Biology subjects

Hahn, U.

Publications and source records attributed to Hahn, U..

3 recordsLinked to original sources

bioRxiv2022

GePI: Retrieval of fully automated recognition and extraction of gene and protein interaction mentions from unstructured literature

MotivationKnowledge about interactions between genes and proteins is vital for bio-molecular research. A large part of this knowledge is published in written text and not accessible in a structured way. To remedy this situation, several repositories of automatically extracted interaction facts were proposed over the years. However, existing solutions lack key features such as permanently updated data resources, easy accessibility and structured result generation ready to be used for downstream analyses. ResultsWe propose GePI, a database portal for fully automated extraction and presentation of molecular interaction facts from scientific literature. GePI offers batch queries, immediate inspection of textual evidence and full text filters. To this end, GePI leverages two gene recognition and normalization approaches as well as optimized runtime for molecular event extraction. The resulting natural language processing pipeline is applied to the full set of publicly available documents from PubMed and the PubMed Central open access subset accounting for more than 33M abstracts and 4.2M complete articles as of 2022. To accommodate the rapid growth of the scientific literature, the fact database is automatically updated several times per week. In summary, our web application GePI allows for the first time a free and easy-to-use investigation of gene and protein interaction information as soon as they are published with unique query possibilities. Availability and ImplementationThe GePI web interface is available at http://gepi.coling.uni-jena.de. Contacterik.faessler@uni-jena.de

bioinformatics↗

bioRxiv2022

The limited place in cognitive space

The idea that objects can be represented within multi-dimensional cognitive spaces remains popular within psychology and neuroscience, and yet the restrictive topology of such spaces is seldom considered. Here, we show that it is possible, even within a simple set of items, to break such models by imposing neighbourhood relations that are incompatible with a purely spatial representation. These results highlight the fundamental limits of cognitive space as a representational format for complex cognition.

neuroscience↗

bioRxiv2021

On the generality and cognitive basis of base-rate neglect

Base rate neglect refers to peoples apparent tendency to underweight or even ignore base rate information when estimating posterior probabilities for events, such as the probability that a person with a positive cancer-test outcome actually does have cancer. While often replicated, almost all evidence for the phenomenon comes from studies that used problems with extremely low base rates, high hit rates, and low false alarm rates. It is currently unclear whether the effect generalizes to reasoning problems outside this "corner" of the entire problem space. Another limitation of previous studies is that they have focused on describing empirical patterns of the effect at the group level and not so much on the underlying strategies and individual differences. Here, we address these two limitations by testing participants on a broader problem space and modelling their responses at a single-participant level. We find that the empirical patterns that have served as evidence for base-rate neglect generalize to a larger problem space, albeit with large individual differences in the extent with which participants "neglect" base rates. In particular, we find a bi-modal distribution consisting of one group of participants who almost entirely ignore the base rate and another group who almost entirely account for it. This heterogeneity is reflected in the cognitive modeling results: participants in the former group were best captured by a linear-additive model, while participants in the latter group were best captured by a Bayesian model. We find little evidence for heuristic models. Altogether, these results suggest that the effect known as "base-rate neglect" generalizes to a large set of reasoning problems, but varies largely across participants and may need a reinterpretation in terms of the underlying cognitive mechanisms.

animal behavior and cognition↗