Using Predicted Bioactivity Profiles to Improve Predictive Modeling

Predictive modeling is a cornerstone in early drug development. Using information for multiple domains or across prediction tasks has the potential to improve the performance of predictive modeling. However, aggregating data often leads to incomplete data matrices that might be limiting for modeling. In line with previous studies, we show that by generating predicted bioactivity profiles, and using these as additional features, prediction accuracy of biological endpoints can be improved. Using conformal prediction, a type of confidence predictor, we present a robust framework for the calculation of these profiles and the evaluation of their impact. We report on the outcomes from several approaches to generate the predicted profiles on 16 datasets in cytotoxicity and bioactivity and show that efficiency is improved the most when including the p-values from conformal prediction as bioactivity profiles

Synergy conformal prediction applied to large-scale bioactivity datasets and in federated learning

Confidence predictors can deliver predictions with the associated confidence required for decision making and can play an important role in drug discovery and toxicity predictions. In this work we investigate a recently introduced version of conformal prediction, synergy conformal prediction, focusing on the predictive performance when applied to bioactivity data. We compare the performance to other variants of conformal predictors for multiple partitioned datasets and demonstrate the utility of synergy conformal predictors for federated learning where data cannot be pooled in one location. Our results show that synergy conformal predictors based on training data randomly sampled with replacement can compete with other conformal setups, while using completely separate training sets often results in worse performance. However, in a federated setup where no method has access to all the data, synergy conformal prediction is shown to give promising results. Based on our study, we conclude that synergy conformal predictors are a valuable addition to the conformal prediction toolbox

Intelligent Algorithm for Enhancing MPEG-DASH QoE in eMBMS

[EN] Multimedia streaming is the most demanding and bandwidth hungry application in today¿s world of Internet. MPEG-DASH as a video technology standard is designed for delivering live or on-demand streams in Internet to deliver best quality content with the fewest dropouts and least possible buffering. Hybrid architecture of DASH and eMBMS has attracted a great attention from the telecommunication industry and multimedia services. It is deployed in response to the immense demand in multimedia traffic. However, handover and limited available resources of the system affected on dropping segments of the adaptive video streaming in eMBMS and it creates an adverse impact on Quality of Experience (QoE), which is creating trouble for service providers and network providers towards delivering the service. In this paper, we derive a case study in eMBMS to approach to provide test measures evaluating MPEG-DASH QoE, by defining the metrics are influenced on QoE in eMBMS such as bandwidth and packet loss then we observe the objective metrics like stalling (number, duration and place), buffer length and accumulative video time. Moreover, we build a smart algorithm to predict rate of segments are lost in multicast adaptive video streaming. The algorithm deploys an estimation decision regards how to recover the lost segments. According to the obtained results based on our proposal algorithm, rate of lost segments is highly decreased by comparing to the traditional approach of MPEG-DASH multicast and unicast for high number of users.This work has been partially supported by the Postdoctoral Scholarship Contratos Postdoctorales UPV 2014 (PAID-10-14) of the Universitat Politècnica de València , by the Programa para la Formación de Personal Investigador (FPI-2015-S2-884) of the Universitat Politècnica de València , by the Ministerio de Economía y Competitividad , through the Convocatoria 2014. Proyectos I+D - Programa Estatal de Investigación Científica y Técnica de Excelencia in the Subprograma Estatal de Generación de Conocimiento , project TIN2014-57991-C3-1-P and through the Convocatoria 2017 - Proyectos I+D+I - Programa Estatal de Investigación, Desarrollo e Innovación, convocatoria excelencia (Project TIN2017-84802-C2-1-P).Abdullah, MT.; Jimenez, JM.; Canovas Solbes, A.; Lloret, J. (2017). Intelligent Algorithm for Enhancing MPEG-DASH QoE in eMBMS. Network Protocols and Algorithms. 9(3-4):94-114. https://doi.org/10.5296/npa.v9i3-4.12573S9411493-

Deep Learning-Based Conformal Prediction of Toxicity

Predictive modeling for toxicity can help reduce risks in a range of applications and potentially serve as the basis for regulatory decisions. However, the utility of these predictions can be limited if the associated uncertainty is not adequately quantified. With recent studies showing great promise for deep learning-based models also for toxicity predictions, we investigate the combination of deep learning-based predictors with the conformal prediction framework to generate highly predictive models with well-defined uncertainties. We use a range of deep feedforward neural networks and graph neural networks in a conformal prediction setting and evaluate their performance on data from the Tox21 challenge. We also compare the results from the conformal predictors to those of the underlying machine learning models. The results indicate that highly predictive models can be obtained that result in very efficient conformal predictors even at high confidence levels. Taken together, our results highlight the utility of conformal predictors as a convenient way to deliver toxicity predictions with confidence, adding both statistical guarantees on the model performance as well as better predictions of the minority class compared to the underlying models

Predicting Information Diffusion on Social Media

Sotsiaalmeedia on saanud moodsa elu osaks. Pidevalt tekib juurde informatsiooni, mida maailmaga jagatakse. Informatsiooni hajumist on varasemalt uuritud paljude teadlaste poolt, kuna sel on rakendusi erinevates valdkondades, nagu näiteks sotsiaalmeediaturundamine ja uudiste levimise uurimine. Informatsiooni leviku kiirust mõjutab selle olulisus inimestele. Käesolevas töös uuritakse info hajumist sotsiaalvõrgustikus ja ennustatakse sisu populaarsust kasutades juhendatud masinõppe algoritme. Kolme Twitterist pärit andmestikku analüüsitakse ja kasutatakse erinevate masinõppe mudelite konstrueerimiseks.Defineerisime säutsu populaarsuse kui taaspostituste arvu, mida iga originaalsäuts sai, ning püstitasime uurimisprobleemid binaarsete ja mitmeklassiliste ennustusülesannetena. Uurisime, kuidas esialgne säutsude taaspostitamise käitumine mõjutab mudelite ennustusvõimekust. Lisaks analüüsisime, kas viimase tunni taaspostituskäitumine aitab ennustada taas-postituskäitumist järgneva tunni jooksul. Täiendav tähelepanu oli suunatud ka ennustuseks tähtsate tunnuste leidmiseks.Binaarse ennustuse puhul näitasid mudelid tulemusi AUC (area under curve) kuni 95% ning F1-skoori kuni 87%. Mitmeklassiliste ennustuste puhul suutsid mudelid saavutada kuni 60% üldise täpsuse ning F1-skoori kuni 67%. Paremad ennustustäpsused saavutati siis, kui postitustel olid väga madalad või väga kõrged taaspostituste arvud. Me genereerisime mudelid kasutades üht andmestikku ning testisime neid ülejäänud kahe peal. See näitas, et mudelid on piisavalt robustsed, et tegeleda erinevate teemadega.Social media has become a part of the everyday life of modern society. A lot of infor-mation is created and shared with the world continuously. Predicting information has been studied in the past by many researchers since it has its applications in various domains such as viral marketing, news propagation etc.Some information spreads faster compared to others depending on what interests people. In this thesis, by using supervised machine learning algorithms, we studied information diffusion in a social network and predicted content popularity. Three datasets from Twitter are collected and analysed for building and testing various models based on different ma-chine learning algorithms.We defined tweet popularity as number of retweets any original message received and stated our research problems as binary and multiclass prediction tasks. We investigated how initial retweeting behaviour of a message affects the predictive power of a model. We also analysed if a recent one-hour retweeting behaviour can help to predict a tweet popu-larity of the following hour. Besides that, main focus is made on finding features im-portant for the prediction.For binary prediction, the models showed performance of AUC up to 95% and F1 up to 87%. For multiclass prediction, the models were able to predict up to 60% of overall accu-racy and 67% of F1, with more accurate performance of classes with messages with very low and high retweet counts comparing to others. We created our models using one da-taset and tested our approach on the other two datasets, which showed that the models are robust enough to deal with multiple topics