooking the potential of non-Euclidean spaces. Besides, to address the prevalent issue of limited supervision in real NAD tasks, previous methods tend to leverage synthetic data to collect auxiliary information, which is not an effective solution as shown in our experiments. To overcome these challenges, we introduce a novel SpaceGNN model designed for NAD tasks with extremely limited labels. Specifically, we provide deeper insights into a task-relevant framework by empirically analyzing the benefits of different spaces for node representations, based on which, we design a Learnable Space Projection function that effectively encodes nodes into suitable spaces. Besides, we introduce the concept of weighted homogeneity, which we empirically and theoretically validate as an effective coefficient during information propagation. This concept inspires the design of the Distance Aware Propagation module. Furthermore, we propose the Multiple Space Ensemble module, which extracts comprehensive information for NAD under conditions of extremely limited supervision. Our findings indicate that this module is more beneficial than data augmentation techniques for NAD. Extensive experiments conducted on 9 real datasets confirm the superiority of SpaceGNN, which outperforms the best rival by an average of 8.55% in AUC and 4.31% in F1 scores. Our code is available at https://github.com/xydong127/SpaceGNN.

Zhaoqi Dong, Zhinan Wang, Quanqi Zheng et al.

Traditional rule-based decision-making methods with interpretable advantage, such as finite state machine, suffer from the jitter or deadlock(JoD) problems in extremely dynamic scenarios. To realize agent swarm confrontation, decision conflicts causing many JoD problems are a key issue to be solved. Here, we propose a novel decision-making framework that integrates probabilistic finite state machine, deep convolutional networks, and reinforcement learning to implement interpretable intelligence into agents. Our framework overcomes state machine instability and JoD problems, ensuring reliable and adaptable decisions in swarm confrontation. The proposed approach demonstrates effective performance via enhanced human-like cooperation and competitive strategies in the rigorous evaluation of real experiments, outperforming other methods.

Xihan Li, Xing Li, Lei Chen et al.

While deep learning has achieved significant success in various domains, its application to logic circuit design has been limited due to complex constraints and strict feasibility requirement. However, a recent generative deep neural model, "Circuit Transformer", has shown promise in this area by enabling equivalence-preserving circuit transformation on a small scale. In this paper, we introduce a logic synthesis rewriting operator based on the Circuit Transformer model, named "ctrw" (Circuit Transformer Rewriting), which incorporates the following techniques: (1) a two-stage training scheme for the Circuit Transformer tailored for logic synthesis, with iterative improvement of optimality through self-improvement training; (2) integration of the Circuit Transformer with state-of-the-art rewriting techniques to address scalability issues, allowing for guided DAG-aware rewriting. Experimental results on the IWLS 2023 contest benchmark demonstrate the effectiveness of our proposed rewriting methods.

Luyu Qiu, Yi Yang, Caleb Chen Cao et al.

With the rapid development of eXplainable Artificial Intelligence (XAI), perturbation-based XAI algorithms have become quite popular due to their effectiveness and ease of implementation. The vast majority of perturbation-based XAI techniques face the challenge of Out-of-Distribution (OoD) data -- an artifact of randomly perturbed data becoming inconsistent with the original dataset. OoD data leads to the over-confidence problem in model predictions, making the existing XAI approaches unreliable. To our best knowledge, the OoD data problem in perturbation-based XAI algorithms has not been adequately addressed in the literature. In this work, we address this OoD data problem by designing an additional module quantifying the affinity between the perturbed data and the original dataset distribution, which is integrated into the process of aggregation. Our solution is shown to be compatible with the most popular perturbation-based XAI algorithms, such as RISE, OCCLUSION, and LIME. Experiments have confirmed that our methods demonstrate a significant improvement in general cases using both computational and cognitive metrics. Especially in the case of degradation, our proposed approach demonstrates outstanding performance comparing to baselines. Besides, our solution also resolves a fundamental problem with the faithfulness indicator, a commonly used evaluation metric of XAI algorithms that appears to be sensitive to the OoD issue.

Xiao-Hui Li, Yuhan Shi, Haoyang Li et al.

It has been long debated that eXplainable AI (XAI) is an important topic, but it lacks rigorous definition and fair metrics. In this paper, we briefly summarize the status quo of the metrics, along with an exhaustive experimental study based on them, including faithfulness, localization, false-positives, sensitivity check, and stability. With the experimental results, we conclude that among all the methods we compare, no single explanation method dominates others in all metrics. Nonetheless, Gradient-weighted Class Activation Mapping (Grad-CAM) and Randomly Input Sampling for Explanation (RISE) perform fairly well in most of the metrics. Utilizing a set of filtered metrics, we further present a case study to diagnose the classification bases for models. While providing a comprehensive experimental study of metrics, we also examine measuring factors that are missed in current metrics and hope this valuable work could serve as a guide for future research.

Brighter Agyemang, Wei-Ping Wu, Michael Yelpengne Kpiebaareh et al.

The drug discovery stage is a vital aspect of the drug development process and forms part of the initial stages of the development pipeline. In recent times, machine learning-based methods are actively being used to model drug-target interactions for rational drug discovery due to the successful application of these methods in other domains. In machine learning approaches, the numerical representation of molecules is critical to the performance of the model. While significant progress has been made in molecular representation engineering, this has resulted in several descriptors for both targets and compounds. Also, the interpretability of model predictions is a vital feature that could have several pharmacological applications. In this study, we propose a self-attention-based multi-view representation learning approach for modeling drug-target interactions. We evaluated our approach using three benchmark kinase datasets and compared the proposed method to some baseline models. Our experimental results demonstrate the ability of our method to achieve competitive prediction performance and offer biologically plausible drug-target interaction interpretations.

Shuhang Wang, Szu-Yeu Hu, Eugene Cheah et al.

This paper proposes a novel U-Net variant using stacked dilated convolutions for medical image segmentation (SDU-Net). SDU-Net adopts the architecture of vanilla U-Net with modifications in the encoder and decoder operations (an operation indicates all the processing for feature maps of the same resolution). Unlike vanilla U-Net which incorporates two standard convolutions in each encoder/decoder operation, SDU-Net uses one standard convolution followed by multiple dilated convolutions and concatenates all dilated convolution outputs as input to the next operation. Experiments showed that SDU-Net outperformed vanilla U-Net, attention U-Net (AttU-Net), and recurrent residual U-Net (R2U-Net) in all four tested segmentation tasks while using parameters around 40% of vanilla U-Net's, 17% of AttU-Net's, and 15% of R2U-Net's.