The age of data-driven proteomics : how machine learning enables novel workflows

A lot of energy in the field of proteomics is dedicated to the application of challenging experimental workflows, which include metaproteomics, proteogenomics, data independent acquisition (DIA), non-specific proteolysis, immunopeptidomics, and open modification searches. These workflows are all challenging because of ambiguity in the identification stage; they either expand the search space and thus increase the ambiguity of identifications, or, in the case of DIA, they generate data that is inherently more ambiguous. In this context, machine learning-based predictive models are now generating considerable excitement in the field of proteomics because these predictive models hold great potential to drastically reduce the ambiguity in the identification process of the above-mentioned workflows. Indeed, the field has already produced classical machine learning and deep learning models to predict almost every aspect of a liquid chromatography-mass spectrometry (LC-MS) experiment. Yet despite all the excitement, thorough integration of predictive models in these challenging LC-MS workflows is still limited, and further improvements to the modeling and validation procedures can still be made. In this viewpoint we therefore point out highly promising recent machine learning developments in proteomics, alongside some of the remaining challenges

Optimal length-constrained segmentation and subject-adaptive learning for real-time arrhythmia detection

© 2018 Association for Computing Machinery. An algorithm of data segmentation with length constraints for each segment is presented and applied in the context of arrhythmia detection. The additivity property of the cost function for each segment yields the induction proof of the exact global optimal solution. The experiments were conducted on the MIT-BIH arrhythmia dataset with the heartbeat categories recommended by the ANSI/AAMI EC57:1998 standard. The heartbeat classification task is enhanced by an adaptive learning scheme. Incremental support vector machine is used to integrate a small number of expert-annotated samples specific to the subject into the existing classifier previously learned from the dataset. The proposed segmentation scheme obtains the sensitivity of 99.89% and the positive predictivity of 99.83%. The classification sensitivities of ventricular and supraventricular detection are significantly boosted from 85.9% and 83.5% (subject-unadaptive) to 97.7% and 93.2% (subject-adaptive), respectively. Similarly the pre-dictivities increase from 94.8% to 99.3% (ventricular), and from 67.7% to 88.0% (supraventricular) when plugging in the adaptive learning method. The signal processing framework is conducted in a simulated real-time model. As compared to the previously reported studies we achieve a competitive performance in terms of all assessment measures

High-performance RF coil inductors on silicon

Strong demand for wireless communication devices has motivated research directed toward monolithic integration of transceivers. The fundamental electronic component least compatible with silicon integrated circuits is the inductor, although a number of inductors are required to implement oscillators, filters and matching networks in cellular devices. Spiral inductors have been integrated into the silicon IC metallization sequence but have not performed adequately due to coupling to the silicon which results in parasitic capacitance and loss. We have, for the first time, fabricated three dimensional coil inductors on silicon which have significantly lower capacitive coupling and loss and which now exceed the requirements of potential applications. Quality factors of 30 at 1 GHz have been measured in single turn devices and Q > 16 in 2 and 4 turn devices. The reduced Q for multiturn devices appears to be related to eddy currents in outer turns generated by magnetic fields from current in neighboring turns. Higher Q values significantly in excess of 30 are anticipated using modified coil designs

Using data mining for wine quality assessment

Certification and quality assessment are crucial issues within the wine industry. Currently, wine quality is mostly assessed by physico- chemical (e.g alcohol levels) and sensory (e.g. human expert evaluation) tests. In this paper, we propose a data mining approach to predict wine preferences that is based on easily available analytical tests at the certifi- cation step. A large dataset is considered with white vinho verde samples from the Minho region of Portugal. Wine quality is modeled under a re- gression approach, which preserves the order of the grades. Explanatory knowledge is given in terms of a sensitivity analysis, which measures the response changes when a given input variable is varied through its do- main. Three regression techniques were applied, under a computationally efficient procedure that performs simultaneous variable and model selec- tion and that is guided by the sensitivity analysis. The support vector machine achieved promising results, outperforming the multiple regres- sion and neural network methods. Such model is useful for understand- ing how physicochemical tests affect the sensory preferences. Moreover, it can support the wine expert evaluations and ultimately improve the production

Support vector machine versus logistic regression modeling for prediction of hospital mortality in critically ill patients with haematological malignancies

Background: Several models for mortality prediction have been constructed for critically ill patients with haematological malignancies in recent years. These models have proven to be equally or more accurate in predicting hospital mortality in patients with haematological malignancies than ICU severity of illness scores such as the APACHE II or SAPS II [1]. The objective of this study is to compare the accuracy of predicting hospital mortality in patients with haematological malignancies admitted to the ICU between models based on multiple logistic regression (MLR) and support vector machine (SVM) based models. Methods: 352 patients with haematological malignancies admitted to the ICU between 1997 and 2006 for a life-threatening complication were included. 252 patient records were used for training of the models and 100 were used for validation. In a first model 12 input variables were included for comparison between MLR and SVM. In a second more complex model 17 input variables were used. MLR and SVM analysis were performed independently from each other. Discrimination was evaluated using the area under the receiver operating characteristic (ROC) curves (+/- SE). Results: The area under ROC curve for the MLR and SVM in the validation data set were 0.768 (+/- 0.04) vs. 0.802 (+/- 0.04) in the first model (p = 0.19) and 0.781 (+/- 0.05) vs. 0.808 (+/- 0.04) in the second more complex model (p = 0.44). SVM needed only 4 variables to make its prediction in both models, whereas MLR needed 7 and 8 variables in the first and second model respectively. Conclusion: The discriminative power of both the MLR and SVM models was good. No statistically significant differences were found in discriminative power between MLR and SVM for prediction of hospital mortality in critically ill patients with haematological malignancies

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011

Measurements of Higgs boson production and couplings in diboson final states with the ATLAS detector at the LHC

Measurements are presented of production properties and couplings of the recently discovered Higgs boson using the decays into boson pairs, H →γ γ, H → Z Z∗ →4l and H →W W∗ →lνlν. The results are based on the complete pp collision data sample recorded by the ATLAS experiment at the CERN Large Hadron Collider at centre-of-mass energies of √s = 7 TeV and √s = 8 TeV, corresponding to an integrated luminosity of about 25 fb−1. Evidence for Higgs boson production through vector-boson fusion is reported. Results of combined fits probing Higgs boson couplings to fermions and bosons, as well as anomalous contributions to loop-induced production and decay modes, are presented. All measurements are consistent with expectations for the Standard Model Higgs boson

Measurement of the top quark pair cross section with ATLAS in pp collisions at √s=7 TeV using final states with an electron or a muon and a hadronically decaying τ lepton

A measurement of the cross section of top quark pair production in proton-proton collisions recorded with the ATLAS detector at the Large Hadron Collider at a centre-of-mass energy of 7 TeV is reported. The data sample used corresponds to an integrated luminosity of 2.05 fb -1. Events with an isolated electron or muon and a τ lepton decaying hadronically are used. In addition, a large missing transverse momentum and two or more energetic jets are required. At least one of the jets must be identified as originating from a b quark. The measured cross section, σtt-=186±13(stat.)±20(syst.)±7(lumi.) pb, is in good agreement with the Standard Model prediction