Relational Attention: Generalizing Transformers for Graph-Structured Tasks

Transformers flexibly operate over sets of real-valued vectors representing task-specific entities and their attributes, where each vector might encode one word-piece token and its position in a sequence, or some piece of information that carries no position at all. But as set processors, transformers are at a disadvantage in reasoning over more general graph-structured data where nodes represent entities and edges represent relations between entities. To address this shortcoming, we generalize transformer attention to consider and update edge vectors in each transformer layer. We evaluate this relational transformer on a diverse array of graph-structured tasks, including the large and challenging CLRS Algorithmic Reasoning Benchmark. There, it dramatically outperforms state-of-the-art graph neural networks expressly designed to reason over graph-structured data. Our analysis demonstrates that these gains are attributable to relational attention's inherent ability to leverage the greater expressivity of graphs over sets.Comment: The Eleventh International Conference on Learning Representations, ICLR'2

MolCPT: Molecule Continuous Prompt Tuning to Generalize Molecular Representation Learning

Molecular representation learning is crucial for the problem of molecular property prediction, where graph neural networks (GNNs) serve as an effective solution due to their structure modeling capabilities. Since labeled data is often scarce and expensive to obtain, it is a great challenge for GNNs to generalize in the extensive molecular space. Recently, the training paradigm of "pre-train, fine-tune" has been leveraged to improve the generalization capabilities of GNNs. It uses self-supervised information to pre-train the GNN, and then performs fine-tuning to optimize the downstream task with just a few labels. However, pre-training does not always yield statistically significant improvement, especially for self-supervised learning with random structural masking. In fact, the molecular structure is characterized by motif subgraphs, which are frequently occurring and influence molecular properties. To leverage the task-related motifs, we propose a novel paradigm of "pre-train, prompt, fine-tune" for molecular representation learning, named molecule continuous prompt tuning (MolCPT). MolCPT defines a motif prompting function that uses the pre-trained model to project the standalone input into an expressive prompt. The prompt effectively augments the molecular graph with meaningful motifs in the continuous representation space; this provides more structural patterns to aid the downstream classifier in identifying molecular properties. Extensive experiments on several benchmark datasets show that MolCPT efficiently generalizes pre-trained GNNs for molecular property prediction, with or without a few fine-tuning steps

Building Capacity for Cancer Research in the Era of COVID-19: Implementation and Results From an International Virtual Clinical Research Training Program in Zambia

DOI: 10.1200/GO.21.00372 JCO Global Oncology no. 8 (2022) Published online May 20, 2022. PMID: 35594499https://openworks.mdanderson.org/mozart/1024/thumbnail.jp

Perspectives of Zambian Clinical Oncology Trainees in the MD Anderson and Zambia Virtual Clinical Research Training Program (MOZART)

Published in The Oncologist, 2022;, oyac110, https://doi.org/10.1093/oncolo/oyac110 PMID 35689473https://openworks.mdanderson.org/mozart/1025/thumbnail.jp

The effect of a preparation of minerals, vitamins and trace elements on the cardiac gene expression pattern in male diabetic rats

BACKGROUND: Diabetic patients have an increased risk of developing cardiovascular diseases, which are the leading cause of death in developed countries. Although multivitamin products are widely used as dietary supplements, the effects of these products have not been investigated in the diabetic heart yet. Therefore, here we investigated if a preparation of different minerals, vitamins, and trace elements (MVT) affects the cardiac gene expression pattern in experimental diabetes. METHODS: Two-day old male Wistar rats were injected with streptozotocin (i.p. 100 mg/kg) or citrate buffer to induce diabetes. From weeks 4 to 12, rats were fed with a vehicle or a MVT preparation. Fasting blood glucose measurement and oral glucose tolerance test were performed at week 12, and then total RNA was isolated from the myocardium and assayed by rat oligonucleotide microarray for 41012 oligonucleotides. RESULTS: Significantly elevated fasting blood glucose concentration and impaired glucose tolerance were markedly improved by MVT-treatment in diabetic rats at week 12. Genes with significantly altered expression due to diabetes include functional clusters related to cardiac hypertrophy (e.g. caspase recruitment domain family, member 9; cytochrome P450, family 26, subfamily B, polypeptide; FXYD domain containing ion transport regulator 3), stress response (e.g. metallothionein 1a; metallothionein 2a; interleukin-6 receptor; heme oxygenase (decycling) 1; and glutathione S-transferase, theta 3), and hormones associated with insulin resistance (e.g. resistin; FK506 binding protein 5; galanin/GMAP prepropeptide). Moreover the expression of some other genes with no definite cardiac function was also changed such as e.g. similar to apolipoprotein L2; brain expressed X-linked 1; prostaglandin b2 synthase (brain). MVT-treatment in diabetic rats showed opposite gene expression changes in the cases of 19 genes associated with diabetic cardiomyopathy. In healthy hearts, MVT-treatment resulted in cardiac gene expression changes mostly related to immune response (e.g. complement factor B; complement component 4a; interferon regulatory factor 7; hepcidin). CONCLUSIONS: MVT-treatment improved diagnostic markers of diabetes. This is the first demonstration that MVT-treatment significantly alters cardiac gene expression profile in both control and diabetic rats. Our results and further studies exploring the mechanistic role of individual genes may contribute to the prevention or diagnosis of cardiac complications in diabetes

Características clínico-epidemiológicas de pacientes hipertensos en un Consultorio Médico de Santa Clara

High blood pressure is a chronic non-transmittable disease, which is also a risk factor for the development of other clinical conditions. The incidence of arterial hypertension in the Cuban population is high.Aim: to characterize the evolution of arterial hypertension in a Family Doctor's Office.Methods: an observational, descriptive and cross-sectional study was carried out at the Family Doctor's Office 17-19 in the municipality of Santa Clara. The study covered the months of January to March 2020. Of the 256 hypertensive patients, a sample of 52 was selected by a simple random method.Results: Males predominated (53.84 %), together with the age group between 40 and 49 years (28.84 %). A total of 63.46 % of the patients were white-skinned. 51.61% presented risk factors. The risk factors with the highest incidence were smoking, followed by obesity and sedentary lifestyle.Conclusions: the most affected hypertensive patients are male. Most patients have a family history of high blood pressure. Smoking is a high incidence risk factor in the hypertensive population.Introducción: la hipertensión arterial es una enfermedad crónica no transmisible, que a la vez constituye un factor de riesgo para el desarrollo de otras enfermedades. La incidencia de la hipertensión arterial en la población de Cuba es alta.Objetivo: caracterizar el comportamiento de la hipertensión arterial en un Consultorio Médico de Familia.Métodos: se realizó un estudio observacional, descriptivo y transversal en el Consultorio Médico de Familia 17-19 del municipio Santa Clara. El período de estudio comprendió los meses de enero a marzo del 2020. La población fue de 256 hipertensos y se escogió una muestra de 52 hipertensos por muestreo aleatorio simple.Resultados: predominó el sexo masculino (53,84 %), y el grupo de edad entre 40 y 49 años (28,84 %). El 63,46 % de los pacientes fueron de color de la piel blanca. El 51,61 % presentaron factores de riesgo. Los factores de riesgo de mayor incidencia fueron el tabaquismo, seguido por la obesidad y el sedentarismo.Conclusiones: los pacientes hipertensos más afectados son los del sexo masculino. La mayor parte de los pacientes tienen antecedentes familiares de hipertensión arterial. El tabaquismo es un factor de riesgo de alta incidencia en la población hipertensa

Distributions of Ice Supersaturation and Ice Crystals From Airborne Observations in Relation to Upper Tropospheric Dynamical Boundaries

Cirrus clouds are one of the largest sources of uncertainties in predicting future climate. Ice nucleation and ice crystal growth inside cirrus clouds require ice supersaturation (ISS). Previously, remote sensing observations have shown that the locations of cirrus clouds’ cloud top height are highly correlated with the thermal tropopause height (Pan and Munchak, 2011). However, it is unclear if the initial conditions of cirrus clouds – ice supersaturated region (ISSRs) – have similar features in the extratropical upper troposphere and lower stratosphere (UT/LS). In fact, the dynamical processes and conditions that contribute to ISS formation from the microscale (~100 m) to the mesoscale (~100 km) are still not well understood. In this work, we present in-situ observations of ISS and ice crystals with ~200 m horizontal resolution at temperatures ≤ -40°C. Our analyses are based on the NSF Stratosphere Troposphere Analyses of Regional Transport (START08) Campaign, which sampled chemical and microphysical variables under various dynamical conditions near the extratropical tropopause and upper level jets. One of the key analyses is about the influences of jet stream and extratropical thermal tropopause on the formation of ice supersaturated regions (ISSRs) and ice crystals. We found that most of the ISSRs are vertically constrained by the thermal tropopause height, agreeing with the findings of cirrus cloud top constraint (Pan and Munchak, 2011). In addition, the number of ISSRs observed on the anti-cyclonic side of the jet is ~1.6 times of that on the cyclonic side, consistent with previous model simulations (Gierens and Brinkop, 2012). Based on the O3-CO and O3-H2O tracer-tracer correlations, two different air mass mixing scenarios are found: stratosphere-troposphere mixing and troposphere-troposphere mixing. These different mixing scenarios are also associated with different dynamical conditions: small-scale waves/turbulence and large scale uplifting, respectively. Understanding the dynamical conditions of ISSR and cirrus clouds and the related microphysical properties will ultimately improve the simulation of cirrus clouds and the prediction of their radiative forcing in the future climate

Distributions of Ice Supersaturation and Ice Crystals From Airborne Observations in Relation to Upper Tropospheric Dynamical Boundaries

Ice supersaturation (ISS) is the prerequisite condition for cirrus cloud formation. To examine multiscale dynamics\u27 influences on ISS formation, we analyze in situ aircraft observations (~200 m scale) over North America in coordinates relative to dynamical boundaries in the upper troposphere and lower stratosphere. Two case studies demonstrate that ISS formation is likely influenced by mesoscale uplifting, small-scale waves, and turbulence. A collective analysis of 15 flights in April–June 2008 shows that the top layers of ISS and ice crystal distributions are strongly associated with thermal tropopause height. In addition, the average occurrence frequencies of ISS and ice crystals on the anticyclonic side of the jet stream are ~1.5–2 times of those on the cyclonic side. By defining five cirrus evolution phases based on the spatial relationships between ice-supersaturated and in-cloud regions, we find that their peak occurrence frequencies are located at decreasing altitudes with respect to the thermal tropopause: (phase 1) clear-sky ISS around the tropopause, (phase 2) nucleation phase around 2 km below the tropopause, (phases 3 and 4) early and later growth phases around 6 km below the tropopause, and (phase 5) sedimentation/sublimation around 2–6 km below the tropopause. Consistent with this result, chemical tracer correlation analysis shows that the majority (~80%) of the earlier cirrus phases (clear-sky ISS and nucleation) occurs inside the chemical tropopause transition layer, while the later phases happen mostly below that layer. These results shed light on the role of dynamical environment in facilitating cirrus cloud formation and evolution