Automatic Generation of Cognitive Theories using Genetic Programming

Cognitive neuroscience is the branch of neuroscience that studies the neural mechanisms underpinning cognition and develops theories explaining them. Within cognitive neuroscience, computational neuroscience focuses on modeling behavior, using theories expressed as computer programs. Up to now, computational theories have been formulated by neuroscientists. In this paper, we present a new approach to theory development in neuroscience: the automatic generation and testing of cognitive theories using genetic programming. Our approach evolves from experimental data cognitive theories that explain “the mental program” that subjects use to solve a specific task. As an example, we have focused on a typical neuroscience experiment, the delayed-match-to-sample (DMTS) task. The main goal of our approach is to develop a tool that neuroscientists can use to develop better cognitive theories

Evolving structure-function mappings in cognitive neuroscience using genetic programming

A challenging goal of psychology and neuroscience is to map cognitive functions onto neuroanatomical structures. This paper shows how computational methods based upon evolutionary algorithms can facilitate the search for satisfactory mappings by efficiently combining constraints from neuroanatomy and physiology (the structures) with constraints from behavioural experiments (the functions). This methodology involves creation of a database coding for known neuroanatomical and physiological constraints, for mental programs made of primitive cognitive functions, and for typical experiments with their behavioural results. The evolutionary algorithms evolve theories mapping structures to functions in order to optimize the fit with the actual data. These theories lead to new, empirically testable predictions. The role of the prefrontal cortex in humans is discussed as an example. This methodology can be applied to the study of structures or functions alone, and can also be used to study other complex systems. (This article does not exactly replicate the final version published in the Journal of Swiss Psychology. It is not a copy of the original published article and is not suitable for citation.

RegenBase: a knowledge base of spinal cord injury biology for translational research.

Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. SCI experimental methods, data and domain knowledge are locked in the largely unstructured text of scientific publications, making large scale integration with existing bioinformatics resources and subsequent analysis infeasible. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources. By querying RegenBase, we have identified novel biological hypotheses linking the effects of perturbagens to observed behavioral outcomes after SCI. RegenBase is publicly available for browsing, querying and download.Database URL:http://regenbase.org

Online Resources for Identifying Evidence-Based, Out-of-School Time Programs: A User's Guide

Summarizes general information, select program outcomes, and evidence levels of searchable databases, interactive summaries, and documents online on evidence-based intervention programs. Outlines considerations and assessments for selecting programs

N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana

Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N termini encoded in the Arabidopsis thaliana genome. After a stringent false discovery rate filtering, 117 protein N termini compliant with N-terminal methionine excision specificity and indicative of translation initiation were found. These include N-terminal protein extensions and translation from transposable elements and pseudogenes. Gene prediction provided supporting protein-coding models for approximately half of the protein N termini. Besides the prediction of functional domains (partially) contained within the newly predicted ORFs, further supporting evidence of translation was found in the recently released Araport11 genome re-annotation of Arabidopsis and computational translations of sequences stored in public repositories. Most interestingly, complementary evidence by ribosome profiling was found for 23 protein N termini. Finally, by analyzing protein N-terminal peptides, an in silico analysis demonstrates the applicability of our N-terminal proteogenomics strategy in revealing protein-coding potential in species with well-and poorly-annotated genomes

Understanding the Internet: Model, Metaphor, and Analogy

published or submitted for publicatio

Characterizing lab instructors' self-reported learning goals to inform development of an experimental modeling skills assessment

The ability to develop, use, and refine models of experimental systems is a nationally recognized learning outcome for undergraduate physics lab courses. However, no assessments of students' model-based reasoning exist for upper-division labs. This study is the first step toward development of modeling assessments for optics and electronics labs. In order to identify test objectives that are likely relevant across many institutional contexts, we interviewed 35 lab instructors about the ways they incorporate modeling in their course learning goals and activities. The study design was informed by the Modeling Framework for Experimental Physics. This framework conceptualizes modeling as consisting of multiple subtasks: making measurements, constructing system models, comparing data to predictions, proposing causes for discrepancies, and enacting revisions to models or apparatus. We found that each modeling subtask was identified by multiple instructors as an important learning outcome for their course. Based on these results, we argue that test objectives should include probing students' competence with most modeling subtasks, and test items should be designed to elicit students' justifications for choosing particular modeling pathways. In addition to discussing these and other implications for assessment, we also identify future areas of research related to the role of modeling in optics and electronics labs.Comment: 24 pages, 2 figures, 5 tables; submitted to Phys. Rev. PE

A Rigorous Evaluation of Family Finding in North Carolina

Child Trends evaluated Family Finding services in nine North Carolina counties through a rigorous impact evaluation and an accompanying process study. The impact evaluation involved random assignment of eligible children to a treatment or control group. The treatment group received Family Finding services in addition to traditional child welfare services, whereas the control group received traditional child welfare services only. Eligible children were in foster care; were 10 or older at the time of referral; did not have a goal of reunification; and lacked an identified permanent placement. The accompanying process study examined program outputs, outcomes, and linkages between the project components and other contextual factors