Z-score-based modularity for community detection in networks

Identifying community structure in networks is an issue of particular interest in network science. The modularity introduced by Newman and Girvan [Phys. Rev. E 69, 026113 (2004)] is the most popular quality function for community detection in networks. In this study, we identify a problem in the concept of modularity and suggest a solution to overcome this problem. Specifically, we obtain a new quality function for community detection. We refer to the function as Z-modularity because it measures the Z-score of a given division with respect to the fraction of the number of edges within communities. Our theoretical analysis shows that Z-modularity mitigates the resolution limit of the original modularity in certain cases. Computational experiments using both artificial networks and well-known real-world networks demonstrate the validity and reliability of the proposed quality function.Comment: 8 pages, 10 figure

Additive Approximation Algorithms for Modularity Maximization

The modularity is a quality function in community detection, which was introduced by Newman and Girvan (2004). Community detection in graphs is now often conducted through modularity maximization: given an undirected graph $G=(V,E)$, we are asked to find a partition $\mathcal{C}$ of $V$ that maximizes the modularity. Although numerous algorithms have been developed to date, most of them have no theoretical approximation guarantee. Recently, to overcome this issue, the design of modularity maximization algorithms with provable approximation guarantees has attracted significant attention in the computer science community. In this study, we further investigate the approximability of modularity maximization. More specifically, we propose a polynomial-time $\left(\cos\left(\frac{3-\sqrt{5}}{4}\pi\right) - \frac{1+\sqrt{5}}{8}\right)$-additive approximation algorithm for the modularity maximization problem. Note here that $\cos\left(\frac{3-\sqrt{5}}{4}\pi\right) - \frac{1+\sqrt{5}}{8} < 0.42084$ holds. This improves the current best additive approximation error of $0.4672$, which was recently provided by Dinh, Li, and Thai (2015). Interestingly, our analysis also demonstrates that the proposed algorithm obtains a nearly-optimal solution for any instance with a very high modularity value. Moreover, we propose a polynomial-time $0.16598$-additive approximation algorithm for the maximum modularity cut problem. It should be noted that this is the first non-trivial approximability result for the problem. Finally, we demonstrate that our approximation algorithm can be extended to some related problems.Comment: 23 pages, 4 figure

The Densest Subgraph Problem with a Convex/Concave Size Function

we propose a linear-programming-based polynomial-time exact algorithm. It should be emphasized that this algorithm obtains not only an optimal solution to the problem but also subsets of vertices corresponding to the extreme points of the upper convex hull of {(|S|, w(S)) | S subseteq V }, which we refer to as the dense frontier points. We also propose a flow-based combinatorial exact algorithm for unweighted graphs that runs in O(n^3) time. Finally, we propose a nearly-linear-time 3-approximation algorithm

Stochastic Solutions for Dense Subgraph Discovery in Multilayer Networks

Network analysis has played a key role in knowledge discovery and data mining. In many real-world applications in recent years, we are interested in mining multilayer networks, where we have a number of edge sets called layers, which encode different types of connections and/or time-dependent connections over the same set of vertices. Among many network analysis techniques, dense subgraph discovery, aiming to find a dense component in a network, is an essential primitive with a variety of applications in diverse domains. In this paper, we introduce a novel optimization model for dense subgraph discovery in multilayer networks. Our model aims to find a stochastic solution, i.e., a probability distribution over the family of vertex subsets, rather than a single vertex subset, whereas it can also be used for obtaining a single vertex subset. For our model, we design an LP-based polynomial-time exact algorithm. Moreover, to handle large-scale networks, we also devise a simple, scalable preprocessing algorithm, which often reduces the size of the input networks significantly and results in a substantial speed-up. Computational experiments demonstrate the validity of our model and the effectiveness of our algorithms.Comment: Accepted to WSDM 202

CXCR4 expression in papillary thyroid carcinoma: induction by nitric oxide and correlation with lymph node metastasis

<p>Abstract</p> <p>Background</p> <p>Metastasis to regional lymph nodes is a common step in the progression of cancer. Recent evidence suggests that tumor production of CXCR4 promotes lymph node metastasis. Nitric oxide (NO) may also increase metastatic ability in human cancers.</p> <p>Methods</p> <p>Nitrite/nitrate levels and functional CXCR4 expression were assessed in K1 and B-CPAP papillary thyroid carcinoma (PTC) cells after induction and/or inhibition of NO synthesis. CXCR4 expression was also analyzed in primary human PTC. The relationship between nitrotyrosine levels, which are a biomarker for peroxynitrate formation from NO in vivo, CXCR4 expression, and lymph node status was also analyzed.</p> <p>Results</p> <p>Production of nitrite/nitrate and functional CXCR4 expression in both cell lines was increased by treatment with the NO donor DETA NONOate. The NOS inhibitor L-NAME eliminated this increase. Positive CXCR4 immunostaining was observed in 60.7% (34/56) of PTCs. CXCR4 expression was significantly correlated with nitrotyrosine levels and lymph node metastasis in human PTC.</p> <p>Conclusion</p> <p>Our data indicate that NO stimulates CXCR4 expression in vitro. Formation of the NO biomarker nitrotyrosine was also correlated with CXCR4 expression and lymph node metastasis in human PTC. NO may induce lymph node metastasis via CXCR4 induction in papillary thyroid carcinoma.</p

Network-dependent modulation of brain activity during sleep

AbstractBrain activity dynamically changes even during sleep. A line of neuroimaging studies has reported changes in functional connectivity and regional activity across different sleep stages such as slow-wave sleep (SWS) and rapid-eye-movement (REM) sleep. However, it remains unclear whether and how the large-scale network activity of human brains changes within a given sleep stage. Here, we investigated modulation of network activity within sleep stages by applying the pairwise maximum entropy model to brain activity obtained by functional magnetic resonance imaging from sleeping healthy subjects. We found that the brain activity of individual brain regions and functional interactions between pairs of regions significantly increased in the default-mode network during SWS and decreased during REM sleep. In contrast, the network activity of the fronto-parietal and sensory-motor networks showed the opposite pattern. Furthermore, in the three networks, the amount of the activity changes throughout REM sleep was negatively correlated with that throughout SWS. The present findings suggest that the brain activity is dynamically modulated even in a sleep stage and that the pattern of modulation depends on the type of the large-scale brain networks

National survey of catheter ablation for atrial fibrillation: The Japanese catheter ablation registry of atrial fibrillation (J-CARAF)

AbstractTo assess the current status of atrial fibrillation (AF) ablation in Japan, the Japanese Heart Rhythm Society (JHRS) instituted a national registry, the Japanese Catheter Ablation Registry of AF (J-CARAF).MethodsUsing an online questionnaire, the JHRS invited electrophysiology centers in Japan to voluntarily and retrospectively register data regarding the AF ablation procedures performed in September, 2011.ResultsA total of 128 centers submitted data regarding AF ablation procedures in 932 patients (age 62.1±10.4 years; male 76.8%; paroxysmal AF 65.7%, CHADS2 score 1.0±1.0). The majority received oral anticoagulant therapy during and following the procedure (68.9% and 97.5%, respectively). Pulmonary vein isolation (PVI) was performed in 97.5% of the patients; ipsilateral encircling PVI was the preferred technique (79.7%). Three-dimensional (3D) mapping systems and irrigated-tip catheters were used in 94.8% and 87.7% of the procedures, respectively. Ablation methods other than PVI were performed in 78.8% of all the patients and 73.5% of the patients with paroxysmal AF. Acute complications were reported in 6.2% of the patients, but no early deaths were recorded.ConclusionsIpsilateral encircling PVI, using 3D mapping and irrigated-tip catheters, is the standard AF ablation method in Japan. However, adjunctive ablations were performed frequently, even in patients with paroxysmal AF

Japanese Lung Cancer Society Guidelines for Stage IV NSCLC With EGFR Mutations

Patients with NSCLC in East Asia, including Japan, frequently contain EGFR mutations. In 2018, we published the latest full clinical practice guidelines on the basis of those provided by the Japanese Lung Cancer Society Guidelines Committee. The purpose of this study was to update those recommendations, especially for the treatment of metastatic or recurrent EGFR-mutated NSCLC. We conducted a literature search of systematic reviews of randomized controlled and nonrandomized trials published between 2018 and 2019 that multiple physicians had reviewed independently. On the basis of those studies and the advice from the Japanese Society of Lung Cancer Expert Panel, we developed updated guidelines according to the Grading of Recommendations, Assessment, Development, and Evaluation system. We also evaluated the benefits of overall and progression-free survival, end points, toxicities, and patients’ reported outcomes. For patients with NSCLC harboring EGFR-activating mutations, the use of EGFR tyrosine kinase inhibitors (EGFR TKIs), especially osimertinib, had the best recommendation as to first-line treatment. We also recommended the combination of EGFR TKI with other agents (platinum-based chemotherapy or antiangiogenic agents); however, it can lead to toxicity. In the presence of EGFR uncommon mutations, except for an exon 20 insertion, we also recommended the EGFR TKI treatment. However, we could not provide recommendations for the treatment of EGFR mutations with immune checkpoint inhibitors, including monotherapy, and its combination with cytotoxic chemotherapy, because of the limited evidence present in the literature. The 2020 Japanese Lung Cancer Society Guidelines can help community-based physicians to determine the most appropriate treatments and adequately provide medical care to their patients

Amlodipine versus angiotensin II receptor blocker; control of blood pressure evaluation trial in diabetics (ADVANCED-J)

BACKGROUND: The coexistence of type 2 diabetes mellitus and hypertension increases the risk of cardiovascular diseases. The U.K. Prospective Diabetes Study has shown that blood pressure control as well as blood glucose control is efficient for prevention of complications in hypertensive patients with diabetes mellitus. However, some reports have shown that it is difficult to control the blood pressure and the concomitant use of a plurality of drugs is needed in hypertensive patients with diabetes mellitus. In recent years renin-angiotensin system depressants are increasingly used for the blood pressure control in diabetic patients. Particularly in Japan, angiotensin II (A II) antagonists are increasingly used. However, there is no definite evidence of the point of which is efficient for the control, the increase in dose of A II antagonist or the concomitant use of another drug, in hypertensive patients whose blood pressure levels are inadequately controlled with A II antagonist. METHODS/DESIGN: Hypertensive patients of age 20 years or over with type 2 diabetes mellitus who have been treated by the single use of AII antagonist at usual doses for at least 8 weeks or patients who have been treated by the concomitant use of AII antagonist and an antihypertensive drug other than calcium channel blockers and ACE inhibitors at usual doses for at least 8 weeks are included. DISCUSSION: We designed a multi-center, prospective, randomized, open label, blinded-endpoint trial, ADVANCED-J, to compare the increases in dose of A II antagonist and the concomitant use of a Ca-channel blocker (amlodipine) and A II antagonist in hypertensive patients with diabetes mellitus, whose blood pressure levels were inadequately controlled with A II antagonist. This study is different from the usual previous studies in that home blood pressures are assessed as indicators of evaluation of blood pressure. The ADVANCED-J study may have much influence on selection of antihypertensive drugs for treatment in hypertensive patients with diabetes mellitus. It is expected to give an important hint for considering the validity of selection of antihypertensive drugs from the aspects not only of the antihypertensive effect but medical cost-effectiveness