SOM-based aggregation for graph convolutional neural networks

Graph property prediction is becoming more and more popular due to the increasing availability of scientific and social data naturally represented in a graph form. Because of that, many researchers are focusing on the development of improved graph neural network models. One of the main components of a graph neural network is the aggregation operator, needed to generate a graph-level representation from a set of node-level embeddings. The aggregation operator is critical since it should, in principle, provide a representation of the graph that is isomorphism invariant, i.e. the graph representation should be a function of graph nodes treated as a set. DeepSets (in: Advances in neural information processing systems, pp 3391–3401, 2017) provides a framework to construct a set-aggregation operator with universal approximation properties. In this paper, we propose a DeepSets aggregation operator, based on Self-Organizing Maps (SOM), to transform a set of node-level representations into a single graph-level one. The adoption of SOMs allows to compute node representations that embed the information about their mutual similarity. Experimental results on several real-world datasets show that our proposed approach achieves improved predictive performance compared to the commonly adopted sum aggregation and many state-of-the-art graph neural network architectures in the literature

Linear graph convolutional networks

Many neural networks for graphs are based on the graph convolution operator, proposed more than a decade ago. Since then, many alternative definitions have been proposed, that tend to add complexity (and non-linearity) to the model. In this paper, we follow the opposite direction by proposing a linear graph convolution operator. Despite its simplicity, we show that our convolution operator is more theoretically grounded than many proposals in literature, and shows improved predictive performance

First-line erlotinib and fixed dose-rate gemcitabine for advanced pancreatic cancer

AIM: To investigate activity, toxicity, and prognostic factors for survival of erlotinib and fixed dose-rate gemcitabine (FDR-Gem) in advanced pancreatic cancer. METHODS: We designed a single-arm prospective, multicentre, open-label phase II study to evaluate the combination of erlotinib (100 mg/d, orally) and weekly FDR-Gem (1000 mg/m2, infused at 10 mg/m2per minute) in a population of previously untreated patients with locally advanced, inoperable, or metastatic pancreatic cancer. Primary endpoint was the rate of progression-free survival at 6 mo (PFS-6); secondary endpoints were overall response rate (ORR), response duration, tolerability, overall survival (OS), and clinical benefit. Treatment was not considered to be of further interest if the PFS-6 was < 20% (p0 = 20%), while a PFS-6 > 40% would be of considerable interest (p1 = 40%); with a 5% rejection error (α = 5%) and a power of 80%, 35 fully evaluable patients with metastatic disease were required to be enrolled in order to complete the study. Analysis of prognostic factors for survival was also carried out. RESULTS: From May 2007 to September 2009, 46 patients were enrolled (male/female: 25/21; median age: 64 years; median baseline carbohydrate antigen 19-9 (CA 19-9): 897 U/mL; locally advanced/metastatic disease: 5/41). PFS-6 and median PFS were 30.4% and 14 wk (95%CI: 10-19), respectively; 1-year and median OS were 20.2% and 26 wk (95%CI: 8-43). Five patients achieved an objective response (ORR: 10.9%, 95%CI: 1.9-19.9); disease control rate was 56.5% (95%CI: 42.2-70.8); clinical benefit rate was 43.5% (95%CI: 29.1-57.8). CA 19-9 serum levels were decreased by > 25% as compared to baseline in 14/23 evaluable patients (63.6%). Treatment was well-tolerated, with skin rash being the most powerful predictor of both longer PFS (P < 0.0001) and OS (P = 0.01) at multivariate analysis (median OS for patients with or without rash: 42 wk vs 15 wk, respectively, Log-rank P = 0.03). Additional predictors of better outcome were: CA 19-9 reduction, female sex (for PFS), and good performance status (for OS). CONCLUSION: Primary study endpoint was not met. However, skin rash strongly predicted erlotinib efficacy, suggesting that a pharmacodynamic-based strategy for patient selection deserves further investigation

Towards a new osteometric method for sexing ancient cremated human remains. Analysis of Late Bronze Age and Iron Age samples from Italy with gendered grave goods

Sex estimation of human remains is one of the most important research steps for physical anthropologists and archaeologists dealing with funerary contexts and trying to reconstruct the demographic structure of ancient societies. However, it is well known that in the case of cremations sex assessment might be complicated by the destructive/transformative effect of the fire on bones. Osteometric standards built on unburned human remains and contemporary cremated series are often inadequate for the analysis of ancient cremations, and frequently result in a significant number of misclassifications. This work is an attempt to overcome the scarcity of methods that could be applied to pre-proto-historic Italy and serve as methodological comparison for other European contexts. A set of 24 anatomical traits were measured on 124 Bronze Age and Iron Age cremated individuals with clearly engendered grave goods. Assuming gender largely correlated to sex, male and female distributions of each individual trait measured were compared to evaluate sexual dimorphism through inferential statistics and Chaktaborty and Majumder\u2019s index. The discriminatory power of each variable was evaluated by cross-validation tests. Eight variables yielded an accuracy equal to or greater than 80%. Four of these variables also show a similar degree of precision for both sexes. The most diagnostic measurements are from radius, patella, mandible, talus, femur, first metatarsal, lunate and humerus. Overall, the degree of sexual dimorphism and the reliability of estimates obtained from our series are similar to those of a modern cremated sample recorded by Gon\ue7alves and collaborators. Nevertheless, mean values of the male and female distributions in our case study are lower, and the application of the cut-off point calculated from the modern sample to our ancient individuals produces a considerable number of misclassifications. This result confirms the need to build population-specific methods for sexing the cremated remains of ancient individuals

Adversarial Edit Attacks for Tree Data

Many machine learning models can be attacked with adversarial examples, i.e. inputs close to correctly classified examples that are classified incorrectly. However, most research on adversarial attacks to date is limited to vectorial data, in particular image data. In this contribution, we extend the field by introducing adversarial edit attacks for tree-structured data with potential applications in medicine and automated program analysis. Our approach solely relies on the tree edit distance and a logarithmic number of black-box queries to the attacked classifier without any need for gradient information. We evaluate our approach on two programming and two biomedical data sets and show that many established tree classifiers, like tree-kernel-SVMs and recursive neural networks, can be attacked effectively.Comment: accepted at the 20th International Conference on Intelligent Data Engineering and Automated Learning (IDEAL

Is transperitoneal laparoscopic adrenalectomy for pheochromocytoma really more challenging? A propensity score-matched analysis

Purpose Minimally invasive surgery is the gold standard treatment for adrenal masses, but it may be a challenging procedure in the case of pheochromocytoma (PHEO). The aim of the present study is to report the results of transperitoneal laparoscopic adrenalectomy (TLA) in cases of PHEO in comparison to other types of adrenal lesions. Methods From 1994 to 2021, 629 patients underwent adrenalectomy. Twenty-two and thirty-five patients, respectively, were excluded because they underwent bilateral and open adrenalectomy, leaving 572 patients for inclusion. Of these, 114 patients had PHEO (Group A), and 458 had other types of lesions (Group B). To adjust for potential baseline confounders, a propensity score matching (PSM) analysis was conducted. Results After PSM, 114 matched pairs of patients were identified from each group. Statistically significant differences were not observed when comparing the median operative time (85 and 90 min in Groups A and B, respectively, p = 0.627), conversion rate [6 (5.3%) in each group, p = 1.000], transfusion rate [4 (3.5%) and 3 (2.6%) in Groups A and B, respectively, p = 1.000], complication rate [7 (6.1%) and 9 (7.9%) in Groups A and B, respectively, p = 0.796), median postoperative hospital stay (3.9 and 3.6 days in Groups A and B, respectively, p = 0.110), and mortality rate [1 (0.9%) in each group, p = 1.000]. Conclusions Based on this analysis, the results of TLA for PHEO are equivalent to those of TLA for other types of adrenal lesions, but the fundamental requirements are multidisciplinary patient management and adequate surgeon experience. Further prospective studies are required to draw definitive conclusions

Abiraterone acetate in metastatic castration-resistant prostate cancer after chemotherapy. A retrospective “Real Life” analysis of activity and safety

Abiraterone acetate (AA) is a potent, selective androge (CYP17) biosynthesis inhibitor, which showed to improve overall survival (HR = 0.646) in mCRPC patients progressing after docetaxel. In this retrospective analysis we assessed the safety and efficacy of AA in patients affected with mCRPC progressing after chemotherapy, treated in the normal clinical practice, in several Italian Oncologic Units, after the approval of the drug from the Italian Drug Agency (AIFA)

Quality of life of therapies for hormone receptor positive advanced/metastatic breast cancer: Regulatory aspects and clinical impact in Europe

In recent years, the number of trials incorporating health-related quality of life (HRQoL) data has increased. The impact of HRQoL on regulatory decision making in the European context and on clinical practice is not well established. We conducted an analysis of the role of QoL data extracted from the clinical trials of the drugs approved for hormone receptor positive/HER2-negative advanced/metastatic breast cancer (mBC). The results from the HRQoL were collected and a meta-analysis was performed to evaluate the impact of experimental drugs compared to standard treatments. The results showed a non-detrimental effect in HRQoL from the new treatments. As regards the approval process, from an examination of the European Medicine Agency (EMA) documents, HRQoL was reported nonextensively and contained and discussed in the European assessment reports (EPARs) for eleven trials in the approval process and cited in three cases in the EPARs and summary of medicinal product characteristics (SmPC). An effort should be made by all the stakeholders to increase the visibility of the HRQoL results in order to allow increased consideration in the approval process to make QoL data more easily and visibly available for the clinician and the patients. The evaluation should be reflected in the SmPC in order to increase the amount of information provided to the physician

Triple positive breast cancer. A distinct subtype?

Breast cancer is a heterogeneous disease, and within the HER-2 positive subtype this is highly exemplified by the presence of substantial phenotypical and clinical heterogeneity, mostly related to hormonal receptor (HR) expression. It is well known how HER-2 positivity is commonly associated with a more aggressive tumor phenotype and decreased overall survival and, moreover, with a reduced benefit from endocrine treatment. Preclinical studies corroborate the role played by functional crosstalks between HER-2 and estrogen receptor (ER) signaling in endocrine resistance and, more recently, the activation of ER signaling is emerging as a possible mechanism of resistance to HER-2 blocking agents. Indeed, HER-2 positive breast cancer heterogeneity has been suggested to underlie the variability of response not only to endocrine treatments, but also to HER-2 blocking agents. Among HER-2 positive tumors, HR status probably defines two distinct subtypes, with dissimilar clinical behavior and different sensitivity to anticancer agents. The triple positive subtype, namely, ER/PgR/Her-2 positive tumors, could be considered the subset which most closely resembles the HER-2 negative/HR positive tumors, with substantial differences in biology and clinical outcome. We argue on whether in this subgroup the "standard" treatment may be considered, in selected cases, i.e., small tumors, low tumor burden, high expression of both hormonal receptors, an overtreatment. This article review the existing literature on biologic and clinical data concerning the HER-2/ER/PgR positive tumors, in an attempt to better define the HER-2 subtypes and to optimize the use of HER-2 targeted agents, chemotherapy and endocrine treatments in the various subsets