Moussab/ORKG-training-evaluation-set huggingface dataset:
Research field: Bioinformatics
Title: Integrated Assessment of Behavioral and Environmental Risk Factors for Lyme Disease Infection on Block Island, Rhode Island
Abstract: Peridomestic exposure to Borrelia burgdorferi-infected Ixodes scapularis nymphs is considered the dominant means of infection with black-legged tick-borne pathogens in the eastern United States. Population level studies have detected a positive association between the density of infected nymphs and Lyme disease incidence. At a finer spatial scale within endemic communities, studies have focused on individual level risk behaviors, without accounting for differences in peridomestic nymphal density. This study simultaneously assessed the influence of peridomestic tick exposure risk and human behavior risk factors for Lyme disease infection on Block Island, Rhode Island. Tick exposure risk on Block Island properties was estimated using remotely sensed landscape metrics that strongly correlated with tick density at the individual property level. Behavioral risk factors and Lyme disease serology were assessed using a longitudinal serosurvey study. Significant factors associated with Lyme disease positive serology included one or more self-reported previous Lyme disease episodes, wearing protective clothing during outdoor activities, the average number of hours spent daily in tick habitat, the subject’s age and the density of shrub edges on the subject’s property. The best fit multivariate model included previous Lyme diagnoses and age. The strength of this association with previous Lyme disease suggests that the same sector of the population tends to be repeatedly infected. The second best multivariate model included a combination of environmental and behavioral factors, namely hours spent in vegetation, subject’s age, shrub edge density (increase risk) and wearing protective clothing (decrease risk). Our findings highlight the importance of concurrent evaluation of both environmental and behavioral factors to design interventions to reduce the risk of tick-borne infections.
Extracted statement — uses: ENVI
Research field: Bioinformatics
Title: GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations
Abstract: Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics.
Extracted statement — creates: GEMINI
Research field: Bioinformatics
Title: GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations
Abstract: Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics.
Extracted statement — uses: GEMINI
Research field: Bioinformatics
Title: GINI: From ISH Images to Gene Interaction Networks
Abstract: Accurate inference of molecular and functional interactions among genes, especially in multicellular organisms such as Drosophila, often requires statistical analysis of correlations not only between the magnitudes of gene expressions, but also between their temporal-spatial patterns. The ISH (in-situ-hybridization)-based gene expression micro-imaging technology offers an effective approach to perform large-scale spatial-temporal profiling of whole-body mRNA abundance. However, analytical tools for discovering gene interactions from such data remain an open challenge due to various reasons, including difficulties in extracting canonical representations of gene activities from images, and in inference of statistically meaningful networks from such representations. In this paper, we present GINI, a machine learning system for inferring gene interaction networks from Drosophila embryonic ISH images. GINI builds on a computer-vision-inspired vector-space representation of the spatial pattern of gene expression in ISH images, enabled by our recently developed system; and a new multi-instance-kernel algorithm that learns a sparse Markov network model, in which, every gene (i.e., node) in the network is represented by a vector-valued spatial pattern rather than a scalar-valued gene intensity as in conventional approaches such as a Gaussian graphical model. By capturing the notion of spatial similarity of gene expression, and at the same time properly taking into account the presence of multiple images per gene via multi-instance kernels, GINI is well-positioned to infer statistically sound, and biologically meaningful gene interaction networks from image data. Using both synthetic data and a small manually curated data set, we demonstrate the effectiveness of our approach in network building. Furthermore, we report results on a large publicly available collection of Drosophila embryonic ISH images from the Berkeley Drosophila Genome Project, where GINI makes novel and interesting predictions of gene interactions. Software for GINI is available at http://sailing.cs.cmu.edu/Drosophila_ISH_images/
Extracted statement — creates: GINI
Research field: Bioinformatics
Title: GINI: From ISH Images to Gene Interaction Networks
Abstract: Accurate inference of molecular and functional interactions among genes, especially in multicellular organisms such as Drosophila, often requires statistical analysis of correlations not only between the magnitudes of gene expressions, but also between their temporal-spatial patterns. The ISH (in-situ-hybridization)-based gene expression micro-imaging technology offers an effective approach to perform large-scale spatial-temporal profiling of whole-body mRNA abundance. However, analytical tools for discovering gene interactions from such data remain an open challenge due to various reasons, including difficulties in extracting canonical representations of gene activities from images, and in inference of statistically meaningful networks from such representations. In this paper, we present GINI, a machine learning system for inferring gene interaction networks from Drosophila embryonic ISH images. GINI builds on a computer-vision-inspired vector-space representation of the spatial pattern of gene expression in ISH images, enabled by our recently developed system; and a new multi-instance-kernel algorithm that learns a sparse Markov network model, in which, every gene (i.e., node) in the network is represented by a vector-valued spatial pattern rather than a scalar-valued gene intensity as in conventional approaches such as a Gaussian graphical model. By capturing the notion of spatial similarity of gene expression, and at the same time properly taking into account the presence of multiple images per gene via multi-instance kernels, GINI is well-positioned to infer statistically sound, and biologically meaningful gene interaction networks from image data. Using both synthetic data and a small manually curated data set, we demonstrate the effectiveness of our approach in network building. Furthermore, we report results on a large publicly available collection of Drosophila embryonic ISH images from the Berkeley Drosophila Genome Project, where GINI makes novel and interesting predictions of gene interactions. Software for GINI is available at http://sailing.cs.cmu.edu/Drosophila_ISH_images/
Extracted statement — deposits: GINI
Research field: Bioinformatics
Title: IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform
Abstract: Since its identification in 1983, HIV-1 has been the focus of a research effort unprecedented in scope and difficulty, whose ultimate goals — a cure and a vaccine – remain elusive. One of the fundamental challenges in accomplishing these goals is the tremendous genetic variability of the virus, with some genes differing at as many as 40% of nucleotide positions among circulating strains. Because of this, the genetic bases of many viral phenotypes, most notably the susceptibility to neutralization by a particular antibody, are difficult to identify computationally. Drawing upon open-source general-purpose machine learning algorithms and libraries, we have developed a software package IDEPI (IDentify EPItopes) for learning genotype-to-phenotype predictive models from sequences with known phenotypes. IDEPI can apply learned models to classify sequences of unknown phenotypes, and also identify specific sequence features which contribute to a particular phenotype. We demonstrate that IDEPI achieves performance similar to or better than that of previously published approaches on four well-studied problems: finding the epitopes of broadly neutralizing antibodies (bNab), determining coreceptor tropism of the virus, identifying compartment-specific genetic signatures of the virus, and deducing drug-resistance associated mutations. The cross-platform Python source code (released under the GPL 3.0 license), documentation, issue tracking, and a pre-configured virtual machine for IDEPI can be found at https://github.com/veg/idepi.
Extracted statement — creates: IDEPI
Research field: Bioinformatics
Title: IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform
Abstract: Since its identification in 1983, HIV-1 has been the focus of a research effort unprecedented in scope and difficulty, whose ultimate goals — a cure and a vaccine – remain elusive. One of the fundamental challenges in accomplishing these goals is the tremendous genetic variability of the virus, with some genes differing at as many as 40% of nucleotide positions among circulating strains. Because of this, the genetic bases of many viral phenotypes, most notably the susceptibility to neutralization by a particular antibody, are difficult to identify computationally. Drawing upon open-source general-purpose machine learning algorithms and libraries, we have developed a software package IDEPI (IDentify EPItopes) for learning genotype-to-phenotype predictive models from sequences with known phenotypes. IDEPI can apply learned models to classify sequences of unknown phenotypes, and also identify specific sequence features which contribute to a particular phenotype. We demonstrate that IDEPI achieves performance similar to or better than that of previously published approaches on four well-studied problems: finding the epitopes of broadly neutralizing antibodies (bNab), determining coreceptor tropism of the virus, identifying compartment-specific genetic signatures of the virus, and deducing drug-resistance associated mutations. The cross-platform Python source code (released under the GPL 3.0 license), documentation, issue tracking, and a pre-configured virtual machine for IDEPI can be found at https://github.com/veg/idepi.
Extracted statement — deposits: IDEPI
Research field: Bioinformatics
Title: LINNAEUS: A species name identification system for biomedical literature
Abstract: Abstract Background The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles. Results In this paper we describe an open-source species name recognition and normalization software system, LINNAEUS, and evaluate its performance relative to several automatically generated biomedical corpora, as well as a novel corpus of full-text documents manually annotated for species mentions. LINNAEUS uses a dictionary-based approach (implemented as an efficient deterministic finite-state automaton) to identify species names and a set of heuristics to resolve ambiguous mentions. When compared against our manually annotated corpus, LINNAEUS performs with 94% recall and 97% precision at the mention level, and 98% recall and 90% precision at the document level. Our system successfully solves the problem of disambiguating uncertain species mentions, with 97% of all mentions in PubMed Central full-text documents resolved to unambiguous NCBI taxonomy identifiers. Conclusions LINNAEUS is an open source, stand-alone software system capable of recognizing and normalizing species name mentions with speed and accuracy, and can therefore be integrated into a range of bioinformatics and text-mining applications. The software and manually annotated corpus can be downloaded freely at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://linnaeus.sourceforge.net/" ext-link-type="uri">http://linnaeus.sourceforge.net/</jats:ext-link>.
Extracted statement — model: LINNAEUS
Research field: Bioinformatics
Title: Multi task sequence learning for depression scale prediction from video
Abstract: Depression is a typical mood disorder, which affects people in mental and even physical problems. People who suffer depression always behave abnormal in visual behavior and the voice. In this paper, an audio visual based multimodal depression scale prediction system is proposed. Firstly, features are extracted from video and audio are fused in feature level to represent the audio visual behavior. Secondly, long short memory recurrent neural network (LSTM-RNN) is utilized to encode the dynamic temporal information of the abnormal audio visual behavior. Thirdly, emotion information is utilized by multi-task learning to boost the performance further. The proposed approach is evaluated on the Audio-Visual Emotion Challenge (AVEC2014) dataset. Experiments results show the dimensional emotion recognition helps to depression scale prediction.
Extracted statement — Used models: LSTM
Research field: Bioinformatics
Title: Detection of mood disorder using speech emotion profiles and LSTM
Abstract: In mood disorder diagnosis, bipolar disorder (BD) patients are often misdiagnosed as unipolar depression (UD) on initial presentation. It is crucial to establish an accurate distinction between BD and UD to make a correct and early diagnosis, leading to improvements in treatment and course of illness. To deal with this misdiagnosis problem, in this study, we experimented on eliciting subjects' emotions by watching six eliciting emotional video clips. After watching each video clips, their speech responses were collected when they were interviewing with a clinician. In mood disorder detection, speech emotions play an import role to detect manic or depressive symptoms. Therefore, speech emotion profiles (EP) are obtained by using the support vector machine (SVM) which are built via speech features adapted from selected databases using a denoising autoencoder-based method. Finally, a Long Short-Term Memory (LSTM) recurrent neural network is employed to characterize the temporal information of the EPs with respect to six emotional videos. Comparative experiments clearly show the promising advantage and efficacy of the LSTM-based approach for mood disorder detection.
Extracted statement — Used models: LSTM
Research field: Bioinformatics
Title: DepAudioNet: An Efficient Deep Model for Audio based Depression Classification
Abstract: This paper presents a novel and effective audio based method on depression classification. It focuses on two important issues, \emph{i.e.} data representation and sample imbalance, which are not well addressed in literature. For the former one, in contrast to traditional shallow hand-crafted features, we propose a deep model, namely DepAudioNet, to encode the depression related characteristics in the vocal channel, combining Convolutional Neural Network (CNN) and Long Short-Term Memory (LSTM) to deliver a more comprehensive audio representation. For the latter one, we introduce a random sampling strategy in the model training phase to balance the positive and negative samples, which largely alleviates the bias caused by uneven sample distribution. Evaluations are carried out on the DAIC-WOZ dataset for the Depression Classification Sub-challenge (DCC) at the 2016 Audio-Visual Emotion Challenge (AVEC), and the experimental results achieved clearly demonstrate the effectiveness of the proposed approach.
Extracted statement — Used models: LSTM
Research field: Bioinformatics
Title: Mood disorder identification using deep bottleneck features of elicited speech
Abstract: In the diagnosis of mental health disorder, a large portion of the Bipolar Disorder (BD) patients is likely to be misdiagnosed as Unipolar Depression (UD) on initial presentation. As speech is the most natural way to express emotion, this work focuses on tracking emotion profile of elicited speech for short-term mood disorder identification. In this work, the Deep Scattering Spectrum (DSS) and Low Level Descriptors (LLDs) of the elicited speech signals are extracted as the speech features. The hierarchical spectral clustering (HSC) algorithm is employed to adapt the emotion database to the mood disorder database to alleviate the data bias problem. The denoising autoencoder is then used to extract the bottleneck features of DSS and LLDs for better representation. Based on the bottleneck features, a long short term memory (LSTM) is applied to generate the time-varying emotion profile sequence. Finally, given the emotion profile sequence, the HMM-based identification and verification model is used to determine mood disorder. This work collected the elicited emotional speech data from 15 BDs, 15 UDs and 15 healthy controls for system training and evaluation. Five-fold cross validation was employed for evaluation. Experimental results show that the system using the bottleneck feature achieved an identification accuracy of 73.33%, improving by 8.89%, compared to that without bottleneck features. Furthermore, the system with verification mechanism, improving by 4.44%, outperformed that without verification.
Extracted statement — Used models: LSTM
Research field: Bioinformatics
Title: Exploring microscopic fluctuation of facial expression for mood disorder classification
Abstract: In clinical diagnosis of mood disorder, depression is one of the most common psychiatric disorders. There are two major types of mood disorders: major depressive disorder (MDD) and bipolar disorder (BPD). A large portion of BPD are misdiagnosed as MDD in the diagnostic of mood disorders. Short-term detection which could be used in early detection and intervention is thus desirable. This study investigates microscopic facial expression changes for the subjects with MDD, BPD and control group (CG), when elicited by emotional video clips. This study uses eight basic orientations of motion vector (MV) to characterize the subtle changes in microscopic facial expression. Then, wavelet decomposition is applied to extract entropy and energy of different frequency bands. Next, an autoencoder neural network is adopted to extract the bottleneck features for dimensionality reduction. Finally, the long short term memory (LSTM) is employed for modeling the long-term variation among different mood disorders types. For evaluation of the proposed method, the elicited data from 36 subjects (12 for each of MDD, BPD and CG) were considered in the K-fold (K=12) cross validation experiments, and the performance for distinguishing among MDD, BPD and CG achieved 67.7% accuracy.
Extracted statement — Used models: LSTM
Research field: Bioinformatics
Title: Cell-Coupled Long Short-Term Memory With $L$ -Skip Fusion Mechanism for Mood Disorder Detection Through Elicited Audiovisual Features
Abstract: In early stages, patients with bipolar disorder are often diagnosed as having unipolar depression in mood disorder diagnosis. Because the long-term monitoring is limited by the delayed detection of mood disorder, an accurate and one-time diagnosis is desirable to avoid delay in appropriate treatment due to misdiagnosis. In this paper, an elicitation-based approach is proposed for realizing a one-time diagnosis by using responses elicited from patients by having them watch six emotion-eliciting videos. After watching each video clip, the conversations, including patient facial expressions and speech responses, between the participant and the clinician conducting the interview were recorded. Next, the hierarchical spectral clustering algorithm was employed to adapt the facial expression and speech response features by using the extended Cohn–Kanade and eNTERFACE databases. A denoizing autoencoder was further applied to extract the bottleneck features of the adapted data. Then, the facial and speech bottleneck features were input into support vector machines to obtain speech emotion profiles (EPs) and the modulation spectrum (MS) of the facial action unit sequence for each elicited response. Finally, a cell-coupled long short-term memory (LSTM) network with an $L$ -skip fusion mechanism was proposed to model the temporal information of all elicited responses and to loosely fuse the EPs and the MS for conducting mood disorder detection. The experimental results revealed that the cell-coupled LSTM with the $L$ -skip fusion mechanism has promising advantages and efficacy for mood disorder detection.
Extracted statement — Used models: LSTM