Fusion Techniques in Biomedical Information Retrieval

For difficult cases clinicians usually use their experience and also the information found in textbooks to determine a diagnosis. Computer tools can help them supply the relevant information now that much medical knowledge is available in digital form. A biomedical search system such as developed in the Khresmoi project (that this chapter partially reuses) has the goal to fulfil information needs of physicians. This chapter concentrates on information needs for medical cases that contain a large variety of data, from free text, structured data to images. Fusion techniques will be compared to combine the various information sources to supply cases similar to an example case given. This can supply physicians with answers to problems similar to the one they are analyzing and can help in diagnosis and treatment planning

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Global lake responses to climate change

Climate change is one of the most severe threats to global lake ecosystems. Lake surface conditions, such as ice cover, surface temperature, evaporation and water level, respond dramatically to this threat, as observed in recent decades. In this Review, we discuss physical lake variables and their responses to climate change. Decreases in winter ice cover and increases in lake surface temperature modify lake mixing regimes and accelerate lake evaporation. Where not balanced by increased mean precipitation or inflow, higher evaporation rates will favour a decrease in lake level and surface water extent. Together with increases in extreme-precipitation events, these lake responses will impact lake ecosystems, changing water quantity and quality, food provisioning, recreational opportunities and transportation. Future research opportunities, including enhanced observation of lake variables from space (particularly for small water bodies), improved in situ lake monitoring and the development of advanced modelling techniques to predict lake processes, will improve our global understanding of lake responses to a changing climate

The scientific legacy of Harold Edwin Hurst (1880\u20131978)

Emanating from his remarkable characterization of long-term variability in geophysical records in the early 1950s, Hurst\u2019s scientific legacy to hydrology and other disciplines is explored. A statistical explanation of the so-called \u201cHurst Phenomenon\u201d did not emerge until 1968 when Mandelbrot and co-authors proposed fractional Gaussian noise based on the hypothesis of infinite memory. A vibrant hydrological literature ensued where alternative modelling representations were explored and debated, e.g. ARMA models, the Broken Line model, shifting mean models with no memory, FARIMA models, and Hurst-Kolmogorov dynamics, acknowledging a link with the work of Kolmogorov in 1940. The diffusion of Hurst\u2019s work beyond hydrology is summarized by discipline and citations, showing that he arguably has the largest scientific footprint of any hydrologist in the last century. Its particular relevance to the modelling of long-term climatic variability in the era of climate change is discussed. Links to various long-term modes of variability in the climate system, driven by fluctuations in sea surface temperatures and ocean dynamics, are explored. Several issues related to the Hurst Phenomenon in hydrology remain as a challenge for future research. Editor M. Acreman; Associate editor A. Carstean