Disease-related concept mining by knowledge-based two-dimensional gene mapping

There is a strong need to systematically organize and comprehend the rapidly expanding stores of biomedical knowledge to formulate hypotheses on disease mechanisms. However, no method is available that automatically structuralizes fragmentary knowledge along with domain-specific expressions for a large-scale integration. A method presented here, cross-subspace analysis (CSA), produces a holistic view of over 3,000 human genes with a two-dimensional (2D) arrangement. The genes are plotted in relation to functions determined by machine learning from the occurrence patterns of various biomedical terms in MEDLINE abstracts. By focusing on the 2D distributions of gene plots that share the same biomedical concepts, as defined by databases such as Gene Ontology, relevant biomedical concepts can be computationally extracted. In an analysis where myocardial infarction and ischemic stroke were taken as examples, we found valid relations with lifestyle, diet-related metabolism, and host immune responses, all of which are known risk factors for the diseases. These results demonstrate that systematizing accumulated gene knowledge can lead to hypothesis generation and knowledge discovery, regardless of the area of inquiry or discipline.     

Instance-based concept learning from multiclass DNA microarray data

Background  

Various statistical and machine learning methods have been successfully applied to the classification of DNA microarray data. Simple instance-based classifiers such as nearest neighbor (NN) approaches perform remarkably well in comparison to more complex models, and are currently experiencing a renaissance in the analysis of data sets from biology and biotechnology. While binary classification of microarray data has been extensively investigated, studies involving multiclass data are rare. The question remains open whether there exists a significant difference in performance between NN approaches and more complex multiclass methods. Comparative studies in this field commonly assess different models based on their classification accuracy only; however, this approach lacks the rigor needed to draw reliable conclusions and is inadequate for testing the null hypothesis of equal performance. Comparing novel classification models to existing approaches requires focusing on the significance of differences in performance.     

Successive two-item same-different discrimination and concept learning by pigeons

Four pigeons were trained in a successive same/different procedure involving the alternation of two stimuli per trial. Using a go/no-go procedure, two different or two identical color photographs were alternated, with a brief, dark, inter-stimulus interval, on a computer screen for 20s. Pigeons learned to discriminate between same (S+) and different (D-) sequences with moderate to large contrasts between successive pictures. Analyses of pecking behavior within single trials revealed this discrimination emerged at the earliest possible point in the sequence (i.e. by the presentation of the second item). Pigeons transferred to novel color and gray-scale pictures, and showed savings in tests with novel video stimuli. These results suggest that same/different discrimination and concept formation can be acquired with successively presented pairs of stimuli by pigeons. When combined with results using simultaneous same/different presentations, these findings further support a qualitative similarity among birds and primates in their capacity to judge certain types of stimulus relations.     

生物学教学中引入概念图策略的实验研究

在一些国家,概念图作为有意义学习的一种有效策略已广泛研究和应用。以高中学生为研究对象,以概念图作为教与学的策略,研究了在生物学教学中使用概念图策略对于提高高中学生生物学学业成绩的效果。     

Use of concept mapping in an undergraduate introductory exercise physiology course

Physiology is often considered a challenging course for students. It is up to teachers to structure courses and create learning opportunities that will increase the chance of student success. In an undergraduate exercise physiology course, concept maps are assigned to help students actively process and organize information into manageable and meaningful chunks and to teach them to recognize the patterns and regularities of physiology. Students are first introduced to concept mapping with a commonly relatable nonphysiology concept and are then assigned a series of maps that become more and more complex. Students map the acute response to a drop in blood pressure, the causes of the acute increase in stroke volume during cardiorespiratory exercise, and the factors contributing to an increase in maximal O(2) consumption with cardiorespiratory endurance training. In the process, students draw the integrative nature of physiology, identify causal relationships, and learn about general models and core principles of physiology.     

On the application of the information concept to learning theory

A learning curve derived by H. D. Landahl (Bull. Math. Biophysics,3, 71–77, 1941) from postulated neurological structures is shown to be derivable from simplified assumptions by introducing the information measure of the uncertainty of response. The possible significance of this approach to learning theory is discussed.     

A ‘species identification’ approach to concept mapping in the classroom

ABSTRACT

The detailed analysis and scoring of concept maps may not be necessary in order for students to gain from their use in the classroom. A simplified recognition of different types (‘species’) of map may increase the likelihood of teachers employing maps in their classrooms so that more teachers and students might benefit from concept mapping on a regular basis. A greater familiarity and level of engagement with concept maps is likely to support an increase in the level of mapping expertise developed by both teachers and students, enabling maps to be used to support higher order thinking skills – as intended. The counter-intuitive conclusion to this prospect is that the adoption of a non-analytical consideration of maps may actually make them a more valuable classroom asset. However, this requires a greater level of expertise in the application of concept maps on the part of the teacher. A simplified typology of ‘map species’ is presented to support the development of this perspective.     

Distance learning techniques for ontology similarity measuring and ontology mapping

Recent years, a large amount of ontology learning algorithms have been applied in different disciplines and engineering. The ontology model is presented as a graph and the key of ontology algorithms is similarity measuring between concepts. In the learning frameworks, the information of each ontology vertex is expressed as a vector, thus the similarity measuring can be determined via the distance of the corresponding vector. In this paper, we study how to get an optimal distance function in the ontology setting. The tricks we presented are divided into two parts: first, the ontology distance learning technology in the setting that the ontology data have no labels; then, the distance learning approaches in the setting that the given ontology data are carrying real numbers as their labels. The result data of the four simulation experiments reveal that our new ontology trick has high efficiency and accuracy in ontology similarity measure and ontology mapping in special engineering applications.     

Vasopressin analog (DDAVP) facilitates concept learning in human males

The effects of desmopressin acetate (DDAVP) were studied in normal males. Subjects were given 60μg of DDAVP, a placebo, or no treatment and were given several behavioral tests. DDAVP enhanced learning of all problems on a concept shift task but had no effect on visual memory, anxiety, blood pressure or heart rate. It was suggested that DDAVP may influence memory via its actions on attention.     

Same/different concept learning by capuchin monkeys in matching-to-sample tasks

The ability to understand similarities and analogies is a fundamental aspect of human advanced cognition. Although subject of considerable research in comparative cognition, the extent to which nonhuman species are capable of analogical reasoning is still debated. This study examined the conditions under which tufted capuchin monkeys (Cebus apella) acquire a same/different concept in a matching-to-sample task on the basis of relational similarity among multi-item stimuli. We evaluated (i) the ability of five capuchin monkeys to learn the same/different concept on the basis of the number of items composing the stimuli and (ii) the ability to match novel stimuli after training with both several small stimulus sets and a large stimulus set. We found the first evidence of same/different relational matching-to-sample abilities in a New World monkey and demonstrated that the ability to match novel stimuli is within the capacity of this species. Therefore, analogical reasoning can emerge in monkeys under specific training conditions.     

Mechanisms of same/different concept learning in primates and avians

Mechanisms of same/different concept learning by rhesus monkeys, capuchin monkeys, and pigeons were studied in terms of how these species learned the task (e.g., item-specific learning versus relational learning) and how rapidly they learned the abstract concept, as the training set size was doubled. They had similar displays, training stimuli, test stimuli, and contingencies. The monkey species learned the abstract concept at similar rates and more rapidly than pigeons, thus showing a quantitative difference across species. All species eventually showed full concept learning (novel-stimulus transfer equivalent to baseline: 128-item set size for monkeys; 256-item set for pigeons), thus showing a qualitative similarity across species. Issues of stimulus regularity/symmetry, generalization from item pairs, and familiarity processing were not considered to be major factors in the final performances, converging on the conclusion that these species were increasingly controlled by the sample-test relationship (i.e., relational processing) leading to full abstract-concept learning.     

Association mapping and fine mapping with TreeLD

SUMMARY: The program package TreeLD implements a unified approach to association mapping and fine mapping of complex trait loci and a novel approach to visualizing association data, based on an inferred ancestry of the sample. Fundamentally, the TreeLD approach is based on the idea that the evidence for association at a particular position is contained in the ancestral tree relating the sampled chromosomes at that position. TreeLD provides an easy-to-use interface and can be applied to case-control, TDT trio and quantitative trait data.     

Quantitative concept mapping in pulmonary physiology: comparison of student and faculty knowledge structures

Quantitative concept mapping, in contrast with qualitative approaches, is rigorous scientifically and permits statistical analyses of data about concept learning. This study extends past quantitative research on the structure of student concept learning in pulmonary physiology. Pathfinder scaling is used to derive concept maps for medical and veterinary students and their physiology instructors at Northwestern University and the University of Wisconsin, respectively. The concept maps are evaluated for coherence (internal consistency), student-instructor similarity, and correlation of similarity with final examination scores. Results show that student and instructor concept maps are coherent and that student concept maps become increasingly similar to instructors' concept maps from pre- to postinstruction, but that student-instructor concept map similarity does not correlate with examination performance. Research outcomes are discussed concerning possible sources of variation in student and faculty knowledge structures.