SSumM: Sparse Summarization of Massive Graphs

Given a graph G and the desired size k in bits, how can we summarize G within k bits, while minimizing the information loss? Large-scale graphs have become omnipresent, posing considerable computational challenges. Analyzing such large graphs can be fast and easy if they are compressed sufficiently to fit in main memory or even cache. Graph summarization, which yields a coarse-grained summary graph with merged nodes, stands out with several advantages among graph compression techniques. Thus, a number of algorithms have been developed for obtaining a concise summary graph with little information loss or equivalently small reconstruction error. However, the existing methods focus solely on reducing the number of nodes, and they often yield dense summary graphs, failing to achieve better compression rates. Moreover, due to their limited scalability, they can be applied only to moderate-size graphs. In this work, we propose SSumM, a scalable and effective graph-summarization algorithm that yields a sparse summary graph. SSumM not only merges nodes together but also sparsifies the summary graph, and the two strategies are carefully balanced based on the minimum description length principle. Compared with state-of-the-art competitors, SSumM is (a) Concise: yields up to 11.2X smaller summary graphs with similar reconstruction error, (b) Accurate: achieves up to 4.2X smaller reconstruction error with similarly concise outputs, and (c) Scalable: summarizes 26X larger graphs while exhibiting linear scalability. We validate these advantages through extensive experiments on 10 real-world graphs.Comment: to be published in the 26th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD '20

X-SNS: Cross-Lingual Transfer Prediction through Sub-Network Similarity

Cross-lingual transfer (XLT) is an emergent ability of multilingual language models that preserves their performance on a task to a significant extent when evaluated in languages that were not included in the fine-tuning process. While English, due to its widespread usage, is typically regarded as the primary language for model adaption in various tasks, recent studies have revealed that the efficacy of XLT can be amplified by selecting the most appropriate source languages based on specific conditions. In this work, we propose the utilization of sub-network similarity between two languages as a proxy for predicting the compatibility of the languages in the context of XLT. Our approach is model-oriented, better reflecting the inner workings of foundation models. In addition, it requires only a moderate amount of raw text from candidate languages, distinguishing it from the majority of previous methods that rely on external resources. In experiments, we demonstrate that our method is more effective than baselines across diverse tasks. Specifically, it shows proficiency in ranking candidates for zero-shot XLT, achieving an improvement of 4.6% on average in terms of NDCG@3. We also provide extensive analyses that confirm the utility of sub-networks for XLT prediction.Comment: Accepted to EMNLP 2023 (Findings

Prevalence and clinical impact of vitamin D deficiency in critically ill Korean patients with traumatic injuries: a single-center, prospective, observational study

Background This study investigated the prevalence and impact of 25-hydroxyvitamin D (25(OH) vitamin D) deficiency in critically ill Korean patients with traumatic injuries. Methods This prospective observational cohort study assessed the 25(OH) vitamin D status of consecutive trauma patients admitted to the trauma intensive care unit (TICU) of Kyungpook National University Hospital between January and December 2018. We analyzed the prevalence of 25(OH) vitamin D deficiency and its impact on clinical outcomes. Results There were no significant differences in the duration of mechanical ventilation (MV), lengths of TICU and hospital stays, and rates of nosocomial infection and mortality between patients with 25(OH) vitamin D <20 ng/ml and those with 25(OH) vitamin D ≥20 ng/ml within 24 hours of TICU admission. The duration of MV and lengths of TICU and hospital stays were shorter and the rate of nosocomial infection was lower in patients with 25(OH) vitamin D level ≥20 ng/ml on day 7 of hospitalization. The duration of MV, lengths of TICU and hospital stays, and nosocomial infection rate were significantly lower in patients with increased concentrations compared with those with decreased concentrations on day 7 of hospitalization, but the mortality rate did not differ significantly. Conclusions The 25(OH) vitamin D level measured within 24 hours after TICU admission was unrelated to clinical outcomes in critically ill patients with traumatic injuries. However, patients with increased 25(OH) vitamin D level after 7 days of hospitalization had better clinical outcomes than those with decreased levels

Hydrophobically Modified let-7b miRNA Enhances Biodistribution to NSCLC and Downregulates HMGA2 In Vivo

MicroRNAs (miRNAs) have increasingly been shown to be involved in human cancer, and interest has grown about the potential use of miRNAs for cancer therapy. miRNA levels are known to be altered in cancer cells, including in non-small cell lung cancer (NSCLC), a subtype of lung cancer that is the most prevalent form of cancer worldwide and that lacks effective therapies. The let-7 miRNA is involved in the regulation of oncogene expression in cells and directly represses cancer growth in the lung. let-7 is therefore a potential molecular target for tumor therapy. However, applications of RNA interference for cancer research have been limited by a lack of simple and efficient methods to deliver oligonucleotides (ONs) to cancer cells. In this study, we have used in vitro and in vivo approaches to show that HCC827 cells internalize hydrophobically modified let-7b miRNAs (hmiRNAs) added directly to the culture medium without the need for lipid formulation. We identified functional let-7b hmiRNAs targeting the HMGA2 mRNA, one of the let-7 target genes upregulated in NSCLC, and show that direct uptake in HCC827 cells induced potent and specific gene silencing in vitro and in vivo. Thus, hmiRNAs constitute a novel class of ONs that enable functional studies of genes involved in cancer biology and are potentially therapeutic molecules

REDOG and Its Performance Analysis

We propose a REinforced modified Dual-Ouroboros based on Gabidulin codes, shortly called REDOG. This is a code-based cryptosystem based on the well-known rank metric codes, Gabidulin codes. The public key sizes of REDOG are 14KB, 33KB, 63KB at the security levels of 128, 192, 256 bits respectively. There is no decoding failure in decryption. REDOG is IND-CPA. As a new result, we give the performance results of implementing REDOG including the time for Key generation, encryption, and decryption for each security level

Development of brain PET using GAPD arrays

Purpose: In recent times, there has been great interest in the use of Geiger-mode avalanche photodiodes (GAPDs) as scintillator readout in positron emission tomography (PET) detectors because of their advantages, such as high gain, compact size, low power consumption, and magnetic field insensitivity. The purpose of this study was to develop a novel PET system based on GAPD arrays for brain imaging. Methods: The PET consisted of 72 detector modules arranged in a ring of 330 mm diameter. Each PET module was composed of a 4 Â 4 matrix of 3 Â 3 Â 20 mm 3 cerium-doped lutetium yttrium orthosilicate (LYSO) crystals coupled with a 4 Â 4 array three-side tileable GAPD. The signals from each PET module were fed into preamplifiers using a 3 m long flat cable and then sent to a position decoder circuit (PDC), which output a digital address and an analog pulse of the interacted channel among 64 preamplifier signals tranmitted from four PET detector modules. The PDC outputs were fed into field programmable gate array (FPGA)-embedded data acquisition (DAQ) boards. The analog signal was then digitized, and arrival time and energy of the signal were calculated and stored. Results: The energy and coincidence timing resolutions measured for 511 keV gamma rays were 18.4 6 3.1% and 2.6 ns, respectively. The transaxial spatial resolution and sensitivity in the center of field of view (FOV) were 3.1 mm and 0.32% cps/Bq, respectively. The rods down to a diameter of 2.5 mm were resolved in a hot-rod phantom image, and activity distribution patterns between the white and gray matters in the Hoffman brain phantom were well imaged. Conclusions: Experimental results indicate that a PET system can be developed using GAPD arrays and the GAPD-based PET system can provide high-quality PET imaging

Peritumoral imaging features of thymic epithelial tumors for the prediction of transcapsular invasion: beyond intratumoral analysis

PURPOSEThe purpose of this study was to differentiate cases without transcapsular invasion (Masaoka–Koga stage I) from cases with transcapsular invasion (Masaoka–Koga stage II or higher) in patients with thymic epithelial tumors (TETs) using tumoral and peritumoral computed tomography (CT) features.METHODSThis retrospective study included 116 patients with pathological diagnoses of TETs. Two radiologists evaluated clinical variables and CT features, including size, shape, capsule integrity, presence of calcification, internal necrosis, heterogeneous enhancement, pleural effusion, pericardial effusion, and vascularity grade. Vascularity grade was defined as the extent of peritumoral vascular structures in the anterior mediastinum. The factors associated with transcapsular invasion were analyzed using multivariable logistic regression. In addition, the interobserver agreement for CT features was assessed using Cohen’s or weighted kappa coefficients. The difference between the transcapsular invasion group and that without transcapsular invasion was evaluated statistically using the Student’s t-test, Mann–Whitney U test, chi-square test, and Fisher’s exact test.RESULTSBased on pathology reports, 37 TET cases without and 79 with transcapsular invasion were identified. Lobular or irregular shape [odds ratio (OR): 4.19; 95% confidence interval (CI): 1.53–12.09; P = 0.006], partial complete capsule integrity (OR: 5.03; 95% CI: 1.85–15.13; P = 0.002), and vascularity grade 2 (OR: 10.09; 95% CI: 2.59–45.48; P = 0.001) were significantly associated with transcapsular invasion. The interobserver agreement for shape classification, capsule integrity, and vascularity grade was 0.840, 0.526, and 0.752, respectively (P < 0.001 for all).CONCLUSIONShape, capsule integrity, and vascularity grade were independently associated with transcapsular invasion of TETs. Furthermore, three CT TET features demonstrated good reproducibility and help differentiate between TET cases with and without transcapsular invasion

MET gene alterations predict poor survival following chemotherapy in patients with advanced cancer

Background: To aid in oncology drug development, we investigated MET proto-oncogene receptor tyrosine kinase gene aberrations in 2,239 oncology patients who underwent next-generation sequencing (NGS) in clinical practice.Materials and methods: From November 2019 to January 2021, 2,239 patientswith advanced solid tumors who visited oncology clinics underwent NGS. The NGS panel included &gt;500 comprehensive NGS tests using archival tissue specimens. Programmed death-ligand 1(PD-L1) 22C3 assay results and clinical records regarding initial chemotherapy were available for 1,137 (50.8%) and 1,761 (78.7%) patients, respectively for overall survival (OS) analysis.Results: The 2,239 patients represented 37 types of cancer. The NGS panel included &gt;500 genes, microsatellite instability status, tumor mutational burden, and fusions. The most common cancer types were colorectal (N = 702), gastric (N = 481), and sarcoma (N = 180). MET aberrations were detected in 212 patients. All MET-amplified tumors had microsatellite stable status, and 8 had a high tumor mutational burden. Of 46 patients with MET-amplified cancers, 8 had MET-positive protein expression by immunohistochemistry (2+ and 3+). MET fusion was detected in 10 patients. Partner genes of MET fusion included ST7, TFEC, LRRD1, CFTR, CAV1, PCM1, HLA-DRB1, and CAPZA2. In survival analysis, patients with amplification of MET gene fusion had shorter OS and progression-free survival (PFS) than those without. Thus, MET aberration was determined to be a factor of response to chemotherapy.Conclusion: Approximately 2.1% and 0.4% of patients with advanced solid tumors demonstrated MET gene amplification and fusion, respectively, and displayed a worse response to chemotherapy and significantly shorter OS and PFS than those without MET gene amplification or fusion

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe