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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. 

In eukaryotic organisms, protein kinases regulate diverse protein activities and signaling pathways through phosphorylation of specific protein substrates. Isolating and characterizing kinase substrates is vital for defining downstream signaling pathways. The Kinase Client (KiC) assay is an in vitro synthetic peptide LC-MS/MS phosphorylation assay that has enabled identification of protein substrates (i.e., clients) for various protein kinases. For example, previous use of a 2,100-member (2k) peptide library identified substrates for the extracellular ATP receptor-like kinase, P2K1. Many P2K1 clients were confirmed by additional in vitro and in planta studies, including Integrin-Linked Kinase 4 (ILK4), for which we provide the evidence herein. In addition, we developed a new KiC peptide library containing 8,000 (8k) peptides based on phosphorylation sites primarily from Arabidopsis thaliana datasets. The 8k peptides are enriched for sites with conservation in other angiosperm plants, with the paired goals of representing functionally conserved sites and usefulness for screening kinases from diverse plants. Screening the 8k library with the active P2K1 kinase domain identified 177 phosphopeptides, including calcineurin B-like protein (CBL9) and G protein alpha subunit 1 (GPA1), which functions in cellular calcium signaling. We confirmed that P2K1 directly phosphorylates CBL9 and GPA1 through in vitro kinase assays. This expanded 8k KiC assay will be a useful tool for identifying novel substrates across diverse plant protein kinases, ultimately facilitating the exploration of previously undiscovered signaling pathways. 

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.