Zijun Zhang

Michail Chatzianastasis, Michalis Vazirgiannis, Zijun Zhang

The identification of cancer genes is a critical yet challenging problem in cancer genomics research. Existing computational methods, including deep graph neural networks, fail to exploit the multilayered gene-gene interactions or provide limited explanation for their predictions. These methods are restricted to a single biological network, which cannot capture the full complexity of tumorigenesis. Models trained on different biological networks often yield different and even opposite cancer gene predictions, hindering their trustworthy adaptation. Here, we introduce an Explainable Multilayer Graph Neural Network (EMGNN) approach to identify cancer genes by leveraging multiple genegene interaction networks and pan-cancer multi-omics data. Unlike conventional graph learning on a single biological network, EMGNN uses a multilayered graph neural network to learn from multiple biological networks for accurate cancer gene prediction. Our method consistently outperforms all existing methods, with an average 7.15% improvement in area under the precision-recall curve (AUPR) over the current state-of-the-art method. Importantly, EMGNN integrated multiple graphs to prioritize newly predicted cancer genes with conflicting predictions from single biological networks. For each prediction, EMGNN provided valuable biological insights via both model-level feature importance explanations and molecular-level gene set enrichment analysis. Overall, EMGNN offers a powerful new paradigm of graph learning through modeling the multilayered topological gene relationships and provides a valuable tool for cancer genomics research.

Qiao Li, Cong Wu, Jing Chen et al.

Deep neural networks (DNNs) are increasingly used in critical applications such as identity authentication and autonomous driving, where robustness against adversarial attacks is crucial. These attacks can exploit minor perturbations to cause significant prediction errors, making it essential to enhance the resilience of DNNs. Traditional defense methods often rely on access to detailed model information, which raises privacy concerns, as model owners may be reluctant to share such data. In contrast, existing black-box defense methods fail to offer a universal defense against various types of adversarial attacks. To address these challenges, we introduce DUCD, a universal black-box defense method that does not require access to the target model's parameters or architecture. Our approach involves distilling the target model by querying it with data, creating a white-box surrogate while preserving data privacy. We further enhance this surrogate model using a certified defense based on randomized smoothing and optimized noise selection, enabling robust defense against a broad range of adversarial attacks. Comparative evaluations between the certified defenses of the surrogate and target models demonstrate the effectiveness of our approach. Experiments on multiple image classification datasets show that DUCD not only outperforms existing black-box defenses but also matches the accuracy of white-box defenses, all while enhancing data privacy and reducing the success rate of membership inference attacks.

Luoxiao Yang, Yun Wang, Xinqi Fan et al.

Time series forecasting (TSF) possesses great practical values in various fields, including power and energy, transportation, etc. TSF methods have been studied based on knowledge from classical statistics to modern deep learning. Yet, all of them were developed based on one fundamental concept, the numerical data fitting. Thus, the models developed have long been known to be problem-specific and lacking application generalizability. Practitioners expect a TSF foundation model that serves TSF tasks in different applications. The central question is then how to develop such a TSF foundation model. This paper offers one pioneering study in the TSF foundation model development method and proposes a vision intelligence-powered framework, ViTime, for the first time. ViTime fundamentally shifts TSF from numerical fitting to operations based on a binary image-based time series metric space and naturally supports both point and probabilistic forecasting. We also provide rigorous theoretical analyses of ViTime, including quantization-induced system error bounds and principled strategies for optimal parameter selection. Furthermore, we propose RealTS, an innovative synthesis algorithm generating diverse and realistic training samples, effectively enriching the training data and significantly enhancing model generalizability. Extensive experiments demonstrate ViTime's state-of-the-art performance. In zero-shot scenarios, ViTime outperforms TimesFM by 9-15\%. With just 10\% fine-tuning data, ViTime surpasses both leading foundation models and fully-supervised benchmarks, a gap that widens with 100\% fine-tuning. ViTime also exhibits exceptional robustness, effectively handling missing data and outperforming TimesFM by 20-30\% under various data perturbations, validating the power of its visual space data operation paradigm.

Zijun Zhang, Linqi Zhou, Liangke Gou et al.

We report a neural architecture search framework, BioNAS, that is tailored for biomedical researchers to easily build, evaluate, and uncover novel knowledge from interpretable deep learning models. The introduction of knowledge dissimilarity functions in BioNAS enables the joint optimization of predictive power and biological knowledge through searching architectures in a model space. By optimizing the consistency with existing knowledge, we demonstrate that BioNAS optimal models reveal novel knowledge in both simulated data and in real data of functional genomics. BioNAS provides a useful tool for domain experts to inject their prior belief into automated machine learning and therefore making deep learning easily accessible to practitioners. BioNAS is available at https://github.com/zj-zhang/BioNAS-pub.

Huixin Zhan, Zijun Zhang

Clinical variant classification of pathogenic versus benign genetic variants remains a pivotal challenge in clinical genetics. Recently, the proposition of protein language models has improved the generic variant effect prediction (VEP) accuracy via weakly-supervised or unsupervised training. However, these VEPs are not disease-specific, limiting their adaptation at point-of-care. To address this problem, we propose a disease-specific \textsc{pro}tein language model for variant \textsc{path}ogenicity, termed ProPath, to capture the pseudo-log-likelihood ratio in rare missense variants through a siamese network. We evaluate the performance of ProPath against pre-trained language models, using clinical variant sets in inherited cardiomyopathies and arrhythmias that were not seen during training. Our results demonstrate that ProPath surpasses the pre-trained ESM1b with an over $5\%$ improvement in AUC across both datasets. Furthermore, our model achieved the highest performances across all baselines for both datasets. Thus, our ProPath offers a potent disease-specific variant effect prediction, particularly valuable for disease associations and clinical applicability.

Huixin Zhan, Ying Nian Wu, Zijun Zhang

Although DNA foundation models have advanced the understanding of genomes, they still face significant challenges in the limited scale and diversity of genomic data. This limitation starkly contrasts with the success of natural language foundation models, which thrive on substantially larger scales. Furthermore, genome understanding involves numerous downstream genome annotation tasks with inherent data heterogeneity, thereby necessitating more efficient and robust fine-tuning methods tailored for genomics. Here, we present \textsc{Lingo}: \textsc{L}anguage prefix f\textsc{In}e-tuning for \textsc{G}en\textsc{O}mes. Unlike DNA foundation models, \textsc{Lingo} strategically leverages natural language foundation models' contextual cues, recalibrating their linguistic knowledge to genomic sequences. \textsc{Lingo} further accommodates numerous, heterogeneous downstream fine-tune tasks by an adaptive rank sampling method that prunes and stochastically reintroduces pruned singular vectors within small computational budgets. Adaptive rank sampling outperformed existing fine-tuning methods on all benchmarked 14 genome understanding tasks, while requiring fewer than 2\% of trainable parameters as genomic-specific adapters. Impressively, applying these adapters on natural language foundation models matched or even exceeded the performance of DNA foundation models. \textsc{Lingo} presents a new paradigm of efficient and scalable genome understanding via genomic-specific adapters on language models.

Zijun Zhang, Adam R. Lamson, Michael Shelley et al.

Finely-tuned enzymatic pathways control cellular processes, and their dysregulation can lead to disease. Creating predictive and interpretable models for these pathways is challenging because of the complexity of the pathways and of the cellular and genomic contexts. Here we introduce Elektrum, a deep learning framework which addresses these challenges with data-driven and biophysically interpretable models for determining the kinetics of biochemical systems. First, it uses in vitro kinetic assays to rapidly hypothesize an ensemble of high-quality Kinetically Interpretable Neural Networks (KINNs) that predict reaction rates. It then employs a novel transfer learning step, where the KINNs are inserted as intermediary layers into deeper convolutional neural networks, fine-tuning the predictions for reaction-dependent in vivo outcomes. Elektrum makes effective use of the limited, but clean in vitro data and the complex, yet plentiful in vivo data that captures cellular context. We apply Elektrum to predict CRISPR-Cas9 off-target editing probabilities and demonstrate that Elektrum achieves state-of-the-art performance, regularizes neural network architectures, and maintains physical interpretability.