Liang Hong

Chenqing Hua, Bozitao Zhong, Sitao Luan et al.

Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life, enabling diverse biological processes and adaptations. Predicting enzyme functions is essential for understanding biological pathways, guiding drug development, enhancing bioproduct yields, and facilitating evolutionary studies. Addressing the inherent complexities, we introduce a new approach to annotating enzymes based on their catalyzed reactions. This method provides detailed insights into specific reactions and is adaptable to newly discovered reactions, diverging from traditional classifications by protein family or expert-derived reaction classes. We employ machine learning algorithms to analyze enzyme reaction datasets, delivering a much more refined view on the functionality of enzymes. Our evaluation leverages the largest enzyme-reaction dataset to date, derived from the SwissProt and Rhea databases with entries up to January 8, 2024. We frame the enzyme-reaction prediction as a retrieval problem, aiming to rank enzymes by their catalytic ability for specific reactions. With our model, we can recruit proteins for novel reactions and predict reactions in novel proteins, facilitating enzyme discovery and function annotation (https://github.com/WillHua127/ReactZyme).

Mingchen Li, Liqi Kang, Yi Xiong et al.

Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet, a supervised deep-learning model to predict the fitness for protein mutants by leveraging both sequence and structure information, and exploiting attention mechanism. Our model integrates local evolutionary context from homologous sequences, the global evolutionary context encoding rich semantic from the universal protein sequence space and the structure information accounting for the microenvironment around each residue in a protein. We show that SESNet outperforms state-of-the-art models for predicting the sequence-function relationship on 26 deep mutational scanning datasets. More importantly, we propose a data augmentation strategy by leveraging the data from unsupervised models to pre-train our model. After that, our model can achieve strikingly high accuracy in prediction of the fitness of protein mutants, especially for the higher order variants (> 4 mutation sites), when finetuned by using only a small number of experimental mutation data (<50). The strategy proposed is of great practical value as the required experimental effort, i.e., producing a few tens of experimental mutation data on a given protein, is generally affordable by an ordinary biochemical group and can be applied on almost any protein.

Tao Shen, Zhihang Hu, Siqi Sun et al.

Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design. The structural flexibility of RNA, which leads to scarcity of experimentally determined data, complicates computational prediction efforts. Here, we present RhoFold+, an RNA language model-based deep learning method that accurately predicts 3D structures of single-chain RNAs from sequences. By integrating an RNA language model pre-trained on ~23.7 million RNA sequences and leveraging techniques to address data scarcity, RhoFold+ offers a fully automated end-to-end pipeline for RNA 3D structure prediction. Retrospective evaluations on RNA-Puzzles and CASP15 natural RNA targets demonstrate RhoFold+'s superiority over existing methods, including human expert groups. Its efficacy and generalizability are further validated through cross-family and cross-type assessments, as well as time-censored benchmarks. Additionally, RhoFold+ predicts RNA secondary structures and inter-helical angles, providing empirically verifiable features that broaden its applicability to RNA structure and function studies.

Yutong Hu, Yang Tan, Andi Han et al.

The advent of deep learning has introduced efficient approaches for de novo protein sequence design, significantly improving success rates and reducing development costs compared to computational or experimental methods. However, existing methods face challenges in generating proteins with diverse lengths and shapes while maintaining key structural features. To address these challenges, we introduce CPDiffusion-SS, a latent graph diffusion model that generates protein sequences based on coarse-grained secondary structural information. CPDiffusion-SS offers greater flexibility in producing a variety of novel amino acid sequences while preserving overall structural constraints, thus enhancing the reliability and diversity of generated proteins. Experimental analyses demonstrate the significant superiority of the proposed method in producing diverse and novel sequences, with CPDiffusion-SS surpassing popular baseline methods on open benchmarks across various quantitative measurements. Furthermore, we provide a series of case studies to highlight the biological significance of the generation performance by the proposed method. The source code is publicly available at https://github.com/riacd/CPDiffusion-SS

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.

Yang Tan, Bingxin Zhou, Yuanhong Jiang et al.

Directed evolution plays an indispensable role in protein engineering that revises existing protein sequences to attain new or enhanced functions. Accurately predicting the effects of protein variants necessitates an in-depth understanding of protein structure and function. Although large self-supervised language models have demonstrated remarkable performance in zero-shot inference using only protein sequences, these models inherently do not interpret the spatial characteristics of protein structures, which are crucial for comprehending protein folding stability and internal molecular interactions. This paper introduces a novel pre-training framework that cascades sequential and geometric analyzers for protein primary and tertiary structures. It guides mutational directions toward desired traits by simulating natural selection on wild-type proteins and evaluates the effects of variants based on their fitness to perform the function. We assess the proposed approach using a public database and two new databases for a variety of variant effect prediction tasks, which encompass a diverse set of proteins and assays from different taxa. The prediction results achieve state-of-the-art performance over other zero-shot learning methods for both single-site mutations and deep mutations.

Yang Tan, Yuanxi Yu, Can Wu et al.

Zero-shot mutation prediction is vital for low-resource protein engineering, yet existing protein language models (PLMs) often yield statistically confident results that ignore fundamental biophysical constraints. Currently, selecting candidates for wet-lab validation relies on manual expert auditing of PLM outputs, a process that is inefficient, subjective, and highly dependent on domain expertise. To address this, we propose Rank-and-Reason (VenusRAR), a two-stage agentic framework to automate this workflow and maximize expected wet-lab fitness. In the Rank-Stage, a Computational Expert and Virtual Biologist aggregate a context-aware multi-modal ensemble, establishing a new Spearman correlation record of 0.551 (vs. 0.518) on ProteinGym. In the Reason-Stage, an agentic Expert Panel employs chain-of-thought reasoning to audit candidates against geometric and structural constraints, improving the Top-5 Hit Rate by up to 367% on ProteinGym-DMS99. The wet-lab validation on Cas12i3 nuclease further confirms the framework's efficacy, achieving a 46.7% positive rate and identifying two novel mutants with 4.23-fold and 5.05-fold activity improvements. Code and datasets are released on GitHub (https://github.com/ai4protein/VenusRAR/).

Yang Tan, Mingchen Li, Pan Tan et al.

Large protein language models are adept at capturing the underlying evolutionary information in primary structures, offering significant practical value for protein engineering. Compared to natural language models, protein amino acid sequences have a smaller data volume and a limited combinatorial space. Choosing an appropriate vocabulary size to optimize the pre-trained model is a pivotal issue. Moreover, despite the wealth of benchmarks and studies in the natural language community, there remains a lack of a comprehensive benchmark for systematically evaluating protein language model quality. Given these challenges, PETA trained language models with 14 different vocabulary sizes under three tokenization methods. It conducted thousands of tests on 33 diverse downstream datasets to assess the models' transfer learning capabilities, incorporating two classification heads and three random seeds to mitigate potential biases. Extensive experiments indicate that vocabulary sizes between 50 and 200 optimize the model, whereas sizes exceeding 800 detrimentally affect the model's representational performance. Our code, model weights and datasets are available at https://github.com/ginnm/ProteinPretraining.

Dingyi Rong, Wenzhuo Zheng, Bozitao Zhong et al.

Accurate prediction of enzyme function is crucial for elucidating biological mechanisms and driving innovation across various sectors. Existing deep learning methods tend to rely solely on either sequence data or structural data and predict the EC number as a whole, neglecting the intrinsic hierarchical structure of EC numbers. To address these limitations, we introduce MAPred, a novel multi-modality and multi-scale model designed to autoregressively predict the EC number of proteins. MAPred integrates both the primary amino acid sequence and the 3D tokens of proteins, employing a dual-pathway approach to capture comprehensive protein characteristics and essential local functional sites. Additionally, MAPred utilizes an autoregressive prediction network to sequentially predict the digits of the EC number, leveraging the hierarchical organization of EC classifications. Evaluations on benchmark datasets, including New-392, Price, and New-815, demonstrate that our method outperforms existing models, marking a significant advance in the reliability and granularity of protein function prediction within bioinformatics.

Song Li, Song Ke, Chenxing Yang et al.

Gonadotrophin-releasing hormone receptor (GnRH1R) is a promising therapeutic target for the treatment of uterine diseases. To date, several GnRH1R antagonists are available in clinical investigation without satisfying multiple property constraints. To fill this gap, we aim to develop a deep learning-based framework to facilitate the effective and efficient discovery of a new orally active small-molecule drug targeting GnRH1R with desirable properties. In the present work, a ligand-and-structure combined model, namely LS-MolGen, was firstly proposed for molecular generation by fully utilizing the information on the known active compounds and the structure of the target protein, which was demonstrated by its superior performance than ligand- or structure-based methods separately. Then, a in silico screening including activity prediction, ADMET evaluation, molecular docking and FEP calculation was conducted, where ~30,000 generated novel molecules were narrowed down to 8 for experimental synthesis and validation. In vitro and in vivo experiments showed that three of them exhibited potent inhibition activities (compound 5 IC50 = 0.856 nM, compound 6 IC50 = 0.901 nM, compound 7 IC50 = 2.54 nM) against GnRH1R, and compound 5 performed well in fundamental PK properties, such as half-life, oral bioavailability, and PPB, etc. We believed that the proposed ligand-and-structure combined molecular generative model and the whole computer-aided workflow can potentially be extended to similar tasks for de novo drug design or lead optimization.

Yang Tan, Ruilin Wang, Banghao Wu et al.

Enzyme engineering enables the modification of wild-type proteins to meet industrial and research demands by enhancing catalytic activity, stability, binding affinities, and other properties. The emergence of deep learning methods for protein modeling has demonstrated superior results at lower costs compared to traditional approaches such as directed evolution and rational design. In mutation effect prediction, the key to pre-training deep learning models lies in accurately interpreting the complex relationships among protein sequence, structure, and function. This study introduces a retrieval-enhanced protein language model for comprehensive analysis of native properties from sequence and local structural interactions, as well as evolutionary properties from retrieved homologous sequences. The state-of-the-art performance of the proposed ProtREM is validated on over 2 million mutants across 217 assays from an open benchmark (ProteinGym). We also conducted post-hoc analyses of the model's ability to improve the stability and binding affinity of a VHH antibody. Additionally, we designed 10 new mutants on a DNA polymerase and conducted wet-lab experiments to evaluate their enhanced activity at higher temperatures. Both in silico and experimental evaluations confirmed that our method provides reliable predictions of mutation effects, offering an auxiliary tool for biologists aiming to evolve existing enzymes. The implementation is publicly available at https://github.com/tyang816/ProtREM.

Yang Tan, Mingchen Li, Bingxin Zhou et al.

Fine-tuning Pre-trained protein language models (PLMs) has emerged as a prominent strategy for enhancing downstream prediction tasks, often outperforming traditional supervised learning approaches. As a widely applied powerful technique in natural language processing, employing Parameter-Efficient Fine-Tuning techniques could potentially enhance the performance of PLMs. However, the direct transfer to life science tasks is non-trivial due to the different training strategies and data forms. To address this gap, we introduce SES-Adapter, a simple, efficient, and scalable adapter method for enhancing the representation learning of PLMs. SES-Adapter incorporates PLM embeddings with structural sequence embeddings to create structure-aware representations. We show that the proposed method is compatible with different PLM architectures and across diverse tasks. Extensive evaluations are conducted on 2 types of folding structures with notable quality differences, 9 state-of-the-art baselines, and 9 benchmark datasets across distinct downstream tasks. Results show that compared to vanilla PLMs, SES-Adapter improves downstream task performance by a maximum of 11% and an average of 3%, with significantly accelerated training speed by a maximum of 1034% and an average of 362%, the convergence rate is also improved by approximately 2 times. Moreover, positive optimization is observed even with low-quality predicted structures. The source code for SES-Adapter is available at https://github.com/tyang816/SES-Adapter.

Yang Tan, Lingrong Zhang, Mingchen Li et al.

Protein scientific discovery is bottlenecked by the manual orchestration of information and algorithms, while general agents are insufficient in complex domain projects. VenusFactory2 provides an autonomous framework that shifts from static tool usage to dynamic workflow synthesis via a self-evolving multi-agent infrastructure to address protein-related demands. It outperforms a set of well-known agents on the VenusAgentEval benchmark, and autonomously organizes the discovery and optimization of proteins from a single natural language prompt.

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.

Yang Tan, Wenrui Gou, Bozitao Zhong et al.

Deep learning models have driven significant progress in predicting protein function and interactions at the protein level. While these advancements have been invaluable for many biological applications such as enzyme engineering and function annotation, a more detailed perspective is essential for understanding protein functional mechanisms and evaluating the biological knowledge captured by models. To address this demand, we introduce VenusX, the first large-scale benchmark for fine-grained functional annotation and function-based protein pairing at the residue, fragment, and domain levels. VenusX comprises three major task categories across six types of annotations, including residue-level binary classification, fragment-level multi-class classification, and pairwise functional similarity scoring for identifying critical active sites, binding sites, conserved sites, motifs, domains, and epitopes. The benchmark features over 878,000 samples curated from major open-source databases such as InterPro, BioLiP, and SAbDab. By providing mixed-family and cross-family splits at three sequence identity thresholds, our benchmark enables a comprehensive assessment of model performance on both in-distribution and out-of-distribution scenarios. For baseline evaluation, we assess a diverse set of popular and open-source models, including pre-trained protein language models, sequence-structure hybrids, structure-based methods, and alignment-based techniques. Their performance is reported across all benchmark datasets and evaluation settings using multiple metrics, offering a thorough comparison and a strong foundation for future research. Code and data are publicly available at https://github.com/ai4protein/VenusX.

Yang Tan, Chen Liu, Jingyuan Gao et al.

Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However, interdisciplinary adoption remains limited due to challenges in data collection, task benchmarking, and application. This work presents VenusFactory, a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular fine-tuning of PLMs. VenusFactory supports both computer science and biology communities with choices of both a command-line execution and a Gradio-based no-code interface, integrating $40+$ protein-related datasets and $40+$ popular PLMs. All implementations are open-sourced on https://github.com/tyang816/VenusFactory.

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.

Zhiyu Wang, Bingxin Zhou, Jing Wang et al.

Proteins are essential biological macromolecules that execute life functions. Local motifs within protein structures, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution and enabling protein engineering. Existing computational methods struggle to identify and compare these local structures, which leaves a significant gap in understanding protein structures and harnessing their functions. This study presents PLASMA, the first deep learning framework for efficient and interpretable residue-level protein substructure alignment. We reformulate the problem as a regularized optimal transport task and leverage differentiable Sinkhorn iterations. For a pair of input protein structures, PLASMA outputs a clear alignment matrix with an interpretable overall similarity score. Through extensive quantitative evaluations and three biological case studies, we demonstrate that PLASMA achieves accurate, lightweight, and interpretable residue-level alignment. Additionally, we introduce PLASMA-PF, a training-free variant that provides a practical alternative when training data are unavailable. Our method addresses a critical gap in protein structure analysis tools and offers new opportunities for functional annotation, evolutionary studies, and structure-based drug design. Reproducibility is ensured via our official implementation at https://github.com/ZW471/PLASMA-Protein-Local-Alignment.git.

Pulock Das, Al Amin, Kamrul Hasan et al.

Deep learning (DL) models have achieved strong performance in an intelligence healthcare setting, yet most existing approaches operate as black boxes and ignore the physical processes that govern tumor growth, limiting interpretability, robustness, and clinical trust. To address this limitation, we propose PhysNet, a physics-embedded DL framework that integrates tumor growth dynamics directly into the feature learning process of a convolutional neural network (CNN). Unlike conventional physics-informed methods that impose physical constraints only at the output level, PhysNet embeds a reaction diffusion model of tumor growth within intermediate feature representations of a ResNet backbone. The architecture jointly performs multi-class tumor classification while learning a latent tumor density field, its temporal evolution, and biologically meaningful physical parameters, including tumor diffusion and growth rates, through end-to-end training. This design is necessary because purely data-driven models, even when highly accurate or ensemble-based, cannot guarantee physically consistent predictions or provide insight into tumor behavior. Experimental results on a large brain MRI dataset demonstrate that PhysNet outperforms multiple state-of-the-art DL baselines, including MobileNetV2, VGG16, VGG19, and ensemble models, achieving superior classification accuracy and F1-score. In addition to improved performance, PhysNet produces interpretable latent representations and learned bio-physical parameters that align with established medical knowledge, highlighting physics-embedded representation learning as a practical pathway toward more trustworthy and clinically meaningful medical AI systems.

Haifeng Li, Kaijian Qiu, Li Chen et al.

High-resolution remote sensing images (HRRSIs) contain substantial ground object information, such as texture, shape, and spatial location. Semantic segmentation, which is an important task for element extraction, has been widely used in processing mass HRRSIs. However, HRRSIs often exhibit large intraclass variance and small interclass variance due to the diversity and complexity of ground objects, thereby bringing great challenges to a semantic segmentation task. In this paper, we propose a new end-to-end semantic segmentation network, which integrates lightweight spatial and channel attention modules that can refine features adaptively. We compare our method with several classic methods on the ISPRS Vaihingen and Potsdam datasets. Experimental results show that our method can achieve better semantic segmentation results. The source codes are available at https://github.com/lehaifeng/SCAttNet.

Xinyou Wang, Liang Hong, Jiasheng Ye et al.

Proteins are shaped by gradual evolution under biophysical and functional constraints. Protein language models learn rich evolutionary constraints from large-scale sequences, and discrete diffusion-based protein language models~(\eg, DPLMs) are promising for both understanding and generation. However, existing DPLMs typically rely on masking-based absorbing diffusion that contradicts a simple biological intuition: proteins evolve through accumulated edits, not by emerging from masks. Consequently, these frameworks lack explicit pretraining objectives for substitution and insertion/deletion (indel) operations, limiting both optimization-style post-editing and flexible guided generation. To address these limitations, we present DPLM-Evo, an evolutionary discrete diffusion framework that explicitly predicts substitution, insertion, and deletion operations during denoising. DPLM-Evo decouples an upsampled-length latent alignment space from the variable-length observed sequence space, which makes indel-aware generation tractable and enables adaptive scaffold growth throughout the process with negligible computational overhead. To better align substitutions with real evolution, we further introduce a contextualized evolutionary noising kernel that produces biologically informed, context-dependent mutation patterns. Across tasks, DPLM-Evo improves sequence understanding and achieves state-of-the-art mutation effect prediction performance on ProteinGym in the single-sequence setting. It also enables variable-length simulated evolution, and post-editing/optimization of existing proteins via explicit edit trajectories.

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.

Jiyue Jiang, Pengan Chen, Jiuming Wang et al.

Large language models (LLMs) have become important tools in solving biological problems, offering improvements in accuracy and adaptability over conventional methods. Several benchmarks have been proposed to evaluate the performance of these LLMs. However, current benchmarks can hardly evaluate the performance of these models across diverse tasks effectively. In this paper, we introduce a comprehensive prompting-based benchmarking framework, termed Bio-benchmark, which includes 30 key bioinformatics tasks covering areas such as proteins, RNA, drugs, electronic health records, and traditional Chinese medicine. Using this benchmark, we evaluate six mainstream LLMs, including GPT-4o and Llama-3.1-70b, etc., using 0-shot and few-shot Chain-of-Thought (CoT) settings without fine-tuning to reveal their intrinsic capabilities. To improve the efficiency of our evaluations, we demonstrate BioFinder, a new tool for extracting answers from LLM responses, which increases extraction accuracy by round 30% compared to existing methods. Our benchmark results show the biological tasks suitable for current LLMs and identify specific areas requiring enhancement. Furthermore, we propose targeted prompt engineering strategies for optimizing LLM performance in these contexts. Based on these findings, we provide recommendations for the development of more robust LLMs tailored for various biological applications. This work offers a comprehensive evaluation framework and robust tools to support the application of LLMs in bioinformatics.

Liang Hong

In the current insurance literature, prediction of insurance claims in the regression problem is often performed with a statistical model. This model-based approach may potentially suffer from several drawbacks: (i) model misspecification, (ii) selection effect, and (iii) lack of finite-sample validity. This article addresses these three issues simultaneously by employing conformal prediction -- a general machine learning strategy for valid predictions. The proposed method is both model-free and tuning-parameter-free. It also guarantees finite-sample validity at a pre-assigned coverage probability level. Examples, based on both simulated and real data, are provided to demonstrate the excellent performance of the proposed method and its applications in insurance, especially regarding meeting the solvency capital requirement of European insurance regulation, Solvency II.

Md Atiqur Rahman Mallick, Kamrul Hasan, Pulock Das et al.

Accurate prediction of intersection turning movements is essential for adaptive signal control but remains difficult due to the high volatility of directional flows. This study proposes HFD-TM (Hierarchical Flow-Decomposition for Turning Movement Prediction), a hierarchical deep learning framework that predicts turning movements by first forecasting corridor through-movements and then expanding these predictions to individual turning streams. This design is motivated by empirical traffic structure, where corridor flows account for 65.1% of total volume, exhibit lower volatility than turning movements, and explain 35.5% of turning-movement variance. A physics-informed loss function enforces flow conservation to maintain structural consistency. Evaluated on six months of 15-minute interval LiDAR (Light Detection and Ranging) data from a six-intersection corridor in Nashville, Tennessee, HFD-TM achieves a mean absolute error of 2.49 vehicles per interval, reducing MAE by 5.7% compared to a Transformer and by 27.0% compared to a GRU (Gated Recurrent Unit). Ablation results show that hierarchical decomposition provides the largest performance gain, while training time is 12.8 times lower than DCRNN (Diffusion Convolutional Recurrent Neural Network), demonstrating suitability for real-time traffic applications.

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.

Liang Hong, Noura Raydan Nasreddine

Conformal prediction is a model-free machine learning method for creating prediction regions with a guaranteed coverage probability level. However, a data scientist often faces three challenges in practice: (i) the determination of a conformal prediction region is only approximate, jeopardizing the finite-sample validity of prediction, (ii) the computation required could be prohibitively expensive, and (iii) the shape of a conformal prediction region is hard to control. This article offers new insights into the relationship among the monotonicity of the non-conformity measure, the monotonicity of the plausibility function, and the exact determination of a conformal prediction region. Based on these new insights, we propose a simple strategy to alleviate the three challenges simultaneously.

Yina Hou, Shourav B. Rabbani, Liang Hong et al.

The importance of clinical variables in the prognosis of the disease is explained using statistical correlation or machine learning (ML). However, the predictive importance of these variables may not represent their causal relationships with diseases. This paper uses clinical variables from a heart failure (HF) patient cohort to investigate the causal explainability of important variables obtained in statistical and ML contexts. Due to inherent regression modeling, popular causal discovery methods strictly assume that the cause and effect variables are numerical and continuous. This paper proposes a new computational framework to enable causal structure discovery (CSD) and score the causal strength of mixed-type (categorical, numerical, binary) clinical variables for binary disease outcomes. In HF classification, we investigate the association between the importance rank order of three feature types: correlated features, features important for ML predictions, and causal features. Our results demonstrate that CSD modeling for nonlinear causal relationships is more meaningful than its linear counterparts. Feature importance obtained from nonlinear classifiers (e.g., gradient-boosting trees) strongly correlates with the causal strength of variables without differentiating cause and effect variables. Correlated variables can be causal for HF, but they are rarely identified as effect variables. These results can be used to add the causal explanation of variables important for ML-based prediction modeling.

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

Healthcare industries face challenges when experiencing rare diseases due to limited samples. Artificial Intelligence (AI) communities overcome this situation to create synthetic data which is an ethical and privacy issue in the medical domain. This research introduces the CAT-U-Net framework as a new approach to overcome these limitations, which enhances feature extraction from medical images without the need for large datasets. The proposed framework adds an extra concatenation layer with downsampling parts, thereby improving its ability to learn from limited data while maintaining patient privacy. To validate, the proposed framework's robustness, different medical conditioning datasets were utilized including COVID-19, brain tumors, and wrist fractures. The framework achieved nearly 98% reconstruction accuracy, with a Dice coefficient close to 0.946. The proposed CAT-U-Net has the potential to make a big difference in medical image diagnostics in settings with limited data.

Yang Tan, Lirong Zheng, Bozitao Zhong et al.

Deep learning has become a crucial tool in studying proteins. While the significance of modeling protein structure has been discussed extensively in the literature, amino acid types are typically included in the input as a default operation for many inference tasks. This study demonstrates with structure alignment task that embedding amino acid types in some cases may not help a deep learning model learn better representation. To this end, we propose ProtLOCA, a local geometry alignment method based solely on amino acid structure representation. The effectiveness of ProtLOCA is examined by a global structure-matching task on protein pairs with an independent test dataset based on CATH labels. Our method outperforms existing sequence- and structure-based representation learning methods by more quickly and accurately matching structurally consistent protein domains. Furthermore, in local structure pairing tasks, ProtLOCA for the first time provides a valid solution to highlight common local structures among proteins with different overall structures but the same function. This suggests a new possibility for using deep learning methods to analyze protein structure to infer function.

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.

Bei Liu, Tieyun Qian, Bing Liu et al.

The wide spread of location-based social networks brings about a huge volume of user check-in data, which facilitates the recommendation of points of interest (POIs). Recent advances on distributed representation shed light on learning low dimensional dense vectors to alleviate the data sparsity problem. Current studies on representation learning for POI recommendation embed both users and POIs in a common latent space, and users' preference is inferred based on the distance/similarity between a user and a POI. Such an approach is not in accordance with the semantics of users and POIs as they are inherently different objects. In this paper, we present a novel spatiotemporal aware (STA) representation, which models the spatial and temporal information as \emph{a relationship connecting users and POIs}. Our model generalizes the recent advances in knowledge graph embedding. The basic idea is that the embedding of a $<$time, location$>$ pair corresponds to a translation from embeddings of users to POIs. Since the POI embedding should be close to the user embedding plus the relationship vector, the recommendation can be performed by selecting the top-\emph{k} POIs similar to the translated POI, which are all of the same type of objects. We conduct extensive experiments on two real-world datasets. The results demonstrate that our STA model achieves the state-of-the-art performance in terms of high recommendation accuracy, robustness to data sparsity and effectiveness in handling cold start problem.