How to understand the cell by breaking it: network analysis of gene perturbation screens

Modern high-throughput gene perturbation screens are key technologies at the forefront of genetic research. Combined with rich phenotypic descriptors they enable researchers to observe detailed cellular reactions to experimental perturbations on a genome-wide scale. This review surveys the current state-of-the-art in analyzing perturbation screens from a network point of view. We describe approaches to make the step from the parts list to the wiring diagram by using phenotypes for network inference and integrating them with complementary data sources. The first part of the review describes methods to analyze one- or low-dimensional phenotypes like viability or reporter activity; the second part concentrates on high-dimensional phenotypes showing global changes in cell morphology, transcriptome or proteome.Comment: Review based on ISMB 2009 tutorial; after two rounds of revisio

End-to-end Neural Coreference Resolution

We introduce the first end-to-end coreference resolution model and show that it significantly outperforms all previous work without using a syntactic parser or hand-engineered mention detector. The key idea is to directly consider all spans in a document as potential mentions and learn distributions over possible antecedents for each. The model computes span embeddings that combine context-dependent boundary representations with a head-finding attention mechanism. It is trained to maximize the marginal likelihood of gold antecedent spans from coreference clusters and is factored to enable aggressive pruning of potential mentions. Experiments demonstrate state-of-the-art performance, with a gain of 1.5 F1 on the OntoNotes benchmark and by 3.1 F1 using a 5-model ensemble, despite the fact that this is the first approach to be successfully trained with no external resources.Comment: Accepted to EMNLP 201

Research and Applications of the Processes of Performance Appraisal: A Bibliography of Recent Literature, 1981-1989

[Excerpt] There have been several recent reviews of different subtopics within the general performance appraisal literature. The reader of these reviews will find, however, that the accompanying citations may be of limited utility for one or more reasons. For example, the reference sections of these reviews are usually composed of citations which support a specific theory or practical approach to the evaluation of human performance. Consequently, the citation lists for these reviews are, as they must be, highly selective and do not include works that may have only a peripheral relationship to a given reviewer\u27s target concerns. Another problem is that the citations are out of date. That is, review articles frequently contain many citations that are fifteen or more years old. The generation of new studies and knowledge in this field occurs very rapidly. This creates a need for additional reference information solely devoted to identifying the wealth of new research, ideas, and writing that is changing the field

Sociohydrologic Systems Thinking: An Analysis of Undergraduate Students’ Operationalization and Modeling of Coupled Human-Water Systems

One of the keys to science and environmental literacy is systems thinking. Learning how to think about the interactions between systems, the far-reaching effects of a system, and the dynamic nature of systems are all critical outcomes of science learning. However, students need support to develop systems thinking skills in undergraduate geoscience classrooms. While systems thinking-focused instruction has the potential to benefit student learning, gaps exist in our understanding of students’ use of systems thinking to operationalize and model SHS, as well as their metacognitive evaluation of systems thinking. To address this need, we have designed, implemented, refined, and studied an introductory-level, interdisciplinary course focused on coupled human-water, or sociohydrologic, systems. Data for this study comes from three consecutive iterations of the course and involves student models and explanations for a socio-hydrologic issue (n = 163). To analyze this data, we counted themed features of the drawn models and applied an operationalization rubric to the written responses. Analyses of the written explanations reveal statistically-significant differences between underlying categories of systems thinking (F(5, 768) = 401.6, p \u3c 0.05). Students were best able to operationalize their systems thinking about problem identification (M = 2.22, SD = 0.73) as compared to unintended consequences (M = 1.43, SD = 1.11). Student-generated systems thinking models revealed statistically significant differences between system components, patterns, and mechanisms, F(2, 132) = 3.06, p \u3c 0.05. Students focused most strongly on system components (M = 13.54, SD = 7.15) as compared to related processes or mechanisms. Qualitative data demonstrated three types of model limitation including scope/scale, temporal, and specific components/mechanisms/patterns excluded. These findings have implications for supporting systems thinking in undergraduate geoscience classrooms, as well as insight into links between these two skills

Your click decides your fate: Inferring Information Processing and Attrition Behavior from MOOC Video Clickstream Interactions

In this work, we explore video lecture interaction in Massive Open Online Courses (MOOCs), which is central to student learning experience on these educational platforms. As a research contribution, we operationalize video lecture clickstreams of students into cognitively plausible higher level behaviors, and construct a quantitative information processing index, which can aid instructors to better understand MOOC hurdles and reason about unsatisfactory learning outcomes. Our results illustrate how such a metric inspired by cognitive psychology can help answer critical questions regarding students' engagement, their future click interactions and participation trajectories that lead to in-video & course dropouts. Implications for research and practice are discusse

1st INCF Workshop on Genetic Animal Models for Brain Diseases

The INCF Secretariat organized a workshop to focus on the “role of neuroinformatics in the processes of building, evaluating, and using genetic animal models for brain diseases” in Stockholm, December 13–14, 2009. Eight scientists specialized in the fields of neuroinformatics, database, ontologies, and brain disease participated together with two representatives of the National Institutes of Health and the European Union, as well as three observers of the national INCF nodes of Norway, Poland, and the United Kingdom

Improving fairness in machine learning systems: What do industry practitioners need?

The potential for machine learning (ML) systems to amplify social inequities and unfairness is receiving increasing popular and academic attention. A surge of recent work has focused on the development of algorithmic tools to assess and mitigate such unfairness. If these tools are to have a positive impact on industry practice, however, it is crucial that their design be informed by an understanding of real-world needs. Through 35 semi-structured interviews and an anonymous survey of 267 ML practitioners, we conduct the first systematic investigation of commercial product teams' challenges and needs for support in developing fairer ML systems. We identify areas of alignment and disconnect between the challenges faced by industry practitioners and solutions proposed in the fair ML research literature. Based on these findings, we highlight directions for future ML and HCI research that will better address industry practitioners' needs.Comment: To appear in the 2019 ACM CHI Conference on Human Factors in Computing Systems (CHI 2019