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Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied. 

Signal peptides (SPs) play a crucial role in protein translocation in cells. The development of large protein language models (PLMs) and prompt-based learning provide a new opportunity for SP prediction, especially for the categories with limited annotated data. We present a parameter-efficient fine-tuning (PEFT) framework for SP prediction, PEFT-SP, to effectively utilize pretrained PLMs. We integrated low-rank adaptation (LoRA) into ESM-2 models to better leverage the protein sequence evolutionary knowledge of PLMs. Experiments show that PEFT-SP using LoRA enhances state-of-the-art results, leading to a maximum Matthews correlation coefficient (MCC) gain of 87.3% for SPs with small training samples and an overall MCC gain of 6.1%. Furthermore, we also employed two other PEFT methods, prompt tuning and adapter tuning, in ESM-2 for SP prediction. More elaborate experiments show that PEFT-SP using adapter tuning can also improve the state-of-the-art results by up to 28.1% MCC gain for SPs with small training samples and an overall MCC gain of 3.8%. LoRA requires fewer computing resources and less memory than the adapter tuning during the training stage, making it possible to adapt larger and more powerful protein models for SP prediction. 

Koley et al. indicate that fatty acid oxidation occurs concomitantly with fatty acid biosynthesis in multiple plant tissues, including seeds that are thought to stably house storage reserves. This study suggests that some lipid breakdown and fatty acid oxidation is the rule and not the exception in plant metabolism. 

Deep Neural Networks (DNN) have emerged as an effective approach to tackling real-world problems. However, like human-written software, DNNs are susceptible to bugs and attacks. This has generated significant interests in developing effective and scalable DNN verification techniques and tools. Recent developments in DNN verification have highlighted the potential of constraint-solving approaches that combine abstraction techniques with SAT solving. Abstraction approaches are effective at precisely encode neuron behavior when it is linear, but they lead to overapproximation and combinatorial scaling when behavior is non-linear. SAT approaches in DNN verification have incorporated standard DPLL techniques, but have overlooked important optimizations found in modern SAT solvers that help them scale on industrial benchmarks. In this paper, we present VeriStable, a novel extension of recently proposed DPLL-based constraint DNN verification approach. VeriStable leverages the insight that while neuron behavior may be non-linear across the entire DNN input space, at intermediate states computed during verification many neurons may be constrained to have linear behavior – these neurons are stable. Efficiently detecting stable neurons reduces combinatorial complexity without compromising the precision of abstractions. Moreover, the structure of clauses arising in DNN verification problems shares important characteristics with industrial SAT benchmarks. We adapt and incorporate multi-threading and restart optimizations targeting those characteristics to further optimize DPLL-based DNN verification. We evaluate the effectiveness of VeriStable across a range of challenging benchmarks including fully- connected feedforward networks (FNNs), convolutional neural networks (CNNs) and residual networks (ResNets) applied to the standard MNIST and CIFAR datasets. Preliminary results show that VeriStable is competitive and outperforms state-of-the-art DNN verification tools, including 𝛼-𝛽-CROWN and MN-BaB, the first and second performers of the VNN-COMP, respectively. 

Deep Neural Networks (DNN) have emerged as an effective approach to tackling real-world problems. However, like human-written software, DNNs are susceptible to bugs and attacks. This has generated significant interest in developing effective and scalable DNN verification techniques and tools. Recent developments in DNN verification have highlighted the potential of constraint-solving approaches that combine abstraction techniques with SAT solving. Abstraction approaches are effective at precisely encoding neuron behavior when it is linear, but they lead to overapproximation and combinatorial scaling when behavior is non-linear. SAT approaches in DNN verification have incorporated standard DPLL techniques, but have overlooked important optimizations found in modern SAT solvers that help them scale on industrial benchmarks. In this paper, we present VeriStable, a novel extension of the recently proposed DPLL-based constraint DNN verification approach. VeriStable leverages the insight that while neuron behavior may be non-linear across the entire DNN input space, at intermediate states computed during verification many neurons may be constrained to have linear behavior – these neurons are stable. Efficiently detecting stable neurons reduces combinatorial complexity without compromising the precision of abstractions. Moreover, the structure of clauses arising in DNN verification problems shares important characteristics with industrial SAT benchmarks. We adapt and incorporate multi-threading and restart optimizations targeting those characteristics to further optimize DPLL-based DNN verification. We evaluate the effectiveness of VeriStable across a range of challenging benchmarks including fully- connected feedforward networks (FNNs), convolutional neural networks (CNNs) and residual networks (ResNets) applied to the standard MNIST and CIFAR datasets. Preliminary results show that VeriStable is competitive and outperforms state-of-the-art DNN verification tools, including α-β-CROWN and MN-BaB, the first and second performers of the VNN-COMP, respectively.