Quantum-chemical insights from deep tensor neural networks.

Learning from data has led to paradigm shifts in a multitude of disciplines, including web, text and image search, speech recognition, as well as bioinformatics. Can machine learning enable similar breakthroughs in understanding quantum many-body systems? Here we develop an efficient deep learning approach that enables spatially and chemically resolved insights into quantum-mechanical observables of molecular systems. We unify concepts from many-body Hamiltonians with purpose-designed deep tensor neural networks, which leads to size-extensive and uniformly accurate (1 kcal mol-1) predictions in compositional and configurational chemical space for molecules of intermediate size. As an example of chemical relevance, the model reveals a classification of aromatic rings with respect to their stability. Further applications of our model for predicting atomic energies and local chemical potentials in molecules, reliable isomer energies, and molecules with peculiar electronic structure demonstrate the potential of machine learning for revealing insights into complex quantum-chemical systems.

Near-infrared spectroscopy (NIRS)-based eyes-closed brain-computer interface (BCI) using prefrontal cortex activation due to mental arithmetic.

We propose a near-infrared spectroscopy (NIRS)-based brain-computer interface (BCI) that can be operated in eyes-closed (EC) state. To evaluate the feasibility of NIRS-based EC BCIs, we compared the performance of an eye-open (EO) BCI paradigm and an EC BCI paradigm with respect to hemodynamic response and classification accuracy. To this end, subjects performed either mental arithmetic or imagined vocalization of the English alphabet as a baseline task with very low cognitive loading. The performances of two linear classifiers were compared; resulting in an advantage of shrinkage linear discriminant analysis (LDA). The classification accuracy of EC paradigm (75.6 ± 7.3%) was observed to be lower than that of EO paradigm (77.0 ± 9.2%), which was statistically insignificant (p = 0.5698). Subjects reported they felt it more comfortable (p = 0.057) and easier (p < 0.05) to perform the EC BCI tasks. The different task difficulty may become a cause of the slightly lower classification accuracy of EC data. From the analysis results, we could confirm the feasibility of NIRS-based EC BCIs, which can be a BCI option that may ultimately be of use for patients who cannot keep their eyes open consistently.

Single trial classification of motor imagination using 6 dry EEG electrodes.

BACKGROUND: Brain computer interfaces (BCI) based on electro-encephalography (EEG) have been shown to detect mental states accurately and non-invasively, but the equipment required so far is cumbersome and the resulting signal is difficult to analyze. BCI requires accurate classification of small amplitude brain signal components in single trials from recordings which can be compromised by currents induced by muscle activity. METHODOLOGY/PRINCIPAL FINDINGS: A novel EEG cap based on dry electrodes was developed which does not need time-consuming gel application and uses far fewer electrodes than on a standard EEG cap set-up. After optimizing the placement of the 6 dry electrodes through off-line analysis of standard cap experiments, dry cap performance was tested in the context of a well established BCI cursor control paradigm in 5 healthy subjects using analysis methods which do not necessitate user training. The resulting information transfer rate was on average about 30% slower than the standard cap. The potential contribution of involuntary muscle activity artifact to the BCI control signal was found to be inconsequential, while the detected signal was consistent with brain activity originating near the motor cortex. CONCLUSIONS/SIGNIFICANCE: Our study shows that a surprisingly simple and convenient method of brain activity imaging is possible, and that simple and robust analysis techniques exist which discriminate among mental states in single trials. Within 15 minutes the dry BCI device is set-up, calibrated and ready to use. Peak performance matched reported EEG BCI state of the art in one subject. The results promise a practical non-invasive BCI solution for severely paralyzed patients, without the bottleneck of setup effort and limited recording duration that hampers current EEG recording technique. The presented recording method itself, BCI not considered, could significantly widen the use of EEG for emerging applications requiring long-term brain activity and mental state monitoring.

A novel mechanism for evoked responses in the human brain.

Magnetoencephalographic and electroencephalographic evoked responses are primary real-time objective measures of cognitive and perceptual processes in the human brain. Two mechanisms (additive activity and phase reset) have been debated and considered as the only possible explanations for evoked responses. Here we present theoretical and empirical evidence of a third mechanism contributing to the generation of evoked responses. Interestingly, this mechanism can be deduced entirely from the characteristics of spontaneous oscillations in the absence of stimuli. We show that the amplitude fluctuations of neuronal alpha oscillations at rest are associated with changes in the mean value of ongoing activity in magnetoencephalography, a phenomenon that we term baseline shifts associated with alpha oscillations. When stimuli modulate the amplitude of alpha oscillations, baseline shifts become the basis of a novel mechanism for the generation of evoked responses; the averaging of several trials leads to a cancellation of the oscillatory component but the baseline shift remains, which gives rise to an evoked response. We propose that the presence of baseline shifts associated with alpha oscillations can be explained by the asymmetric flow of inward and outward neuronal currents related to the generation of alpha oscillations. Our findings are relevant to the vast majority of electroencephalographic and magnetoencephalographic studies involving perceptual, cognitive and motor activity.

Improving the Caenorhabditis elegans genome annotation using machine learning.

For modern biology, precise genome annotations are of prime importance, as they allow the accurate definition of genic regions. We employ state-of-the-art machine learning methods to assay and improve the accuracy of the genome annotation of the nematode Caenorhabditis elegans. The proposed machine learning system is trained to recognize exons and introns on the unspliced mRNA, utilizing recent advances in support vector machines and label sequence learning. In 87% (coding and untranslated regions) and 95% (coding regions only) of all genes tested in several out-of-sample evaluations, our method correctly identified all exons and introns. Notably, only 37% and 50%, respectively, of the presently unconfirmed genes in the C. elegans genome annotation agree with our predictions, thus we hypothesize that a sizable fraction of those genes are not correctly annotated. A retrospective evaluation of the Wormbase WS120 annotation [] of C. elegans reveals that splice form predictions on unconfirmed genes in WS120 are inaccurate in about 18% of the considered cases, while our predictions deviate from the truth only in 10%-13%. We experimentally analyzed 20 controversial genes on which our system and the annotation disagree, confirming the superiority of our predictions. While our method correctly predicted 75% of those cases, the standard annotation was never completely correct. The accuracy of our system is further corroborated by a comparison with two other recently proposed systems that can be used for splice form prediction: SNAP and ExonHunter. We conclude that the genome annotation of C. elegans and other organisms can be greatly enhanced using modern machine learning technology.