The olfactory system is known to be associated with emotion during odor stimulation. A well-designed computational model that can correctly recognize preference induced by odor stimulation can be vital in the food and perfume industries. Electroencephalogram (EEG) can be used to study the brain's response to odor stimulation due to its good temporal resolution and low acquisition cost. In this study, we proposed a novel self-attention deep learning framework: Temporal Segment Attention Network (TESANet) to classify the brain state of subjects when they are exposed to pleasant and unpleasant odors. Odor stimulation is a continuous process, the temporal dynamics of the EEG signal should reflect the continuous changes of the brain responses to the given odor, thus we design the model to capture the intercorrelation between time segments of the EEG by utilizing the self-attention mechanism. TESANet consists of a filter-bank layer to extract spectral features, a spatial convolution layer to extract spatial features, a temporal segmentation layer to split the data into overlapping time windows, a Long Short-Term Memory (LSTM) layer to encode the temporal segments, a self-attention layer to decode the temporal dynamics by learning the intercorrelation between time segments, and finally a fully connected layer for classification. Experiments on an olfactory EEG dataset demonstrated that the proposed method outperforms other competing deep learning methods for odor pleasantness classification.

This work aims to develop an end-to-end solution for seizure onset detection. We design the SeizNet, a Convolutional Neural Network for seizure detection. To compare SeizNet with traditional machine learning approach, a baseline classifier is implemented using spectrum band power features with Support Vector Machines (BPsvm). We explore the possibility to use the least number of channels for accurate seizure detection by evaluating SeizNet and BPsvm approaches using all channels and two channels settings respectively. EEG Data is acquired from 29 pediatric patients admitted to KK Woman's and Children's Hospital who were diagnosed as typical absence seizures. We conduct leave-one-out cross validation for all subjects. Using full channel data, BPsvm yields a sensitivity of 86.6% and 0.84 false alarm (per hour) while SeizNet yields overall sensitivity of 95.8 % with 0.17 false alarm. More interestingly, two channels seizNet outperforms full channel BPsvm with a sensitivity of 93.3% and 0.58 false alarm. We further investigate interpretability of SeizNet by decoding the filters learned along convolutional layers. Seizure-like characteristics can be clearly observed in the filters from third and forth convolutional layers.

BACKGROUND: Computer-aided diagnosis for screening utilizes computer-based analytical methodologies to process patient information. Glaucoma is the leading irreversible cause of blindness. Due to the lack of an effective and standard screening practice, more than 50% of the cases are undiagnosed, which prevents the early treatment of the disease. OBJECTIVE: To design an automatic glaucoma diagnosis architecture automatic glaucoma diagnosis through medical imaging informatics (AGLAIA-MII) that combines patient personal data, medical retinal fundus image, and patient's genome information for screening. MATERIALS AND METHODS: 2258 cases from a population study were used to evaluate the screening software. These cases were attributed with patient personal data, retinal images and quality controlled genome data. Utilizing the multiple kernel learning-based classifier, AGLAIA-MII, combined patient personal data, major image features, and important genome single nucleotide polymorphism (SNP) features. RESULTS AND DISCUSSION: Receiver operating characteristic curves were plotted to compare AGLAIA-MII's performance with classifiers using patient personal data, images, and genome SNP separately. AGLAIA-MII was able to achieve an area under curve value of 0.866, better than 0.551, 0.722 and 0.810 by the individual personal data, image and genome information components, respectively. AGLAIA-MII also demonstrated a substantial improvement over the current glaucoma screening approach based on intraocular pressure. CONCLUSIONS: AGLAIA-MII demonstrates for the first time the capability of integrating patients' personal data, medical retinal image and genome information for automatic glaucoma diagnosis and screening in a large dataset from a population study. It paves the way for a holistic approach for automatic objective glaucoma diagnosis and screening.

Automatic medical image classification is difficult because of the lacking of training data. As manual labeling is too costly, we provide an automatic labeling solution to this problem by making use of the radiology report associated with the medical images. We first segment and reconstruct the 3D regions of interest (ROIs) from the medical images, and extract pathology and anatomy information from the associated report. We use an anatomical atlas to map the ROIs to the anatomy part(s) and match the pathology information of the same anatomy part(s) from the text. In this way, the ROIs are automatically labeled with pathology types which can be served as class labels, and a training data set of a large number of training instances is generated automatically. We extract the volume, color, location, and shape features of the ROIs, and classify the types of ROIs using these features. The overall evaluation result is promising to doctors and medical professionals. Our experiment is conducted using traumatic brain injury CT images; however, our framework of automatically labeling and classifying medical cases can be extended to medical images in other modality or of other anatomical part.

Computed tomography (CT) is used widely in traumatic brain injury diagnosis. One axial brain CT scan consists of multiple slices with different heights along the brain axial direction. Indexing of brain CT slices is to order the slices and align each individual slice onto the corresponding brain axial height, which is an important step in content-based image retrieval and computer-assisted diagnosis. Current existing methods for this indexing task are through the image registration techniques by registering 2D image slices onto a 3D brain atlas. In this paper, instead of using the registration methods, we propose a fast indexing method using anatomical feature classification. In our method, the brain CT scan is divided into 6 height levels along the axial direction so that slices in each level share similar anatomical structure. In this way, the indexing problem becomes a classification problem that one series of scan slices are to be classified into 6 classes. Experimental results show that the proposed method is effective and efficient.

Large number of medical images are produced daily in hospitals and medical institutions, the needs to efficiently process, index, search and retrieve these images are great. In this paper, we propose a pathology based medical image annotation framework using a statistical machine translation approach. After pathology terms and regions of interest (ROIs) are extracted from training text and images respectively, we use machine translation model IBM Model 1 to iteratively learn the alignment between the ROIs and the pathology terms and generate an ROI-to-pathology translation table. In testing phase, we annotate the ROI in the image with the pathology label of the highest probability in the translation table. The overall annotation results and the retrieval performance are promising to doctors and medical professionals.

This paper presents a photometric restoration technique that automatically corrects shading within retinal images taken with a fundus camera. The proposed technique is based on the observation that the background of retinal images usually shows flat reflectance variations due to its high similarity in color and texture. It estimates shading through an iterative polynomial interpolation procedure that first estimates a shading image through a horizontal interpolation process and then improves the shading estimation by a vertical interpolation process. Once the shading image is estimated, a reflectance image can accordingly be determined based on the luminance of the retina image under study. Experiments on 161 retinal images of different qualities show promising results.

In intracranial pathological examinations using CT scan, brain midline shift (MLS) is an important diagnostic feature indicating the pathological severity and patient's survival possibility. In this paper, we develop a new method of tracing the brain midline shift in traumatic brain injury (TBI) CT images using its original cause - the hemorrhage. Firstly, we model the relationship between the hemorrhage and the midline deformation caused by it using a linear regression model (H-MLS model). Secondly, using the H-MLS model, the deformed midline is predicted from the hemorrhage detected in CT images. Finally, the predicted deformed midline is adjusted according to the visual symmetry information. Preliminary experiments show that the proposed method is effective and time-efficient.

Medical text mining has gained increasing interest in recent years. Radiology reports contain rich information describing radiologistpsilas observations on the patientpsilas medical conditions in the associated medical images. However, as most reports are in free text format, the valuable information contained in those reports cannot be easily accessed and used, unless proper text mining has been applied. In this paper, we propose a text mining system to extract and use the information in radiology reports. The system consists of three main modules: a medical finding extractor, a report and image retriever, and a text-assisted image feature extractor. In evaluation, the overall precision and recall for medical finding extraction are 95.5% and 87.9% respectively, and for all modifiers of the medical findings 88.2% and 82.8% respectively. The overall result of report and image retrieval module and text-assisted image feature extraction module is satisfactory to radiologists.

Multi-slice computer tomography (CT) scans are widely used in todaypsilas diagnosis of head traumas. It is effective to disclose the bleeding and fractures. In this paper, we present an automated detection of CT scan slices which contain hemorrhages. Our method is robust towards various rotation, displacement and motion blur. Detection of these pathological slices will be useful for further diagnosis and retrieval.

MOTIVATION: Contrasts are useful conceptual vehicles for learning processes and exploratory research of the unknown. For example, contrastive information between proteins can reveal what similarities, divergences and relations there are of the two proteins, leading to invaluable insights for better understanding about the proteins. Such contrastive information are found to be reported in the biomedical literature. However, there have been no reported attempts in current biomedical text mining work that systematically extract and present such useful contrastive information from the literature for exploitation. RESULTS: Our BioContrasts system extracts protein-protein contrastive information from MEDLINE abstracts and presents the information to biologists in a web-application for exploitation. Contrastive information are identified in the text abstracts with contrastive negation patterns such as 'A but not B'. A total of 799 169 pairs of contrastive expressions were successfully extracted from 2.5 million MEDLINE abstracts. Using grounding of contrastive protein names to Swiss-Prot entries, we were able to produce 41 471 pieces of contrasts between Swiss-Prot protein entries. These contrastive pieces of information are then presented via a user-friendly interactive web portal that can be exploited for applications such as the refinement of biological pathways. AVAILABILITY: BioContrasts can be accessed at http://biocontrasts.i2r.a-star.edu.sg. It is also mirrored at http://biocontrasts.biopathway.org. SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.

MOTIVATION: The current need for high-throughput protein interaction detection has resulted in interaction data being generated en masse through such experimental methods as yeast-two-hybrids and protein chips. Such data can be erroneous and they often do not provide adequate functional information for the detected interactions. Therefore, it is useful to develop an in silico approach to further validate and annotate the detected protein interactions. RESULTS: Given that protein-protein interactions involve physical interactions between protein domains, domain-domain interaction information can be useful for validating, annotating, and even predicting protein interactions. However, large-scale, experimentally determined domain-domain interaction data do not exist. Here, we describe an integrative approach to computationally derive putative domain interactions from multiple data sources, including protein interactions, protein complexes, and Rosetta Stone sequences. We further prove the usefulness of such an integrative approach by applying the derived domain interactions to predict and validate protein-protein interactions. AVAILABILITY: A database of putative protein domain interactions derived using the method described in this paper is available at http://interdom.lit.org.sg.