Hong Liang

Chen Qian, Huayi Tang, Zhirui Yang et al.

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text. Recently, the rapid development of Large Language Models (LLMs) has revolutionized the field of NLP. Although it is natural to utilize LLMs to assist in understanding molecules represented by SMILES, the exploration of how LLMs will impact molecular property prediction is still in its early stage. In this work, we advance towards this objective through two perspectives: zero/few-shot molecular classification, and using the new explanations generated by LLMs as representations of molecules. To be specific, we first prompt LLMs to do in-context molecular classification and evaluate their performance. After that, we employ LLMs to generate semantically enriched explanations for the original SMILES and then leverage that to fine-tune a small-scale LM model for multiple downstream tasks. The experimental results highlight the superiority of text explanations as molecular representations across multiple benchmark datasets, and confirm the immense potential of LLMs in molecular property prediction tasks. Codes are available at \url{https://github.com/ChnQ/LLM4Mol}.

Bingxin Zhou, Outongyi Lv, Kai Yi et al.

Directed evolution as a widely-used engineering strategy faces obstacles in finding desired mutants from the massive size of candidate modifications. While deep learning methods learn protein contexts to establish feasible searching space, many existing models are computationally demanding and fail to predict how specific mutational tests will affect a protein's sequence or function. This research introduces a lightweight graph representation learning scheme that efficiently analyzes the microenvironment of wild-type proteins and recommends practical higher-order mutations exclusive to the user-specified protein and function of interest. Our method enables continuous improvement of the inference model by limited computational resources and a few hundred mutational training samples, resulting in accurate prediction of variant effects that exhibit near-perfect correlation with the ground truth across deep mutational scanning assays of 19 proteins. With its affordability and applicability to both computer scientists and biochemical laboratories, our solution offers a wide range of benefits that make it an ideal choice for the community.

Xiaosong Wang, Xiaofan Zhang, Guotai Wang et al.

The emerging trend of advancing generalist artificial intelligence, such as GPTv4 and Gemini, has reshaped the landscape of research (academia and industry) in machine learning and many other research areas. However, domain-specific applications of such foundation models (e.g., in medicine) remain untouched or often at their very early stages. It will require an individual set of transfer learning and model adaptation techniques by further expanding and injecting these models with domain knowledge and data. The development of such technologies could be largely accelerated if the bundle of data, algorithms, and pre-trained foundation models were gathered together and open-sourced in an organized manner. In this work, we present OpenMEDLab, an open-source platform for multi-modality foundation models. It encapsulates not only solutions of pioneering attempts in prompting and fine-tuning large language and vision models for frontline clinical and bioinformatic applications but also building domain-specific foundation models with large-scale multi-modal medical data. Importantly, it opens access to a group of pre-trained foundation models for various medical image modalities, clinical text, protein engineering, etc. Inspiring and competitive results are also demonstrated for each collected approach and model in a variety of benchmarks for downstream tasks. We welcome researchers in the field of medical artificial intelligence to continuously contribute cutting-edge methods and models to OpenMEDLab, which can be accessed via https://github.com/openmedlab.

Al Amin, Kamrul Hasan, Liang Hong et al.

Collaborative machine learning across healthcare institutions promises improved diagnostic accuracy by leveraging diverse datasets, yet privacy regulations such as HIPAA prohibit direct patient data sharing. While federated learning (FL) enables decentralized training without raw data exchange, recent studies show that model gradients in conventional FL remain vulnerable to reconstruction attacks, potentially exposing sensitive medical information. This paper presents a privacy-preserving federated learning framework combining Vision Transformers (ViT) with homomorphic encryption (HE) for secure multi-institutional histopathology classification. The approach leverages the ViT CLS token as a compact 768-dimensional feature representation for secure aggregation, encrypting these tokens using CKKS homomorphic encryption before transmission to the server. We demonstrate that encrypting CLS tokens achieves a 30-fold communication reduction compared to gradient encryption while maintaining strong privacy guarantees. Through evaluation on a three-client federated setup for lung cancer histopathology classification, we show that gradients are highly susceptible to model inversion attacks (PSNR: 52.26 dB, SSIM: 0.999, NMI: 0.741), enabling near-perfect image reconstruction. In contrast, the proposed CLS-protected HE approach prevents such attacks while enabling encrypted inference directly on ciphertexts, requiring only 326 KB of encrypted data transmission per aggregation round. The framework achieves 96.12 percent global classification accuracy in the unencrypted domain and 90.02 percent in the encrypted domain.

Jingru Zhu, Ya Guo, Geng Sun et al.

Semantic segmentation of high-resolution remote sensing imagery (HRSI) suffers from the domain shift, resulting in poor performance of the model in another unseen domain. Unsupervised domain adaptive (UDA) semantic segmentation aims to adapt the semantic segmentation model trained on the labeled source domain to an unlabeled target domain. However, the existing UDA semantic segmentation models tend to align pixels or features based on statistical information related to labels in source and target domain data, and make predictions accordingly, which leads to uncertainty and fragility of prediction results. In this paper, we propose a causal prototype-inspired contrast adaptation (CPCA) method to explore the invariant causal mechanisms between different HRSIs domains and their semantic labels. It firstly disentangles causal features and bias features from the source and target domain images through a causal feature disentanglement module. Then, a causal prototypical contrast module is used to learn domain invariant causal features. To further de-correlate causal and bias features, a causal intervention module is introduced to intervene on the bias features to generate counterfactual unbiased samples. By forcing the causal features to meet the principles of separability, invariance and intervention, CPCA can simulate the causal factors of source and target domains, and make decisions on the target domain based on the causal features, which can observe improved generalization ability. Extensive experiments under three cross-domain tasks indicate that CPCA is remarkably superior to the state-of-the-art methods.

Al Amin, Kamrul Hasan, Sharif Ullah et al.

In the era of data-driven decision-making, ensuring the privacy and security of shared data is paramount across various domains. Applying existing deep neural networks (DNNs) to encrypted data is critical and often compromises performance, security, and computational overhead. To address these limitations, this research introduces a secure framework consisting of a learnable encryption method based on the block-pixel operation to encrypt the data and subsequently integrate it with the Vision Transformer (ViT). The proposed framework ensures data privacy and security by creating unique scrambling patterns per key, providing robust performance against adversarial attacks without compromising computational efficiency and data integrity. The framework was tested on sensitive medical datasets to validate its efficacy, proving its ability to handle highly confidential information securely. The suggested framework was validated with a 94\% success rate after extensive testing on real-world datasets, such as MRI brain tumors and histological scans of lung and colon cancers. Additionally, the framework was tested under diverse adversarial attempts against secure data sharing with optimum performance and demonstrated its effectiveness in various threat scenarios. These comprehensive analyses underscore its robustness, making it a trustworthy solution for secure data sharing in critical applications.

Liang Hong

The extant insurance literature demonstrates a paucity of finite-sample valid prediction intervals of future insurance claims in the regression setting. To address this challenge, this article proposes a new strategy that converts a predictive method in the unsupervised iid (independent identically distributed) setting to a predictive method in the regression setting. In particular, it enables an actuary to obtain infinitely many finite-sample valid prediction intervals in the regression setting.

Henry Onyeka, Emmanuel Samson, Liang Hong et al.

The increasing complexity of IoT edge networks presents significant challenges for anomaly detection, particularly in identifying sophisticated Denial-of-Service (DoS) attacks and zero-day exploits under highly dynamic and imbalanced traffic conditions. This paper proposes SD-CGAN, a Conditional Generative Adversarial Network framework enhanced with Sinkhorn Divergence, tailored for robust anomaly detection in IoT edge environments. The framework incorporates CTGAN-based synthetic data augmentation to address class imbalance and leverages Sinkhorn Divergence as a geometry-aware loss function to improve training stability and reduce mode collapse. The model is evaluated on exploitative attack subsets from the CICDDoS2019 dataset and compared against baseline deep learning and GAN-based approaches. Results show that SD-CGAN achieves superior detection accuracy, precision, recall, and F1-score while maintaining computational efficiency suitable for deployment in edge-enabled IoT environments.

Daryl Mupupuni, Anupama Guntu, Liang Hong et al.

The expanding role of Artificial Intelligence (AI) in diverse engineering domains highlights the challenges associated with deploying AI models in new operational environments, involving substantial investments in data collection and model training. Rapid application of AI necessitates evaluating the feasibility of utilizing pre-trained models in unobserved operational settings with minimal or no additional data. However, interpreting the opaque nature of AI's black-box models remains a persistent challenge. Addressing this issue, this paper proposes a science-based certification methodology to assess the viability of employing pre-trained data-driven models in new operational environments. The methodology advocates a profound integration of domain knowledge, leveraging theoretical and analytical models from physics and related disciplines, with data-driven AI models. This novel approach introduces tools to facilitate the development of secure engineering systems, providing decision-makers with confidence in the trustworthiness and safety of AI-based models across diverse environments characterized by limited training data and dynamic, uncertain conditions. The paper demonstrates the efficacy of this methodology in real-world safety-critical scenarios, particularly in the context of traffic state estimation. Through simulation results, the study illustrates how the proposed methodology efficiently quantifies physical inconsistencies exhibited by pre-trained AI models. By utilizing analytical models, the methodology offers a means to gauge the applicability of pre-trained AI models in new operational environments. This research contributes to advancing the understanding and deployment of AI models, offering a robust certification framework that enhances confidence in their reliability and safety across a spectrum of operational conditions.

Daryl Mupupuni, Anupama Guntu, Liang Hong et al.

The expanding role of Artificial Intelligence (AI) in diverse engineering domains highlights the challenges associated with deploying AI models in new operational environments, involving substantial investments in data collection and model training. Rapid application of AI necessitates evaluating the feasibility of utilizing pre-trained models in unobserved operational settings with minimal or no additional data. However, interpreting the opaque nature of AI's black-box models remains a persistent challenge. Addressing this issue, this paper proposes a science-based certification methodology to assess the viability of employing pre-trained data-driven models in untrained operational environments. The methodology advocates a profound integration of domain knowledge, leveraging theoretical and analytical models from physics and related disciplines, with data-driven AI models. This novel approach introduces tools to facilitate the development of secure engineering systems, providing decision-makers with confidence in the trustworthiness and safety of AI-based models across diverse environments characterized by limited training data and dynamic, uncertain conditions. The paper demonstrates the efficacy of this methodology in real-world safety-critical scenarios, particularly in the context of traffic state estimation. Through simulation results, the study illustrates how the proposed methodology efficiently quantifies physical inconsistencies exhibited by pre-trained AI models. By utilizing analytical models, the methodology offers a means to gauge the applicability of pre-trained AI models in new operational environments. This research contributes to advancing the understanding and deployment of AI models, offering a robust certification framework that enhances confidence in their reliability and safety across a spectrum of operational conditions.

Al Amin, Kamrul Hasan, Saleh Zein-Sabatto et al.

In the healthcare domain, Magnetic Resonance Imaging (MRI) assumes a pivotal role, as it employs Artificial Intelligence (AI) and Machine Learning (ML) methodologies to extract invaluable insights from imaging data. Nonetheless, the imperative need for patient privacy poses significant challenges when collecting data from diverse healthcare sources. Consequently, the Deep Learning (DL) communities occasionally face difficulties detecting rare features. In this research endeavor, we introduce the Ensemble-Based Federated Learning (EBFL) Framework, an innovative solution tailored to address this challenge. The EBFL framework deviates from the conventional approach by emphasizing model features over sharing sensitive patient data. This unique methodology fosters a collaborative and privacy-conscious environment for healthcare institutions, empowering them to harness the capabilities of a centralized server for model refinement while upholding the utmost data privacy standards.Conversely, a robust ensemble architecture boasts potent feature extraction capabilities, distinguishing itself from a single DL model. This quality makes it remarkably dependable for MRI analysis. By harnessing our groundbreaking EBFL methodology, we have achieved remarkable precision in the classification of brain tumors, including glioma, meningioma, pituitary, and non-tumor instances, attaining a precision rate of 94% for the Global model and an impressive 96% for the Ensemble model. Our models underwent rigorous evaluation using conventional performance metrics such as Accuracy, Precision, Recall, and F1 Score. Integrating DL within the Federated Learning (FL) framework has yielded a methodology that offers precise and dependable diagnostics for detecting brain tumors.

Xiufeng Xu, Liang Hong

We investigate the instantaneous and limiting behavior of an n-node blockchain which is under continuous monitoring of the IT department of a company but faces non-stop cyber attacks from a single hacker. The blockchain is functional as far as no data stored on it has been changed, deleted, or locked. Once the IT department detects the attack from the hacker, it will immediately re-set the blockchain, rendering all previous efforts of the hacker in vain. The hacker will not stop until the blockchain is dysfunctional. For arbitrary distributions of the hacking times and detecting times, we derive the limiting functional probability, instantaneous functional probability, and mean functional time of the blockchain. We also show that all these quantities are increasing functions of the number of nodes, substantiating the intuition that the more nodes a blockchain has, the harder it is for a hacker to succeed in a cyber attack.