Selecting informative features, such as accurate biomarkers for disease diagnosis, prognosis and response to treatment, is an essential task in the field of bioinformatics. Medical data often contain thousands of features and identifying potential biomarkers is challenging due to small number of samples in the data, method dependence and non-reproducibility. This paper proposes a novel ensemble feature selection method, named Filter and Wrapper Stacking Ensemble (FWSE), to identify reproducible biomarkers from high-dimensional omics data. In FWSE, filter feature selection methods are run on numerous subsets of the data to eliminate irrelevant features, and then wrapper feature selection methods are applied to rank the top features. The method was validated on four high-dimensional medical datasets related to mental illnesses and cancer. The results indicate that the features selected by FWSE are stable and statistically more significant than the ones obtained by existing methods while also demonstrating biological relevance. Furthermore, FWSE is a generic method, applicable to various high-dimensional datasets in the fields of machine intelligence and bioinformatics.

The article demonstrates for the first time that a brain-inspired spiking neural network (SNN) architecture can be used not only to learn spatio-temporal data, but also to extract fuzzy spatio-temporal rules from such data and to update these rules incrementally in a transfer learning mode. We propose a method, where a SNN model learns incrementally new time-space data related to new classes/tasks/categories, always utilizing some previously learned knowledge, and presents the evolved knowledge as fuzzy spatio-temporal rules. Similarly, to how the brain manifests transfer learning, these SNN models do not need to be restricted in number of layers and neurons in each layer as they adopt self-organizing learning principles. The continuously evolved fuzzy rules from spatio-temporal data are interpretable for a better understanding of the processes that generate the data. The proposed method is based on a brain-inspired SNN architecture NeuCube, which is structured according to a brain three-dimensional structural template. It is illustrated on tasks of incremental and transfer learning and knowledge transfer using spatio-temporal data measuring brain activity, when subjects are performing tasks in space and time. The method is a general one and opens the field to create new types of adaptable and explainable spatio-temporal learning systems across domain areas.

Making good decisions at the top of a search tree is important for finding good solutions early in constraint optimization. In this paper, we propose a method employing frequent pattern mining (FPM), a classic datamining technique, to find good subtrees for solving constraint optimization problems. We demonstrate that applying FPM in a small number of random high-quality feasible solutions enables us to identify subtrees containing optimal solutions in more than 55% of problem instances for four real world benchmark problems. The method works as a plugin that can be combined with any search strategy for branch-and-bound search. Exploring the identified subtrees first, the method brings substantial improvements for four efficient search strategies in both total runtime and runtime of finding optimal solutions.

The paper proposes Maximum Residue (MR) as a notion to evaluate the strength of a symmetry breaking method. We give a proof to improve the best known DoubleLex MR upper bound from m!n! - (m!+n!) to min(m!,n!) for an m x n matrix model. Our result implies that DoubleLex works well on matrix models where min(m, n) is relatively small. We further study the MR bounds of SwapNext and SwapAny, which are extensions to DoubleLex breaking further a small number of composition symmetries. Such theoretical comparisons suggest general principles on selecting Lex-based symmetry breaking methods based on the dimensions of the matrix models. Our experiments confirm the theoretical predictions as well as efficiency of these methods.

Negative symptoms of schizophrenia are often associated with the blunting of emotional affect which creates a serious impediment in the daily functioning of the patients. Affective prosody is almost always adversely impacted in such cases, and is known to exhibit itself through the low-level acoustic signals of prosody. To automate and simplify the process of assessment of severity of emotion related symptoms of schizophrenia, we utilized these low-level acoustic signals to predict the expert subjective ratings assigned by a trained psychologist during an interview with the patient. Specifically, we extract acoustic features related to emotion using the openSMILE toolkit from the audio recordings of the interviews. We analysed the interviews of 78 paid participants (52 patients and 26 healthy controls) in this study. The subjective ratings could be accurately predicted from the objective openSMILE acoustic signals with an accuracy of 61-85% using machine-learning algorithms with leave-one-out cross-validation technique. Furthermore, these objective measures can be reliably utilized to distinguish between the patient and healthy groups, as supervised learning methods can classify the two groups with 79-86% accuracy.

Negative symptoms of schizophrenia significantly affect the daily functioning of patients, especially movement and expressive gestures. The diagnosis of such symptoms is often difficult and require the expertise of a trained clinician. Apart from these subjective methods, there is little research on developing objective methods to quantify the symptoms. Therefore, we explore body movement signals as objective measures of negative symptoms. Specifically, we extract the signals from video recordings of patients being interviewed. We analysed the interviews of 69 paid participants (46 patients and 23 healthy controls) in this study. Correlation between movement signals (linear and angular speeds of upper limbs and head, acceleration and gesture angles) and subjective ratings (assigned during same interview) from the NSA-16 scale were calculated. As hypothesized, the movement signals correlated strongly with the movement impairment aspect of the NSA-16 questionnaire. Also, not quite surprisingly, strong correlations were obtained between the movement signals and speech items of NSA-16, indicating lack of associated gestures in patients during speech. These subjective ratings could also be reasonably predicted from the objective signals with an accuracy of 61-78% using machine-learning algorithms with leave-one-out cross-validation technique. Furthermore, these objective measures can be reliably utilized to distinguish between the patient and healthy groups, as supervised learning methods can classify the two groups with 74-87% accuracy.

Negative symptoms in schizophrenia are associated with significant burden and functional impairment, especially speech production. In clinical practice today, there are no robust treatments for negative symptoms and one obstacle surrounding its research is the lack of an objective measure. To this end, we explore non-verbal speech cues as objective measures. Specifically, we extract these cues while schizophrenic patients are interviewed by psychologists. We have analyzed interviews of 15 patients who were enrolled in an observational study on the effectiveness of Cognitive Remediation Therapy (CRT). The subject (undergoing CRT) and control group (not undergoing CRT) contains 8 and 7 individuals respectively. The patients were recorded during three sessions while being evaluated for negative symptoms over a 12-week follow-up period. In order to validate the non-verbal speech cues, we computed their correlation with the Negative Symptom Assessment (NSA-16). Our results suggest a strong correlation between certain measures of the two rating sets. Supervised prediction of the subjective ratings from the non-verbal speech features with leave-one-person-out cross-validation has reasonable accuracy of 53-80%. Furthermore, the non-verbal cues can be used to reliably distinguish between the subjects and controls, as supervised learning methods can classify the two groups with 80-93% accuracy.