Zekai Chen

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.

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.

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.

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, 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.

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.

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.

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.