Geometry-aware Transformer for molecular property prediction

Recently, graph neural networks (GNNs) have achieved remarkable performances for quantum mechanical problems. However, a graph convolution can only cover a localized region, and cannot capture long-range interactions of atoms. This behavior is contrary to theoretical interatomic potentials, which is a fundamental limitation of the spatial based GNNs. In this work, we propose a novel attention-based framework for molecular property prediction tasks. We represent a molecular conformation as a discrete atomic sequence combined by atom-atom distance attributes, named Geometry-aware Transformer (GeoT). In particular, we adopt a Transformer architecture, which has been widely used for sequential data. Our proposed model trains sequential representations of molecular graphs based on globally constructed attentions, maintaining all spatial arrangements of atom pairs. Our method does not suffer from cost intensive computations, such as angle calculations. The experimental results on several public benchmarks and visualization maps verified that keeping the long-range interatomic attributes can significantly improve the model predictability.Comment: 14 pages, 5 figure

Collective dynamics of pedestrians interacting with attractions

In order to investigate collective effects of interactions between pedestrians and attractions, this study extends the social force model. Such interactions lead pedestrians to form stable clusters around attractions, or even to rush into attractions if the interaction becomes stronger. It is also found that for high pedestrian density and intermediate interaction strength, some pedestrians rush into attractions while others move to neighboring attractions. These collective patterns of pedestrian movements or phases and transitions between them are systematically presented in a phase diagram. The results suggest that safe and efficient use of pedestrian areas can be achieved by moderating the pedestrian density and the strength of attractive interaction, for example, in order to avoid situations involving extreme desire for limited resources.Peer reviewe

Jamming transitions induced by an attraction in pedestrian flow

We numerically study jamming transitions in pedestrian flow interacting with an attraction, mostly based on the social force model for pedestrians who can join the attraction. We formulate the joining probability as a function of social influence from others, reflecting that individual choice behavior is likely influenced by others. By controlling pedestrian influx and the social influence parameter, we identify various pedestrian flow patterns. For the bidirectional flow scenario, we observe a transition from the free flow phase to the freezing phase, in which oppositely walking pedestrians reach a complete stop and block each other. On the other hand, a different transition behavior appears in the unidirectional flow scenario, i.e., from the free flow phase to the localized jam phase and then to the extended jam phase. It is also observed that the extended jam phase can end up in freezing phenomena with a certain probability when pedestrian flux is high with strong social influence. This study highlights that attractive interactions between pedestrians and an attraction can trigger jamming transitions by increasing the number of conflicts among pedestrians near the attraction. In order to avoid excessive pedestrian jams, we suggest suppressing the number of conflicts under a certain level by moderating pedestrian influx especially when the social influence is strong.Peer reviewe

Multi-Signal Reconstruction Using Masked Autoencoder From EEG During Polysomnography

Polysomnography (PSG) is an indispensable diagnostic tool in sleep medicine, essential for identifying various sleep disorders. By capturing physiological signals, including EEG, EOG, EMG, and cardiorespiratory metrics, PSG presents a patient's sleep architecture. However, its dependency on complex equipment and expertise confines its use to specialized clinical settings. Addressing these limitations, our study aims to perform PSG by developing a system that requires only a single EEG measurement. We propose a novel system capable of reconstructing multi-signal PSG from a single-channel EEG based on a masked autoencoder. The masked autoencoder was trained and evaluated using the Sleep-EDF-20 dataset, with mean squared error as the metric for assessing the similarity between original and reconstructed signals. The model demonstrated proficiency in reconstructing multi-signal data. Our results present promise for the development of more accessible and long-term sleep monitoring systems. This suggests the expansion of PSG's applicability, enabling its use beyond the confines of clinics.Comment: Proc. 12th IEEE International Winter Conference on Brain-Computer Interfac

Impact of Nap on Performance in Different Working Memory Tasks Using EEG

Electroencephalography (EEG) has been widely used to study the relationship between naps and working memory, yet the effects of naps on distinct working memory tasks remain unclear. Here, participants performed word-pair and visuospatial working memory tasks pre- and post-nap sessions. We found marked differences in accuracy and reaction time between tasks performed pre- and post-nap. In order to identify the impact of naps on performance in each working memory task, we employed clustering to classify participants as high- or low-performers. Analysis of sleep architecture revealed significant variations in sleep onset latency and rapid eye movement (REM) proportion. In addition, the two groups exhibited prominent differences, especially in the delta power of the Non-REM 3 stage linked to memory. Our results emphasize the interplay between nap-related neural activity and working memory, underlining specific EEG markers associated with cognitive performance.Comment: Submitted to 2024 12th IEEE International Winter Conference on Brain-Computer Interfac