The combined effect of fundamental results about neurocognitive processes and advancements in decoding mental states from ongoing brain signals has brought forth a whole range of potential neurotechnological applications. In this article, we review our developments in this area and put them into perspective. These examples cover a wide range of maturity levels with respect to their applicability. While we assume we are still a long way away from integrating Brain-Computer Interface (BCI) technology in general interaction with computers, or from implementing neurotechnological measures in safety-critical workplaces, results have already now been obtained involving a BCI as research tool. In this article, we discuss the reasons why, in some of the prospective application domains, considerable effort is still required to make the systems ready to deal with the full complexity of the real world.

Motivation Inferring the properties of a protein from its amino acid sequence is one of the key problems in bioinformatics. Most state-of-the-art approaches for protein classification are tailored to single classification tasks and rely on handcrafted features, such as position-specific-scoring matrices from expensive database searches. We argue that this level of performance can be reached or even be surpassed by learning a task-agnostic representation once, using self-supervised language modeling, and transferring it to specific tasks by a simple fine-tuning step. Results We put forward a universal deep sequence model that is pre-trained on unlabeled protein sequences from Swiss-Prot and fine-tuned on protein classification tasks. We apply it to three prototypical tasks, namely enzyme class prediction, gene ontology prediction and remote homology and fold detection. The proposed method performs on par with state-of-the-art algorithms that were tailored to these specific tasks or, for two out of three tasks, even outperforms them. These results stress the possibility of inferring protein properties from the sequence alone and, on more general grounds, the prospects of modern natural language processing methods in omics. Moreover, we illustrate the prospects for explainable machine learning methods in this field by selected case studies. Availability and implementation Source code is available under https://github.com/nstrodt/UDSMProt. Supplementary information Supplementary data are available at Bioinformatics online.

Motivation:Inferring the properties of a protein from its amino acid sequence is one of the key problems in bioinformatics. Most state-of-the-art approaches for protein classification tasks are tailored to single classification tasks and rely on handcrafted features such as position-specific-scoring matrices from expensive database searches. We argue that this level of performance can be reached or even be surpassed by learning a task-agnostic representation once, using self-supervised language modeling, and transferring it to specific tasks by a simple finetuning step. Results: We put forward a universal deep sequence model that is pretrained on unlabeled protein sequences from Swiss-Prot and finetuned on protein classification tasks. We apply it to three prototypical tasks, namely enzyme class prediction, gene ontology prediction and remote homology and fold detection. The proposed method performs on par with state-of-the-art algorithms that were tailored to these specific tasks or, for two out of three tasks, even outperforms them. These results stress the possibility of inferring protein properties from the sequence alone and, on more general grounds, the prospects of modern natural language processing methods in omics. Availability: Source code is available under https://github.com/nstrodt/UDSMProt.

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It is a vital ability of humans to flexibly adapt their behavior to different environmental situations. Constantly, the rules for our sensoryto-motor mappings need to be adapted to the current task demands. For example, the same sensory input might require two different motor responses depending on the actual situation. How does the brain prepare for such different responses? It has been suggested that the functional connections within cortex are biased according to the present rule to guide the flow of information in accordance with the required sensory-to-motor mapping. Here, we investigated with fMRI whether task settings might indeed change the functional connectivity structure in a large-scale brain network. Subjects performed a visuomotor response task that required an interaction between visual and motor cortex: either within each hemisphere or across the two hemispheres of the brain depending on the task condition. A multivariate analysis on the functional connectivity graph of a cortical visuomotor network revealed that the functional integration, i.e., the connectivity structure, is altered according to the task condition already during a preparatory period before the visual cue and the actual movement. Our results show that the topology of connection weights within a single network changes according to and thus predicts the upcoming task. This suggests that the human brain prepares to respond in different conditions by altering its large scale functional connectivity structure even before an action is required.

Objective: Electroencephalography (EEG) and eye tracking can possibly provide information about which items displayed on the screen are relevant for a person. Exploiting this implicit information promises to enhance various software applications. The specific problem addressed by the present study is that items shown in real applications are typically diverse. Accordingly, the saliency of information, which allows to discriminate between relevant and irrelevant items, varies. As a consequence, recognition can happen in foveal or in peripheral vision, i.e., either before or after the saccade to the item. Accordingly, neural processes related to recognition are expected to occur with a variable latency with respect to the eye movements. The aim was to investigate if relevance estimation based on EEG and eye tracking data is possible despite of the aforementioned variability.Approach:Sixteen subjects performed a search task where the target saliency was varied while the EEG was recorded and the unrestrained eye movements were tracked. Based on the acquired data, it was estimated which of the items displayed were targets and which were distractors in the search task.Results: Target prediction was possible also when the stimulus saliencies were mixed. Information contained in EEG and eye tracking data was found to be complementary and neural signals were captured despite of the unrestricted eye movements. The classification algorithm was able to cope with the experimentally induced variable timing of neural activity related to target recognition.Significance: It was demonstrated how EEG and eye tracking data can provide implicit information about the relevance of items on the screen for potential use in online applications.

Digital contact tracing approaches based on Bluetooth low energy (BLE) have the potential to efficiently contain and delay outbreaks of infectious diseases such as the ongoing SARS-CoV-2 pandemic. In this work we propose a machine learning based approach to reliably detect subjects that have spent enough time in close proximity to be at risk of being infected. Our study is an important proof of concept that will aid the battery of epidemiological policies aiming to slow down the rapid spread of COVID-19.

It was demonstrated that the interest of a reader can be inferred online from EEG and eye tracking signals, which can potentially be used in novel types of adaptive software, which enrich the interaction by adding implicit information about the interest of the user to the explicit interaction. The study is characterised by the following novelties. Interpretation with respect to the word meaning was necessary in contrast to the usual practice in brain-computer interfacing where stimulus recognition is sufficient. The typical counting task was avoided because it would not be sensible for implicit relevance detection. Several words were displayed at the same time, in contrast to the typical sequences of single stimuli. Neural activity was related with eye tracking to the words, which were scanned without restrictions on the eye movements.