Yiping Liu

Dan Luo, Xuan Lin, Peng Zhou et al.

Despite the growing availability of cryo-electron microscopy (cryo-EM) density maps, effectively leveraging them for protein representation remains challenging. First, current methods lack a general-purpose protein pretraining framework tailored for cryo-EM density maps, designed for protein-related property prediction. Second, existing approaches typically partition density maps into local box regions and model them independently, overlooking interactions across boxes which are essential for capturing global structural context in cryo-EM density map. To address these challenges, we propose CryoProt, a protein pretraining framework designed for cryo-EM density maps. CryoProt introduces a Map Encoder based on multi-head latent attention (MLA), where box-level representations interact through a shared latent space, enabling explicit modeling of cross-box dependencies within the density map. Furthermore, we adopt a multi-task pretraining strategy to learn generalizable representations that can be effectively transferred to diverse downstream tasks, such as protein flexibility prediction, where cryo-EM density maps are not required and can be inferred implicitly by the pretrained model. Experimental results demonstrate that CryoProt consistently outperforms existing state-of-the-art methods across multiple benchmarks, achieving up to 12% improvement over the best-performing baselines, highlighting the importance of modeling cross-box interactions in cryo-EM data. The source code is publicly available at https://anonymous.4open.science/r/CryoProt.

Pei Liu, Xiangxiang Zeng, Tengfei Ma et al.

Whole-Slide Images (WSIs) are widely used for estimating the prognosis of cancer patients. Current studies generally follow a cancer-specific learning paradigm. However, the available training samples for one cancer type are usually scarce in pathology. Consequently, the model often struggles to learn generalizable knowledge, thus performing worse on the tumor samples with inherent high heterogeneity. Although multi-cancer joint learning and knowledge transfer approaches have been explored recently to address it, they either rely on large-scale joint training or extensive inference across multiple models, posing new challenges in computational efficiency. To this end, this paper proposes a new scheme, Sparse Task Vector Mixup with Hypernetworks (STEPH). Unlike previous ones, it efficiently absorbs generalizable knowledge from other cancers for the target via model merging: i) applying task vector mixup to each source-target pair and then ii) sparsely aggregating task vector mixtures to obtain an improved target model, driven by hypernetworks. Extensive experiments on 13 cancer datasets show that STEPH improves over cancer-specific learning and an existing knowledge transfer baseline by 5.14% and 2.01%, respectively. Moreover, it is a more efficient solution for learning prognostic knowledge from other cancers, without requiring large-scale joint training or extensive multi-model inference. Code is publicly available at https://github.com/liupei101/STEPH.

Kimi Team, Yifan Bai, Yiping Bao et al. · tsinghua

We introduce Kimi K2, a Mixture-of-Experts (MoE) large language model with 32 billion activated parameters and 1 trillion total parameters. We propose the MuonClip optimizer, which improves upon Muon with a novel QK-clip technique to address training instability while enjoying the advanced token efficiency of Muon. Based on MuonClip, K2 was pre-trained on 15.5 trillion tokens with zero loss spike. During post-training, K2 undergoes a multi-stage post-training process, highlighted by a large-scale agentic data synthesis pipeline and a joint reinforcement learning (RL) stage, where the model improves its capabilities through interactions with real and synthetic environments. Kimi K2 achieves state-of-the-art performance among open-source non-thinking models, with strengths in agentic capabilities. Notably, K2 obtains 66.1 on Tau2-Bench, 76.5 on ACEBench (En), 65.8 on SWE-Bench Verified, and 47.3 on SWE-Bench Multilingual -- surpassing most open and closed-sourced baselines in non-thinking settings. It also exhibits strong capabilities in coding, mathematics, and reasoning tasks, with a score of 53.7 on LiveCodeBench v6, 49.5 on AIME 2025, 75.1 on GPQA-Diamond, and 27.1 on OJBench, all without extended thinking. These results position Kimi K2 as one of the most capable open-source large language models to date, particularly in software engineering and agentic tasks. We release our base and post-trained model checkpoints to facilitate future research and applications of agentic intelligence.

Zhexu Wang, Yiping Liu, Yejie Wang et al.

Recent advancements in large language models (LLMs) have demonstrated significant progress in math and code reasoning capabilities. However, existing code benchmark are limited in their ability to evaluate the full spectrum of these capabilities, particularly at the competitive level. To bridge this gap, we introduce OJBench, a novel and challenging benchmark designed to assess the competitive-level code reasoning abilities of LLMs. OJBench comprises 232 programming competition problems from NOI and ICPC, providing a more rigorous test of models' reasoning skills. We conducted a comprehensive evaluation using OJBench on 37 models, including both closed-source and open-source models, reasoning-oriented and non-reasoning-oriented models. Our results indicate that even state-of-the-art reasoning-oriented models, such as o4-mini and Gemini-2.5-pro-exp, struggle with highly challenging competition-level problems. This highlights the significant challenges that models face in competitive-level code reasoning.

Yiling He, Junchi Lei, Hongyu She et al.

Modern security analytics are increasingly powered by deep learning models, but their performance often degrades as threat landscapes evolve and data representations shift. While continual learning (CL) offers a promising paradigm to maintain model effectiveness, many approaches rely on full retraining or data replay, which are infeasible in data-sensitive environments. Moreover, existing methods remain inadequate for security-critical scenarios, facing two coupled challenges in knowledge transfer: preserving prior knowledge without old data and integrating new knowledge with minimal interference. We propose RETROFIT, a data retrospective-free continual learning method that achieves bounded forgetting for effective knowledge transfer. Our key idea is to consolidate previously trained and newly fine-tuned models, serving as teachers of old and new knowledge, through parameter-level merging that eliminates the need for historical data. To mitigate interference, we apply low-rank and sparse updates that confine parameter changes to independent subspaces, while a knowledge arbitration dynamically balances the teacher contributions guided by model confidence. Our evaluation on two representative applications demonstrates that RETROFIT consistently mitigates forgetting while maintaining adaptability. In malware detection under temporal drift, it substantially improves the retention score, from 20.2% to 38.6% over CL baselines, and exceeds the oracle upper bound on new data. In binary summarization across decompilation levels, where analyzing stripped binaries is especially challenging, RETROFIT achieves around twice the BLEU score of transfer learning used in prior work and surpasses all baselines in cross-representation generalization.

Youneng Bao, Yulong Cheng, Yiping Liu et al.

Prevailing quantization techniques in Learned Image Compression (LIC) typically employ a static, uniform bit-width across all layers, failing to adapt to the highly diverse data distributions and sensitivity characteristics inherent in LIC models. This leads to a suboptimal trade-off between performance and efficiency. In this paper, we introduce DynaQuant, a novel framework for dynamic mixed-precision quantization that operates on two complementary levels. First, we propose content-aware quantization, where learnable scaling and offset parameters dynamically adapt to the statistical variations of latent features. This fine-grained adaptation is trained end-to-end using a novel Distance-aware Gradient Modulator (DGM), which provides a more informative learning signal than the standard Straight-Through Estimator. Second, we introduce a data-driven, dynamic bit-width selector that learns to assign an optimal bit precision to each layer, dynamically reconfiguring the network's precision profile based on the input data. Our fully dynamic approach offers substantial flexibility in balancing rate-distortion (R-D) performance and computational cost. Experiments demonstrate that DynaQuant achieves rd performance comparable to full-precision models while significantly reducing computational and storage requirements, thereby enabling the practical deployment of advanced LIC on diverse hardware platforms.

Chengrui Xiang, Tengfei Ma, Xiangzheng Fu et al.

Drug repurposing plays a critical role in accelerating treatment discovery, especially for complex and rare diseases. Biomedical knowledge graphs (KGs), which encode rich clinical associations, have been widely adopted to support this task. However, existing methods largely overlook common-sense biomedical concept knowledge in real-world labs, such as mechanistic priors indicating that certain drugs are fundamentally incompatible with specific treatments. To address this gap, we propose LLaDR, a Large Language Model-assisted framework for Drug Repurposing, which improves the representation of biomedical concepts within KGs. Specifically, we extract semantically enriched treatment-related textual representations of biomedical entities from large language models (LLMs) and use them to fine-tune knowledge graph embedding (KGE) models. By injecting treatment-relevant knowledge into KGE, LLaDR largely improves the representation of biomedical concepts, enhancing semantic understanding of under-studied or complex indications. Experiments based on benchmarks demonstrate that LLaDR achieves state-of-the-art performance across different scenarios, with case studies on Alzheimer's disease further confirming its robustness and effectiveness. Code is available at https://github.com/xiaomingaaa/LLaDR.

Guidong Lu, Yiping Liu, Xiangxiang Zeng

The prevailing paradigm in Automated Heuristic Design (AHD) typically relies on the assumption that a single, fixed algorithm can effectively navigate the shifting dynamics of a combinatorial search. This static approach often proves inadequate for Perturbative Heuristics, where the optimal algorithm for escaping local optima depends heavily on the specific search phase. To address this limitation, we reformulate heuristic design as a Non-stationary Bi-level Control problem and introduce DyACE (Dynamic Algorithm Co-evolution). Distinct from standard open-loop solvers, DyACE use a Receding Horizon Control architecture to continuously co-evolve the heuristic logic alongside the solution population. A core element of this framework is the Look-Ahead Rollout Search, which queries the landscape geometry to extract Search Trajectory Features. This sensory feedback allows the Large Language Model (LLM) to function as a grounded meta-controller, prescribing phase-specific interventions tailored to the real-time search status. We validate DyACE on three representative combinatorial optimization benchmarks. The results demonstrate that our method significantly outperforms state-of-the-art static baselines, exhibiting superior scalability in high-dimensional search spaces. Furthermore, ablation studies confirm that dynamic adaptation fails without grounded perception, often performing worse than static algorithms. This indicates that DyACE's effectiveness stems from the causal alignment between the synthesized logic and the verified gradients of the optimization landscape.

Yiping Liu, Yi Zhou, Zhenxiang Xu et al.

The Generalized Independent Set (GIS) problem extends the classical maximum independent set problem by incorporating profits for vertices and penalties for edges. This generalized problem has been identified in diverse applications in fields such as forest harvest planning, competitive facility location, social network analysis, and even machine learning. However, solving the GIS problem in large-scale, real-world networks remains computationally challenging. In this paper, we explore data reduction techniques to address this challenge. We first propose 14 reduction rules that can reduce the input graph with rigorous optimality guarantees. We then present a reduction-driven local search (RLS) algorithm that integrates these reduction rules into the pre-processing, the initial solution generation, and the local search components in a computationally efficient way. The RLS is empirically evaluated on 278 graphs arising from different application scenarios. The results indicates that the RLS is highly competitive -- For most graphs, it achieves significantly superior solutions compared to other known solvers, and it effectively provides solutions for graphs exceeding 260 million edges, a task at which every other known method fails. Analysis also reveals that the data reduction plays a key role in achieving such a competitive performance.

Tengfei Ma, Yujie Chen, Wen Tao et al.

Molecular interaction prediction plays a crucial role in forecasting unknown interactions between molecules, such as drug-target interaction (DTI) and drug-drug interaction (DDI), which are essential in the field of drug discovery and therapeutics. Although previous prediction methods have yielded promising results by leveraging the rich semantics and topological structure of biomedical knowledge graphs (KGs), they have primarily focused on enhancing predictive performance without addressing the presence of inevitable noise and inconsistent semantics. This limitation has hindered the advancement of KG-based prediction methods. To address this limitation, we propose BioKDN (Biomedical Knowledge Graph Denoising Network) for robust molecular interaction prediction. BioKDN refines the reliable structure of local subgraphs by denoising noisy links in a learnable manner, providing a general module for extracting task-relevant interactions. To enhance the reliability of the refined structure, BioKDN maintains consistent and robust semantics by smoothing relations around the target interaction. By maximizing the mutual information between reliable structure and smoothed relations, BioKDN emphasizes informative semantics to enable precise predictions. Experimental results on real-world datasets show that BioKDN surpasses state-of-the-art models in DTI and DDI prediction tasks, confirming the effectiveness and robustness of BioKDN in denoising unreliable interactions within contaminated KGs

Yiping Liu, Xiaozhe Wang, Geza Joos

Vehicle-to-Grid (V2G) technology allows bidirectional power flow for real-time grid support, making electric vehicles (EVs) well-suited for ancillary services such as frequency regulation. However, existing methods for flexibility estimation and coordinating aggregated EVs often rely on individual EV traveling information (e.g., arrival/departure time) and/or characteristic parameters (e.g., charging efficiency, battery capacity) as well as real-time state-of-charge (SOC), which raises privacy concerns and faces data quality issues. To address these challenges, this paper proposes a data-driven, privacy-preserving modeling and control framework for frequency regulation using aggregated EVs. The proposed method can provide accurate estimation for power outputs and flexibility of aggregated EVs and carry out effective frequency regulation without any individual EV information. %preserving user privacy and ensuring practical scalability. Simulation results validate the accuracy and effectiveness of the proposed method, which also outperforms the model-based and federated learning-based method under SOC data inaccuracies.

Peng Zhou, Jianmin Wang, Chunyan Li et al.

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a multi-constraint molecular generation large language model, TSMMG, which, akin to a student, incorporates knowledge from various small models and tools, namely, the 'teachers'. To train TSMMG, we construct a large set of text-molecule pairs by extracting molecular knowledge from these 'teachers', enabling it to generate novel molecules that conform to the descriptions through various text prompts. We experimentally show that TSMMG remarkably performs in generating molecules meeting complex, natural language-described property requirements across two-, three-, and four-constraint tasks, with an average molecular validity of over 99% and success ratio of 82.58%, 68.03%, and 67.48%, respectively. The model also exhibits adaptability through zero-shot testing, creating molecules that satisfy combinations of properties that have not been encountered. It can comprehend text inputs with various language styles, extending beyond the confines of outlined prompts, as confirmed through empirical validation. Additionally, the knowledge distillation feature of TSMMG contributes to the continuous enhancement of small models, while the innovative approach to dataset construction effectively addresses the issues of data scarcity and quality, which positions TSMMG as a promising tool in the domains of drug discovery and materials science.

Gaël Gendron, Yang Chen, Mitchell Rogers et al.

Better understanding the natural world is a crucial task with a wide range of applications. In environments with close proximity between humans and animals, such as zoos, it is essential to better understand the causes behind animal behaviour and what interventions are responsible for changes in their behaviours. This can help to predict unusual behaviours, mitigate detrimental effects and increase the well-being of animals. There has been work on modelling the dynamics behind swarms of birds and insects but the complex social behaviours of mammalian groups remain less explored. In this work, we propose a method to build behavioural models using causal structure discovery and graph neural networks for time series. We apply this method to a mob of meerkats in a zoo environment and study its ability to predict future actions and model the behaviour distribution at an individual-level and at a group level. We show that our method can match and outperform standard deep learning architectures and generate more realistic data, while using fewer parameters and providing increased interpretability.

Yuqin He, Tengfei Ma, Chaoyi Li et al.

To mitigate the potential adverse health effects of simultaneous multi-drug use, including unexpected side effects and interactions, accurately identifying and predicting drug-drug interactions (DDIs) is considered a crucial task in the field of deep learning. Although existing methods have demonstrated promising performance, they suffer from the bottleneck of limited functional motif-based representation learning, as DDIs are fundamentally caused by motif interactions rather than the overall drug structures. In this paper, we propose an Image-enhanced molecular motif sequence representation framework for \textbf{DDI} prediction, called ImageDDI, which represents a pair of drugs from both global and local structures. Specifically, ImageDDI tokenizes molecules into functional motifs. To effectively represent a drug pair, their motifs are combined into a single sequence and embedded using a transformer-based encoder, starting from the local structure representation. By leveraging the associations between drug pairs, ImageDDI further enhances the spatial representation of molecules using global molecular image information (e.g. texture, shadow, color, and planar spatial relationships). To integrate molecular visual information into functional motif sequence, ImageDDI employs Adaptive Feature Fusion, enhancing the generalization of ImageDDI by dynamically adapting the fusion process of feature representations. Experimental results on widely used datasets demonstrate that ImageDDI outperforms state-of-the-art methods. Moreover, extensive experiments show that ImageDDI achieved competitive performance in both 2D and 3D image-enhanced scenarios compared to other models.

Yifan Dai, Xuanbai Ren, Tengfei Ma et al.

Accurate molecular property prediction (MPP) is a critical step in modern drug development. However, the scarcity of experimental validation data poses a significant challenge to AI-driven research paradigms. Under few-shot learning scenarios, the quality of molecular representations directly dictates the theoretical upper limit of model performance. We present AdaptMol, a prototypical network integrating Adaptive multimodal fusion for Molecular representation. This framework employs a dual-level attention mechanism to dynamically integrate global and local molecular features derived from two modalities: SMILES sequences and molecular graphs. (1) At the local level, structural features such as atomic interactions and substructures are extracted from molecular graphs, emphasizing fine-grained topological information; (2) At the global level, the SMILES sequence provides a holistic representation of the molecule. To validate the necessity of multimodal adaptive fusion, we propose an interpretable approach based on identifying molecular active substructures to demonstrate that multimodal adaptive fusion can efficiently represent molecules. Extensive experiments on three commonly used benchmarks under 5-shot and 10-shot settings demonstrate that AdaptMol achieves state-of-the-art performance in most cases. The rationale-extracted method guides the fusion of two modalities and highlights the importance of both modalities.

Youneng Bao, Yiping Liu, Zhuo Chen et al.

Driven by the ``scale-is-everything'' paradigm, modern machine learning increasingly demands ever-larger datasets and models, yielding prohibitive computational and storage requirements. Dataset distillation mitigates this by compressing an original dataset into a small set of synthetic samples, while preserving its full utility. Yet, existing methods either maximize performance under fixed storage budgets or pursue suitable synthetic data representations for redundancy removal, without jointly optimizing both objectives. In this work, we propose a joint rate-utility optimization method for dataset distillation. We parameterize synthetic samples as optimizable latent codes decoded by extremely lightweight networks. We estimate the Shannon entropy of quantized latents as the rate measure and plug any existing distillation loss as the utility measure, trading them off via a Lagrange multiplier. To enable fair, cross-method comparisons, we introduce bits per class (bpc), a precise storage metric that accounts for sample, label, and decoder parameter costs. On CIFAR-10, CIFAR-100, and ImageNet-128, our method achieves up to $170\times$ greater compression than standard distillation at comparable accuracy. Across diverse bpc budgets, distillation losses, and backbone architectures, our approach consistently establishes better rate-utility trade-offs.

Yiping Liu, Mengxiao Zhang, Jiamou Liu et al.

Machine learning (ML) models have become essential tools in various scenarios. Their effectiveness, however, hinges on a substantial volume of data for satisfactory performance. Model marketplaces have thus emerged as crucial platforms bridging model consumers seeking ML solutions and data owners possessing valuable data. These marketplaces leverage model trading mechanisms to properly incentive data owners to contribute their data, and return a well performing ML model to the model consumers. However, existing model trading mechanisms often assume the data owners are willing to share their data before being paid, which is not reasonable in real world. Given that, we propose a novel mechanism, named Structural Importance based Model Trading (SIMT) mechanism, that assesses the data importance and compensates data owners accordingly without disclosing the data. Specifically, SIMT procures feature and label data from data owners according to their structural importance, and then trains a graph neural network for model consumers. Theoretically, SIMT ensures incentive compatible, individual rational and budget feasible. The experiments on five popular datasets validate that SIMT consistently outperforms vanilla baselines by up to $40\%$ in both MacroF1 and MicroF1.

Li Wang, Xiangzheng Fu, Jiahao Yang et al.

Deep learning holds a big promise for optimizing existing peptides with more desirable properties, a critical step towards accelerating new drug discovery. Despite the recent emergence of several optimized Antimicrobial peptides(AMP) generation methods, multi-objective optimizations remain still quite challenging for the idealism-realism tradeoff. Here, we establish a multi-objective AMP synthesis pipeline (MoFormer) for the simultaneous optimization of multi-attributes of AMPs. MoFormer improves the desired attributes of AMP sequences in a highly structured latent space, guided by conditional constraints and fine-grained multi-descriptor.We show that MoFormer outperforms existing methods in the generation task of enhanced antimicrobial activity and minimal hemolysis. We also utilize a Pareto-based non-dominated sorting algorithm and proxies based on large model fine-tuning to hierarchically rank the candidates. We demonstrate substantial property improvement using MoFormer from two perspectives: (1) employing molecular simulations and scoring interactions among amino acids to decipher the structure and functionality of AMPs; (2) visualizing latent space to examine the qualities and distribution features, verifying an effective means to facilitate multi-objective optimization AMPs with design constraints

Bo Yan, Yiping Liu, Jiamou Liu et al.

Interpersonal ties are pivotal to individual efficacy, status and performance in an agent society. This paper explores three important and interrelated themes in social network theory: the center/periphery partition of the network; network dynamics; and social integration of newcomers. We tackle the question: How would a newcomer harness information brokerage to integrate into a dynamic network going from periphery to center? We model integration as the interplay between the newcomer and the dynamics network and capture information brokerage using a process of relationship building. We analyze theoretical guarantees for the newcomer to reach the center through tactics; proving that a winning tactic always exists for certain types of network dynamics. We then propose three tactics and show their superior performance over alternative methods on four real-world datasets and four network models. In general, our tactics place the newcomer to the center by adding very few new edges on dynamic networks with approximately 14000 nodes.