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Hepatocellular carcinoma (HCC) is one of the most fatal cancers in the world. There is an urgent need to understand the molecular background of HCC to facilitate the identification of biomarkers and discover effective therapeutic targets. Published transcriptomic studies have reported a large number of genes that are individually significant for HCC. However, reliable biomarkers remain to be determined. In this study, built on max-linear competing risk factor models, we developed a machine learning analytical framework to analyze transcriptomic data to identify the most miniature set of differentially expressed genes (DEGs). By analyzing 9 public whole-transcriptome datasets (containing 1184 HCC samples and 672 nontumor controls), we identified 5 critical differentially expressed genes (DEGs) (ie, CCDC107, CXCL12, GIGYF1, GMNN, and IFFO1) between HCC and control samples. The classifiers built on these 5 DEGs reached nearly perfect performance in identification of HCC. The performance of the 5 DEGs was further validated in a US Caucasian cohort that we collected (containing 17 HCC with paired nontumor tissue). The conceptual advance of our work lies in modeling gene-gene interactions and correcting batch effect in the analytic framework. The classifiers built on the 5 DEGs demonstrated clear signature patterns for HCC. The results are interpretable, robust, and reproducible across diverse cohorts/populations with various disease etiologies, indicating the 5 DEGs are intrinsic variables that can describe the overall features of HCC at the genomic level. The analytical framework applied in this study may pave a new way for improving transcriptome profiling analysis of human cancers. 

Abstract Manipulating the frequency and bandwidth of nonclassical light is essential for implementing frequency-encoded/multiplexed quantum computation, communication, and networking protocols, and for bridging spectral mismatch among various quantum systems. However, quantum spectral control requires a strong nonlinearity mediated by light, microwave, or acoustics, which is challenging to realize with high efficiency, low noise, and on an integrated chip. Here, we demonstrate both frequency shifting and bandwidth compression of heralded single-photon pulses using an integrated thin-film lithium niobate (TFLN) phase modulator. We achieve record-high electro-optic frequency shearing of telecom single photons over terahertz range (±641 GHz or ±5.2 nm), enabling high visibility quantum interference between frequency-nondegenerate photon pairs. We further operate the modulator as a time lens and demonstrate over eighteen-fold (6.55 nm to 0.35 nm) bandwidth compression of single photons. Our results showcase the viability and promise of on-chip quantum spectral control for scalable photonic quantum information processing.