Zekai Chen, Min Sha
In this paper, we construct several infinite families of $q$-ary constacyclic codes over a finite field $\mathbb{F}_q$ with length $n$, dimension around $n/2$, and minimum distance at least $cn/\log_q n$ for some positive constant $c$. They contain many constacyclic codes with optimal, or almost-optimal, or best-known parameters. We also consider constacyclic codes of various lengths.
Tianyu Fu, Yichen You, Zekai Chen et al.
Improving reasoning capabilities of Large Language Models (LLMs), especially under parameter constraints, is crucial for real-world applications. Prior work proposes recurrent transformers, which allocate a fixed number of extra iterations per token to improve generation quality. After the first, standard forward pass, instead of verbalization, last-layer hidden states are fed back as inputs for additional iterations to refine token predictions. Yet we identify a latent overthinking phenomenon: easy token predictions that are already correct after the first pass are sometimes revised into errors in additional iterations. To address this, we propose Think-at-Hard (TaH), a dynamic latent thinking method that iterates deeper only at hard tokens. It employs a lightweight neural decider to trigger latent iterations only at tokens that are likely incorrect after the standard forward pass. During latent iterations, Low-Rank Adaptation (LoRA) modules shift the LLM objective from general next-token prediction to focused hard-token refinement. We further introduce a duo-causal attention mechanism that extends attention from the token sequence dimension to an additional iteration depth dimension. This enables cross-iteration information flow while maintaining full sequential parallelism. Experiments show that TaH boosts LLM reasoning performance across five challenging benchmarks while maintaining the same parameter count. Compared with baselines that iterate twice for all output tokens, TaH delivers 8.1-11.3% accuracy gains while exempting 94% of tokens from the second iteration. Against strong single-iteration Qwen3 models finetuned with the same data, it also delivers 4.0-5.0% accuracy gains. When allowing less than 3% additional parameters from LoRA and the iteration decider, the gains increase to 8.5-12.6% and 5.3-5.4%, respectively. Our code is available at https://github.com/thu-nics/TaH.
Zekai Chen, Devansh Agarwal, Kshitij Aggarwal et al.
Recently, masked image modeling (MIM) has gained considerable attention due to its capacity to learn from vast amounts of unlabeled data and has been demonstrated to be effective on a wide variety of vision tasks involving natural images. Meanwhile, the potential of self-supervised learning in modeling 3D medical images is anticipated to be immense due to the high quantities of unlabeled images, and the expense and difficulty of quality labels. However, MIM's applicability to medical images remains uncertain. In this paper, we demonstrate that masked image modeling approaches can also advance 3D medical images analysis in addition to natural images. We study how masked image modeling strategies leverage performance from the viewpoints of 3D medical image segmentation as a representative downstream task: i) when compared to naive contrastive learning, masked image modeling approaches accelerate the convergence of supervised training even faster (1.40$\times$) and ultimately produce a higher dice score; ii) predicting raw voxel values with a high masking ratio and a relatively smaller patch size is non-trivial self-supervised pretext-task for medical images modeling; iii) a lightweight decoder or projection head design for reconstruction is powerful for masked image modeling on 3D medical images which speeds up training and reduce cost; iv) finally, we also investigate the effectiveness of MIM methods under different practical scenarios where different image resolutions and labeled data ratios are applied.
Zekai Chen, Mariann Micsinai Balan, Kevin Brown
Clinical prediction is an essential task in the healthcare industry. However, the recent success of transformers, on which large language models are built, has not been extended to this domain. In this research, we explore the use of transformers and language models in prognostic prediction for immunotherapy using real-world patients' clinical data and molecular profiles. This paper investigates the potential of transformers to improve clinical prediction compared to conventional machine learning approaches and addresses the challenge of few-shot learning in predicting rare disease areas. The study benchmarks the efficacy of baselines and language models on prognostic prediction across multiple cancer types and investigates the impact of different pretrained language models under few-shot regimes. The results demonstrate significant improvements in accuracy and highlight the potential of NLP in clinical research to improve early detection and intervention for different diseases.
Mufeng Chen, Qi Wu, Bingchao Huang et al.
Reliable seizure prediction is a prerequisite for closed-loop neurostimulation therapy, yet existing methods rarely account for the variability in EEG signal quality encountered in real-world deployment, and the overwhelming majority adopt non-strict evaluation protocols that overestimate generalisation performance. We propose CLSP-REQA (Closed-Loop Seizure Prediction with Real-time EEG Quality Assessment), a unified framework that embeds a lightweight signal quality estimator directly within the prediction pipeline. A Real-time EEG Quality Assessment (REQA) module runs in parallel with a Mamba-BiLSTM backbone, producing a scalar quality score q in [0,1] that modulates output confidence through a tiered non-linear fusion function (ECLO). Under strict cross-patient evaluation on the CHB-MIT Scalp EEG Database (n = 23 subjects, 198 seizures), CLSP-REQA achieves an AUC-ROC of 0.7426 +- 0.0199, outperforming the unadapted cross-patient baseline of 0.69 reported by Jemal et al., using only 16 EEG channels compared to 23 in prior work, and without requiring any target-patient data or domain adaptation. On the SIENA Scalp EEG Database (n = 14 subjects, 47 seizures), CLSP-REQA achieves AUC 0.7012 +- 0.0249, substantially surpassing the best domain-adapted cross-patient result of 0.61 on the same dataset, demonstrating strong cross-dataset generalisation. The framework outputs a structured four-tuple (p, q, c, Phi_SHAP) directly compatible with closed-loop neurostimulator interfaces.
Chentao Jia, Ming Hu, Zekai Chen et al.
Although Federated Learning (FL) is promising to enable collaborative learning among Artificial Intelligence of Things (AIoT) devices, it suffers from the problem of low classification performance due to various heterogeneity factors (e.g., computing capacity, memory size) of devices and uncertain operating environments. To address these issues, this paper introduces an effective FL approach named AdaptiveFL based on a novel fine-grained width-wise model pruning strategy, which can generate various heterogeneous local models for heterogeneous AIoT devices. By using our proposed reinforcement learning-based device selection mechanism, AdaptiveFL can adaptively dispatch suitable heterogeneous models to corresponding AIoT devices on the fly based on their available resources for local training. Experimental results show that, compared to state-of-the-art methods, AdaptiveFL can achieve up to 16.83% inference improvements for both IID and non-IID scenarios.
Irsyad Adam, Zekai Chen, David Laprade et al.
Large language models (LLMs) trained with next-word-prediction have achieved success as clinical foundation models. Representations from these language backbones yield strong linear probe performance across biomedical tasks, suggesting that patient semantics emerge from next-token prediction at scale. However, this paradigm treats patients as a document to be summarized rather than a dynamical system to be simulated; a patient's trajectory emerges from their state evolving under interventions and time, requiring models that simulate dynamics rather than predict tokens. To address this, we introduce SMB-Structure, a world model for structured EHR that grounds a joint-embedding prediction architecture (JEPA) with next-token prediction (SFT). SFT grounds our model to reconstruct future patient states in token space, while JEPA predicts those futures in latent space from the initial patient representation alone, forcing trajectory dynamics to be encoded before the next state is observed. We validate across two large-scale cohorts: Memorial Sloan Kettering (23,319 oncology patients; 323,000+ patient-years) and INSPECT (19,402 pulmonary embolism patients). Using a linear probe evaluated at multiple points along the disease trajectory, we demonstrate that our training paradigm learns embeddings that capture disease dynamics not recoverable by autoregressive baselines, enabling SMB-Structure to achieve competitive performance on complex tasks characterized by high patient heterogeneity. Model weights are available at https://huggingface.co/standardmodelbio/SMB-v1-1.7B-Structure.
Zekai Chen, Fuyi Wang, Zhiwei Zheng et al.
Federated learning (FL) enables multiple clients to collaboratively train deep learning models while considering sensitive local datasets' privacy. However, adversaries can manipulate datasets and upload models by injecting triggers for federated backdoor attacks (FBA). Existing defense strategies against FBA consider specific and limited attacker models, and a sufficient amount of noise to be injected only mitigates rather than eliminates FBA. To address these deficiencies, we introduce a Flexible Federated Backdoor Defense Framework (Fedward) to ensure the elimination of adversarial backdoors. We decompose FBA into various attacks, and design amplified magnitude sparsification (AmGrad) and adaptive OPTICS clustering (AutoOPTICS) to address each attack. Meanwhile, Fedward uses the adaptive clipping method by regarding the number of samples in the benign group as constraints on the boundary. This ensures that Fedward can maintain the performance for the Non-IID scenario. We conduct experimental evaluations over three benchmark datasets and thoroughly compare them to state-of-the-art studies. The results demonstrate the promising defense performance from Fedward, moderately improved by 33% $\sim$ 75 in clustering defense methods, and 96.98%, 90.74%, and 89.8% for Non-IID to the utmost extent for the average FBA success rate over MNIST, FMNIST, and CIFAR10, respectively.
Zekai Chen, Kairui Yang, Xunkai Li et al.
Federated graph learning (FGL) enables collaborative training of graph neural networks (GNNs) across decentralized subgraphs without exposing raw data. While existing FGL methods often achieve high overall accuracy, we show that this average performance can conceal severe degradation on disadvantaged node groups. From a fairness perspective, these disparities arise systematically from three coupled sources: label skew toward majority patterns, topology confounding in message propagation, and aggregation dilution of updates from hard clients. To address this, we propose \textbf{BoostFGL}, a boosting-style framework for fairness-aware FGL. BoostFGL introduces three coordinated mechanisms: \ding{182} \emph{Client-side node boosting}, which reshapes local training signals to emphasize systematically under-served nodes; \ding{183} \emph{Client-side topology boosting}, which reallocates propagation emphasis toward reliable yet underused structures and attenuates misleading neighborhoods; and \ding{184} \emph{Server-side model boosting}, which performs difficulty- and reliability-aware aggregation to preserve informative updates from hard clients while stabilizing the global model. Extensive experiments on 9 datasets show that BoostFGL delivers substantial fairness gains, improving Overall-F1 by 8.43\%, while preserving competitive overall performance against strong FGL baselines.
Xunkai Li, Zhengyu Wu, Zekai Chen et al.
Recently, the rapid advancement of multimodal domains has driven a data-centric paradigm shift in graph ML, transitioning from text-attributed to multimodal-attributed graphs. This advancement significantly enhances data representation and expands the scope of graph downstream tasks, such as modality-oriented tasks, thereby improving the practical utility of graph ML. Despite its promise, limitations exist in the current neural paradigms: (1) Neglect Context in Modality Alignment: Most existing methods adopt topology-constrained or modality-specific operators as tokenizers. These aligners inevitably neglect graph context and inhibit modality interaction, resulting in suboptimal alignment. (2) Lack of Adaptation in Modality Fusion: Most existing methods are simple adaptations for 2-modality graphs and fail to adequately exploit aligned tokens equipped with topology priors during fusion, leading to poor generalizability and performance degradation. To address the above issues, we propose LION (c\underline{LI}ff\underline{O}rd \underline{N}eural paradigm) based on the Clifford algebra and decoupled graph neural paradigm (i.e., propagation-then-aggregation) to implement alignment-then-fusion in multimodal-attributed graphs. Specifically, we first construct a modality-aware geometric manifold grounded in Clifford algebra. This geometric-induced high-order graph propagation efficiently achieves modality interaction, facilitating modality alignment. Then, based on the geometric grade properties of aligned tokens, we propose adaptive holographic aggregation. This module integrates the energy and scale of geometric grades with learnable parameters to improve modality fusion. Extensive experiments on 9 datasets demonstrate that LION significantly outperforms SOTA baselines across 3 graph and 3 modality downstream tasks.
Zekai Chen, Haodong Lu, Xunkai Li et al.
Federated graph learning (FGL) enables collaborative training on graph data across multiple clients. With the rise of large language models (LLMs), textual attributes in FGL graphs are gaining attention. Text-attributed graph federated learning (TAG-FGL) improves FGL by explicitly leveraging LLMs to process and integrate these textual features. However, current TAG-FGL methods face three main challenges: \textbf{(1) Overhead.} LLMs for processing long texts incur high token and computation costs. To make TAG-FGL practical, we introduce graph condensation (GC) to reduce computation load, but this choice also brings new issues. \textbf{(2) Suboptimal.} To reduce LLM overhead, we introduce GC into TAG-FGL by compressing multi-hop texts/neighborhoods into a condensed core with fixed LLM surrogates. However, this one-shot condensation is often not client-adaptive, leading to suboptimal performance. \textbf{(3) Interpretability.} LLM-based condensation further introduces a black-box bottleneck: summaries lack faithful attribution and clear grounding to specific source spans, making local inspection and auditing difficult. To address the above issues, we propose \textbf{DANCE}, a new TAG-FGL paradigm with GC. To improve \textbf{suboptimal} performance, DANCE performs round-wise, model-in-the-loop condensation refresh using the latest global model. To enhance \textbf{interpretability}, DANCE preserves provenance by storing locally inspectable evidence packs that trace predictions to selected neighbors and source text spans. Across 8 TAG datasets, DANCE improves accuracy by \textbf{2.33\%} at an \textbf{8\%} condensation ratio, with \textbf{33.42\%} fewer tokens than baselines.
Zekai Chen, Xun Wu, Xunkai Li et al.
Federated graph learning (FGL) enables collaborative training on graph data across multiple clients. As graph data increasingly contain multimodal node attributes such as text and images, multimodal federated graph learning (MM-FGL) has become an important yet substantially harder setting. The key challenge is that clients from different modality domains may not share a common semantic space: even for the same concept, their local encoders can produce inconsistent representations before collaboration begins. This makes direct parameter coordination unreliable and further causes two downstream problems: forcing heterogeneous client representations into a naively shared semantic space may create false semantic agreement, and graph message passing may amplify residual inconsistency across neighborhoods. To address this issue, we propose \textbf{STAGE}, a protocol-first framework for MM-FGL. Instead of relying on direct parameter averaging, STAGE builds a shared semantic space that first translates heterogeneous multimodal features into comparable representations and then regulates how these representations propagate over local graph structures. In this way, STAGE not only improves cross-client semantic calibration, but also reduces the risk of inconsistency amplification during graph learning. Extensive experiments on 8 multimodal-attributed graphs across 5 graph-centric and modality-centric tasks show that STAGE consistently achieves state-of-the-art performance while reducing per-round communication payload.
Sirui Zhang, Haonan Wang, Xunkai Li et al.
Recently, multimodal graph learning (MGL) has garnered significant attention for integrating diverse modality information and structured context to support various network applications. However, real-world graphs are often isolated due to data-sharing limitations across multiple parties, and their modalities are frequently incomplete. This highlights an urgent need to develop a robust federated approach. However, we find that existing methods remain insufficient. On the one hand, centralized MGL methods that handle missing modalities overlook the knowledge sharing and generalization in federated scenarios. On the other hand, while federated MGL methods have become increasingly mature, they primarily target non-graph data. Based on these technologies, we identify a two-stage pipeline wherein client-side completion reconstructs missing modalities, and server-side aggregation integrates the client-updated parameters of both the modality generator and the backbone models. Although this serves as a general solution, we identify two primary challenges in achieving greater robustness: (1) Topology-Isolated Local Completion: Client-side modality generation struggles to effectively leverage global semantics. (2) Reliability-Imbalanced Global Aggregation: Server-side multi-party collaboration is hindered by client updates with varying modality availability and recovery reliability. To address these challenges, we propose \textsc{FedMPO}, which utilizes topology-aware cross-modal generation to recover missing features using comprehensive graph context, missing-aware expert routing to locally filter out noisy recovered signals, and reliability-aware aggregation to appropriately down-weight unreliable updates. Extensive experiments on 3 tasks across 6 datasets demonstrate that FedMPO outperforms baselines, achieving performance gains of up to 4.10% and 5.65% in high-missing and non-IID settings.
Zekai Chen, Xunkai Li, Yinlin Zhu et al.
As a new distributed graph learning paradigm, Federated Graph Learning (FGL) facilitates collaborative model training across local systems while preserving data privacy. We review existing FGL approaches and categorize their optimization mechanisms into: (1) Server-Client (S-C), where clients upload local model parameters for server-side aggregation and global updates; (2) Client-Client (C-C), which allows direct exchange of information between clients and customizing their local training process. We reveal that C-C shows superior potential due to its refined communication structure. However, existing C-C methods broadcast redundant node representations, incurring high communication costs and privacy risks at the node level. To this end, we propose FedC4, which combines graph Condensation with C-C Collaboration optimization. Specifically, FedC4 employs graph condensation technique to refine the knowledge of each client's graph into a few synthetic embeddings instead of transmitting node-level knowledge. Moreover, FedC4 introduces three novel modules that allow the source client to send distinct node representations tailored to the target client's graph properties. Experiments on eight public real-world datasets show that FedC4 outperforms state-of-the-art baselines in both task performance and communication cost. Our code is now available on https://github.com/Ereshkigal1/FedC4.
Zekai Chen, Arda Pekis, Kevin Brown
Multi-modal learning has significantly advanced generative AI, especially in vision-language modeling. Innovations like GPT-4V and open-source projects such as LLaVA have enabled robust conversational agents capable of zero-shot task completions. However, applying these technologies in the biomedical field presents unique challenges. Recent initiatives like LLaVA-Med have started to adapt instruction-tuning for biomedical contexts using large datasets such as PMC-15M. Our research offers three key contributions: (i) we present a new instruct dataset enriched with medical image-text pairs from Claude3-Opus and LLaMA3 70B, (ii) we propose a novel image encoding strategy using hierarchical representations to improve fine-grained biomedical visual comprehension, and (iii) we develop the Llama3-Med model, which achieves state-of-the-art zero-shot performance on biomedical visual question answering benchmarks, with an average performance improvement of over 10% compared to previous methods. These advancements provide more accurate and reliable tools for medical professionals, bridging gaps in current multi-modal conversational assistants and promoting further innovations in medical AI.
Zekai Chen, Fangtian Zhong, Zhumin Chen et al.
User response prediction, which aims to predict the probability that a user will provide a predefined positive response in a given context such as clicking on an ad or purchasing an item, is crucial to many industrial applications such as online advertising, recommender systems, and search ranking. However, due to the high dimensionality and super sparsity of the data collected in these tasks, handcrafting cross features is inevitably time expensive. Prior studies in predicting user response leveraged the feature interactions by enhancing feature vectors with products of features to model second-order or high-order cross features, either explicitly or implicitly. Nevertheless, these existing methods can be hindered by not learning sufficient cross features due to model architecture limitations or modeling all high-order feature interactions with equal weights. This work aims to fill this gap by proposing a novel architecture Deep Cross Attentional Product Network (DCAP), which keeps cross network's benefits in modeling high-order feature interactions explicitly at the vector-wise level. Beyond that, it can differentiate the importance of different cross features in each network layer inspired by the multi-head attention mechanism and Product Neural Network (PNN), allowing practitioners to perform a more in-depth analysis of user behaviors. Additionally, our proposed model can be easily implemented and train in parallel. We conduct comprehensive experiments on three real-world datasets. The results have robustly demonstrated that our proposed model DCAP achieves superior prediction performance compared with the state-of-the-art models. Public codes are available at https://github.com/zachstarkk/DCAP.
Zekai Chen, Xiao Zhang, Xiuzhen Cheng
Many real-world scenarios, such as human activity recognition (HAR) in IoT, can be formalized as a multi-task multi-view learning problem. Each specific task consists of multiple shared feature views collected from multiple sources, either homogeneous or heterogeneous. Common among recent approaches is to employ a typical hard/soft sharing strategy at the initial phase separately for each view across tasks to uncover common knowledge, underlying the assumption that all views are conditionally independent. On the one hand, multiple views across tasks possibly relate to each other under practical situations. On the other hand, supervised methods might be insufficient when labeled data is scarce. To tackle these challenges, we introduce a novel framework ASM2TV for semi-supervised multi-task multi-view learning. We present a new perspective named gating control policy, a learnable task-view-interacted sharing policy that adaptively selects the most desirable candidate shared block for any view across any task, which uncovers more fine-grained task-view-interacted relatedness and improves inference efficiency. Significantly, our proposed gathering consistency adaption procedure takes full advantage of large amounts of unlabeled fragmented time-series, making it a general framework that accommodates a wide range of applications. Experiments on two diverse real-world HAR benchmark datasets collected from various subjects and sources demonstrate our framework's superiority over other state-of-the-arts. The detailed codes are available at https://github.com/zachstarkk/ASM2TV.
Zekai Chen, Dingshuo Chen, Xiao Zhang et al.
Many real-world IoT systems, which include a variety of internet-connected sensory devices, produce substantial amounts of multivariate time series data. Meanwhile, vital IoT infrastructures like smart power grids and water distribution networks are frequently targeted by cyber-attacks, making anomaly detection an important study topic. Modeling such relatedness is, nevertheless, unavoidable for any efficient and effective anomaly detection system, given the intricate topological and nonlinear connections that are originally unknown among sensors. Furthermore, detecting anomalies in multivariate time series is difficult due to their temporal dependency and stochasticity. This paper presented GTA, a new framework for multivariate time series anomaly detection that involves automatically learning a graph structure, graph convolution, and modeling temporal dependency using a Transformer-based architecture. The connection learning policy, which is based on the Gumbel-softmax sampling approach to learn bi-directed links among sensors directly, is at the heart of learning graph structure. To describe the anomaly information flow between network nodes, we introduced a new graph convolution called Influence Propagation convolution. In addition, to tackle the quadratic complexity barrier, we suggested a multi-branch attention mechanism to replace the original multi-head self-attention method. Extensive experiments on four publicly available anomaly detection benchmarks further demonstrate the superiority of our approach over alternative state-of-the-arts. Codes are available at https://github.com/ZEKAICHEN/GTA.
Fuyi Wang, Zekai Chen, Mingyuan Fan et al.
Graph neural networks (GNNs) are powerful tools for analyzing and learning from graph-structured (GS) data, facilitating a wide range of services. Deploying such services in privacy-critical cloud environments necessitates the development of secure inference (SI) protocols that safeguard sensitive GS data. However, existing SI solutions largely focus on convolutional models for image and text data, leaving the challenge of securing GNNs and GS data relatively underexplored. In this work, we design, implement, and evaluate $\sysname$, a lightweight cryptographic scheme for graph-centric inference in the cloud. By hybridizing additive and function secret sharings within secure two-party computation (2PC), $\sysname$ is carefully designed based on a series of novel 2PC interactive protocols that achieve $1.5\times \sim 1.7\times$ speedups for linear layers and $2\times \sim 15\times$ for non-linear layers over state-of-the-art (SotA) solutions. A thorough theoretical analysis is provided to prove $\sysname$'s correctness, security, and lightweight nature. Extensive experiments across four datasets demonstrate $\sysname$'s superior efficiency with $1.3\times \sim 4.7\times$ faster secure predictions while maintaining accuracy comparable to plaintext graph property inference.
Ting Jiang, Yixiao Wang, Hancheng Ye et al.
Diffusion models have achieved remarkable success in generative tasks but suffer from high computational costs due to their iterative sampling process and quadratic attention costs. Existing training-free acceleration strategies that reduce per-step computation cost, while effectively reducing sampling time, demonstrate low faithfulness compared to the original baseline. We hypothesize that this fidelity gap arises because (a) different prompts correspond to varying denoising trajectory, and (b) such methods do not consider the underlying ODE formulation and its numerical solution. In this paper, we propose Stability-guided Adaptive Diffusion Acceleration (SADA), a novel paradigm that unifies step-wise and token-wise sparsity decisions via a single stability criterion to accelerate sampling of ODE-based generative models (Diffusion and Flow-matching). For (a), SADA adaptively allocates sparsity based on the sampling trajectory. For (b), SADA introduces principled approximation schemes that leverage the precise gradient information from the numerical ODE solver. Comprehensive evaluations on SD-2, SDXL, and Flux using both EDM and DPM++ solvers reveal consistent $\ge 1.8\times$ speedups with minimal fidelity degradation (LPIPS $\leq 0.10$ and FID $\leq 4.5$) compared to unmodified baselines, significantly outperforming prior methods. Moreover, SADA adapts seamlessly to other pipelines and modalities: It accelerates ControlNet without any modifications and speeds up MusicLDM by $1.8\times$ with $\sim 0.01$ spectrogram LPIPS.
Zekai Chen, Weeden Daniel, Po-yu Chen et al.
The advent of personalized content generation by LLMs presents a novel challenge: how to efficiently adapt text to meet individual preferences without the unsustainable demand of creating a unique model for each user. This study introduces an innovative online method that employs neural bandit algorithms to dynamically optimize soft instruction embeddings based on user feedback, enhancing the personalization of open-ended text generation by white-box LLMs. Through rigorous experimentation on various tasks, we demonstrate significant performance improvements over baseline strategies. NeuralTS, in particular, leads to substantial enhancements in personalized news headline generation, achieving up to a 62.9% improvement in terms of best ROUGE scores and up to 2.76% increase in LLM-agent evaluation against the baseline.
Zekai Chen, Arda Pekis, Kevin Brown
Electronic Health Records (EHRs) contain rich temporal dynamics that conventional encoding approaches fail to adequately capture. While Large Language Models (LLMs) show promise for EHR modeling, they struggle to reason about sequential clinical events and temporal dependencies. We propose Next Event Prediction (NEP), a framework that enhances LLMs' temporal reasoning through autoregressive fine-tuning on clinical event sequences. By reformulating EHRs as timestamped event chains and predicting future medical events, NEP explicitly models disease progression patterns and causal relationships. Extensive evaluations across oncology survival prediction and clinical diagnosis tasks demonstrate NEP's superiority, outperforming specialized EHR models by 4.6% AUROC and general-purpose LLMs by 7.2% C-index in temporal reasoning tasks. Our analyses reveal dual benefits: state-of-the-art prediction accuracy combined with clinically interpretable attention patterns that align with known disease pathways.
Zekai Chen, Xunkai Li, Sirui Zhang et al.
De novo ligand design is a fundamental task that seeks to generate protein or molecule candidates that can effectively dock with protein receptors and achieve strong binding affinity entirely from scratch. It holds paramount significance for a wide spectrum of biomedical applications. However, most existing studies are constrained by the \textbf{Pseudo De Novo}, \textbf{Limited Docking Modeling}, and \textbf{Inflexible Ligand Type}. To address these issues, we propose MagicDock, a forward-looking framework grounded in the progressive pipeline and differentiable surface modeling. (1) We adopt a well-designed gradient inversion framework. To begin with, general docking knowledge of receptors and ligands is incorporated into the backbone model. Subsequently, the docking knowledge is instantiated as reverse gradient flows by binding prediction, which iteratively guide the de novo generation of ligands. (2) We emphasize differentiable surface modeling in the docking process, leveraging learnable 3D point-cloud representations to precisely capture binding details, thereby ensuring that the generated ligands preserve docking validity through direct and interpretable spatial fingerprints. (3) We introduce customized designs for different ligand types and integrate them into a unified gradient inversion framework with flexible triggers, thereby ensuring broad applicability. Moreover, we provide rigorous theoretical guarantees for each component of MagicDock. Extensive experiments across 9 scenarios demonstrate that MagicDock achieves average improvements of 27.1\% and 11.7\% over SOTA baselines specialized for protein or molecule ligand design, respectively.
Irsyad Adam, Zekai Chen, David Laub et al.
Proteomics data is essential to pathogenic understanding of a disease phenotype. In cancer, analysis of molecular signatures enables precision medicine through the identification of biological processes that drive individualized tumor progression, therapeutic resistance, and clinical heterogeneity. Recent advances in multimodal large language models (LLMs) have shown remarkable capacity to integrate and reason across heterogeneous data modalities. However, performing multi-modal language modeling for molecular understanding of patient-specific proteomics remains a significant challenge due to two barriers: (1) the lack of instruction-tuning datasets that enable clinical interpretation from proteomics data, and (2) the absence of language modeling architectures designed to capture the rich heterogeneity of molecular data. In this work, we introduce CPTAC-PROTSTRUCT, the first instruction tuning dataset for molecular understanding of oncology, comprising over 400k open-ended examples derived from individualized proteomic profiles curated from the largest national proteomics cancer study (CPTAC). Additionally, we propose KRONOS (Knowledge Representation of patient Omics Networks in Oncology via Structured tuning), a novel graph-LLM framework that leverages molecular interaction topology with proteomics to learn patient-specific graph representations for enhanced clinical reasoning. We show that KRONOS achieves competitive performance across benchmark clinical tasks, including molecular classification, temporal trajectory modeling, and tumor stage prediction from proteomics data. Ultimately, this approach empowers LLMs to understand patient-level pathogenesis, advancing precision medicine through more accurate diagnosis, prognosis, and treatment stratification.
Zhengyu Wu, Xunkai Li, Yinlin Zhu et al.
In the era of big data applications, Federated Graph Learning (FGL) has emerged as a prominent solution that reconcile the tradeoff between optimizing the collective intelligence between decentralized datasets holders and preserving sensitive information to maximum. Existing FGL surveys have contributed meaningfully but largely focus on integrating Federated Learning (FL) and Graph Machine Learning (GML), resulting in early stage taxonomies that emphasis on methodology and simulated scenarios. Notably, a data centric perspective, which systematically examines FGL methods through the lens of data properties and usage, remains unadapted to reorganize FGL research, yet it is critical to assess how FGL studies manage to tackle data centric constraints to enhance model performances. This survey propose a two-level data centric taxonomy: Data Characteristics, which categorizes studies based on the structural and distributional properties of datasets used in FGL, and Data Utilization, which analyzes the training procedures and techniques employed to overcome key data centric challenges. Each taxonomy level is defined by three orthogonal criteria, each representing a distinct data centric configuration. Beyond taxonomy, this survey examines FGL integration with Pretrained Large Models, showcases realistic applications, and highlights future direction aligned with emerging trends in GML.
Yu-Lin Tsai, Yizhe Li, Zekai Chen et al.
The integration of Differential Privacy (DP) with diffusion models (DMs) presents a promising yet challenging frontier, particularly due to the substantial memorization capabilities of DMs that pose significant privacy risks. Differential privacy offers a rigorous framework for safeguarding individual data points during model training, with Differential Privacy Stochastic Gradient Descent (DP-SGD) being a prominent implementation. Diffusion method decomposes image generation into iterative steps, theoretically aligning well with DP's incremental noise addition. Despite the natural fit, the unique architecture of DMs necessitates tailored approaches to effectively balance privacy-utility trade-off. Recent developments in this field have highlighted the potential for generating high-quality synthetic data by pre-training on public data (i.e., ImageNet) and fine-tuning on private data, however, there is a pronounced gap in research on optimizing the trade-offs involved in DP settings, particularly concerning parameter efficiency and model scalability. Our work addresses this by proposing a parameter-efficient fine-tuning strategy optimized for private diffusion models, which minimizes the number of trainable parameters to enhance the privacy-utility trade-off. We empirically demonstrate that our method achieves state-of-the-art performance in DP synthesis, significantly surpassing previous benchmarks on widely studied datasets (e.g., with only 0.47M trainable parameters, achieving a more than 35% improvement over the previous state-of-the-art with a small privacy budget on the CelebA-64 dataset). Anonymous codes available at https://anonymous.4open.science/r/DP-LORA-F02F.
Fangtian Zhong, Zekai Chen, Minghui Xu et al.
Malware is a piece of software that was written with the intent of doing harm to data, devices, or people. Since a number of new malware variants can be generated by reusing codes, malware attacks can be easily launched and thus become common in recent years, incurring huge losses in businesses, governments, financial institutes, health providers, etc. To defeat these attacks, malware classification is employed, which plays an essential role in anti-virus products. However, existing works that employ either static analysis or dynamic analysis have major weaknesses in complicated reverse engineering and time-consuming tasks. In this paper, we propose a visualized malware classification framework called VisMal, which provides highly efficient categorization with acceptable accuracy. VisMal converts malware samples into images and then applies a contrast-limited adaptive histogram equalization algorithm to enhance the similarity between malware image regions in the same family. We provided a proof-of-concept implementation and carried out an extensive evaluation to verify the performance of our framework. The evaluation results indicate that VisMal can classify a malware sample within 4.0ms and have an average accuracy of 96.0%. Moreover, VisMal provides security engineers with a simple visualization approach to further validate its performance.
Zekai Chen, Jiaze E, Xiao Zhang et al.
Time series forecasting is a key component in many industrial and business decision processes and recurrent neural network (RNN) based models have achieved impressive progress on various time series forecasting tasks. However, most of the existing methods focus on single-task forecasting problems by learning separately based on limited supervised objectives, which often suffer from insufficient training instances. As the Transformer architecture and other attention-based models have demonstrated its great capability of capturing long term dependency, we propose two self-attention based sharing schemes for multi-task time series forecasting which can train jointly across multiple tasks. We augment a sequence of paralleled Transformer encoders with an external public multi-head attention function, which is updated by all data of all tasks. Experiments on a number of real-world multi-task time series forecasting tasks show that our proposed architectures can not only outperform the state-of-the-art single-task forecasting baselines but also outperform the RNN-based multi-task forecasting method.