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Jinyun Chen

Publications and source records attributed to Jinyun Chen.

2 recordsLinked to original sources

Compilation Is Not Correctness: Scan-by-Scan Evaluation of LLM-Generated PLC Programs

Programmable logic controllers (PLCs) automate industrial processes through repeated scans, each reading inputs, executing control logic, and updating outputs. Engineers write this logic in Structured Text (ST), a high-level textual language defined in IEC 61131-3. Large language models (LLMs) can now generate ST from natural-language requirements, yet compilation success and checks on selected properties or sampled scans can leave behavioral errors undetected. We introduce CycleBench, a benchmark of 301 ST tasks with behavioral requirements, public interfaces, reference programs, and executable scenarios. Its runtime executes each generated program and its reference under aligned inputs, initialization, and logical time, comparing their outputs after every scan. Across eight LLMs and baseline generation methods, execution pass rate trails compilation pass rate by 11.92 percentage points; observed failures include output-update, arithmetic, and timing errors. On fixed traces of programs directly generated by five LLMs, checking outputs only at every fifth scan misses 21.66% of the 157 failures detected by per-scan comparison; across sampling phases, the missed-failure rate ranges from 12.10% to 28.03%. These misses stem from transient output discrepancies, whose detection depends on the sampling phase. Building on this evaluation, we propose CycleGen, which generates multiple candidate ST programs, repairs their compilation errors with bounded compiler feedback, and selects one using runtime self-tests generated in a separate model context. CycleGen improves the execution pass rate over direct generation by 8.68 percentage points. Component ablations distinguish repair and self-test selection; candidate-count analysis shows diminishing returns, with no execution-pass-rate improvement beyond five candidates in our experiments despite 38.8% higher token consumption at eight.

cs.SE↗

Methods for Joint Imaging and RNA-seq Data Analysis

Emerging integrative analysis of genomic and anatomical imaging data which has not been well developed, provides invaluable information for the holistic discovery of the genomic structure of disease and has the potential to open a new avenue for discovering novel disease susceptibility genes which cannot be identified if they are analyzed separately. A key issue to the success of imaging and genomic data analysis is how to reduce their dimensions. Most previous methods for imaging information extraction and RNA-seq data reduction do not explore imaging spatial information and often ignore gene expression variation at genomic positional level. To overcome these limitations, we extend functional principle component analysis from one dimension to two dimension (2DFPCA) for representing imaging data and develop a multiple functional linear model (MFLM) in which functional principal scores of images are taken as multiple quantitative traits and RNA-seq profile across a gene is taken as a function predictor for assessing the association of gene expression with images. The developed method has been applied to image and RNA-seq data of ovarian cancer and KIRC studies. We identified 24 and 84 genes whose expressions were associated with imaging variations in ovarian cancer and KIRC studies, respectively. Our results showed that many significantly associated genes with images were not differentially expressed, but revealed their morphological and metabolic functions. The results also demonstrated that the peaks of the estimated regression coefficient function in the MFLM often allowed the discovery of splicing sites and multiple isoform of gene expressions.

q-bio.GN↗