arXiv subjects

Peilin Xin

Publications and source records attributed to Peilin Xin.

5 recordsLinked to original sources

arXiv2026

Physics-Aligned Deep Learning Enables SERS Resolving and Sequencing of Dynamic Single-Molecule DNA Oligomers in Plasmonic Nanocavity

Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) captures dynamic molecular behavior with ultrahigh sensitivity, but its biopolymer analysis is hindered by strong spectral heterogeneity, transient hotspot sampling, and background interference. Here, we develop a physics-aligned deep learning framework integrating contrastive attention-based multiple-instance learning (CAMIL), a tri-channel multi-kernel CNN classifier, and trajectory-level transition-guided sequence reconstruction to decode single-molecule DNA oligomer dynamics in a plasmonic nanocavity. In this work, CAMIL mines informative spectra enriched with chain-embedded nucleotide and dinucleotide signatures from contrastive positive and negative DNA trajectory bags, generating a single-molecule DNA-segment spectral-states library. This library trains a 12-class CNN to assign query time-resolved DNA SM-SERS frames to high-confidence DNA-segment states, enabling trajectory-level analysis of state composition, dwell length, entropy, switching frequency, and transition matrix. The transition matrix is further converted into state-transition-edge evidence for candidate sequence scoring, enabling asymmetric DNA sequences inference from confined stochastic sampling dynamics. This framework transforms SM-SERS heterogeneity into quantitative analytical information, advancing dynamic single-molecule decoding.

physics.optics↗

arXiv2026

SERS study of single-live-cell electrical permeabilization dynamics via plasmonic nanotubes

There is a growing demand for minimally invasive methods to analyze intracellular processes and signaling activities in individual living cells, including the identification of tumorigenic cell subpopulations. However, most conventional analytical methods require cell lysis, precluding repeated measurements in the same cell over time, or rely on exogenous labels and reporters that may perturb cellular function. Various applications based on vertical nanotubes have been developed that enable live cell monitoring and analysis by electroporation with low voltages. However, the extent and duration of membrane permeability and kinetics of membrane repair remain elusive. Here, we built a plasmonic platform with the capacity of surface enhanced Raman spectroscopy (SERS) to monitor the electroporation-induced membrane permeability dynamics in individual live cells attached onto 100-nm diameter nanotubes of 2 um height. Fibronectin was employed as extracellular matrix (ECM)-coating to facilitate cell attachment onto nanotubes. Using fluorescent-dye delivery as an independent validation method, we show that the fabricated nanostructures induce localized electrical permeabilization of the plasma membrane and enable monitoring of its subsequent recovery. We further use SERS to track molecular changes at the membrane during permeabilization and resealing. The SERS spectra provide molecular-level insight into changes in membrane-associated components and the ECM during electroporation and subsequent membrane recovery. Real time monitoring of pulse induced molecular changes holds great promise for characterizing intracellular signaling, cellular states, and cellular heterogeneity at the single cell level, including the identification of tumorigenic subpopulations. This capacity could facilitate the development of novel biosensing assay.

physics.app-ph↗

arXiv2026

ASAP: Reimagining the Data Lifecycle using Application Semantic-Aware Processing

Across many domains (e.g., observability, networking, security), data processing pipelines face what we refer to as the CSP problem: achieving low Cost at large Scale, while maintaining high Performance. In response, we see several efforts to tackle CSP in various stages of the Collect-Transmit-Store-Analyze data lifecycle; such as approximate query processing in databases or sketches in network routers. Our work is driven by the simple insight: "seeing the forest for the trees". These proposed solutions (e.g., AQP, sketching, compression, rollups) addressing CSP share a common property - they exploit semantic-preserving opportunities to support application needs. In this paper, we make a case for ASAP, a paradigm that makes Application Semantic-Aware Processing (ASAP) a first-class design principle in data processing pipelines. We argue that by taking a unified view across ASAP primitives developed in different domains, across the entire data lifecycle, we can unlock new opportunities to tackle the CSP problem. In particular, we can: (i) enable novel cross-lifecycle optimizations such as analytics run directly on sketches computed at the source; (ii) leverage primitives developed in other application domains; and (iii) enable widespread adoption of these powerful techniques. We discuss research challenges in socializing the benefits of the ASAP paradigm, and show preliminary evidence that adopting ASAP can yield up to 3 orders of magnitude improvements in the CSP tradeoff for many application domains.

cs.DB↗

arXiv2025

SPDZCoder: Combining Expert Knowledge with LLMs for Generating Privacy-Computing Code

Privacy computing receives increasing attention but writing privacy computing code remains challenging for developers due to limited library functions, necessitating function implementation from scratch, and data-oblivious requirement, contradicting intuitive thinking and usual practices of programmers. Automating the generation of privacy computing code with Large Language Models can streamline development effort and lower the barrier to using privacy computing frameworks. However, existing LLMs still encounter challenges in code translation for privacy-preserving computation, such as translating Python to MP-SPDZ, due to the scarcity of MP-SPDZ data required for effective pre-training or fine-tuning. Moreover, the lack of a benchmark further complicates the evaluation of translation quality. To address the limitations, this work proposes SPDZCoder, a rule-based framework that combines LLMs with expert knowledge for generating privacy-computing code without requiring additional training data. Specifically, SPDZCoder employ a rigorous procedure for collecting high-quality expert knowledge to represent the semantic-expressing differences between Python and MP-SPDZ, and to derive transformation rules for translating Python to MP-SPDZ based on these knowledge. Then, SPDZCoder progressively converts Python code into MP-SPDZ code using transformation rules in a three stage pipeline. To evaluate SPDZCoder, we manually constructed a benchmark dataset, SPDZEval, which comprises six data splits, each representing a distinct class of challenging tasks in MP-SPDZ implementation. Extensive experiments show that SPDZCoder achieves superior performance, significantly surpassing baselines in pass@1 and pass@2. Specifically, SPDZCoder attains an overall correctness of 85.94% and 92.01% in pass@1 and pass@2, respectively, whereas the best-performing baseline achieves 63.58% and 76.36%, respectively.

cs.CR↗

arXiv2024

Deep learning assisted SERS detection of prolines and hydroxylated prolines using nitrilotriacetic acid functionalized gold nanopillars

Proline (Pro) is one kind of proteinogenic amino acid and an important signaling molecule in the process of metabolism. Hydroxyproline (Hyp) is a product on Pro oxygen sensing post-translational modification (PTM), which is efficiently modulated tumor cells for angiogenesis. Distinguishing between Pro and Hyp is crucial for diagnosing connective tissue disorders, as elevated levels of Hyp can indicate abnormal collagen metabolism, often associated with diseases like osteogenesis imperfecta or fibrosis. However, there is a very small difference between molecular structures of Pro and Hyp, which is a big challenge for current detection technologies to distinguish them. For surface-enhanced Raman scattering (SERS) sensors, the similar molecule structure leads to similar Raman spectra that are difficult to distinguish. Furthermore, another problem is the weak affinity between amino acids sample and SERS-active substrates by physical adsorption. The selecting capturing of Pro and Hyp in the mixture of amino acids is not easy to achieve. In this work, we designed a new method for Pro and Hyp specifical detection and recognition by using gold nanopillars as the SERS substrate and combing nitrilotriacetic acid (NTA) with nickel (Ni) to form NTA-Ni structure as a specifical affinity agent. One side of NTA-Ni was attached to gold nanopillars through thiol binding. Another side captured the amino acids using reversible binding by receptor-ligand interaction between Ni and amino acids. Because of the different binding time with NTA-Ni and amino acids, the sensor can recognize Pro and Hyp from amino acids mixture. Then we used automatic peak assignment program for data analysis and machine learning model to distinguish between Pro and Hyp. The label-free SERS detection of amino acids PTM using gold nanopillars provides a potential method to further biomolecule detection and specifical capture.

q-bio.BM↗