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Motivation: Biomedical named-entity normalization involves connecting biomedical entities with distinct database identifiers in order to facilitate data integration across various fields of biology. Existing systems for biomedical named…
Ranking functions in information retrieval are often used in search engines to recommend the relevant answers to the query. This paper makes use of this notion of information retrieval and applies onto the problem domain of cognate…
Evaluating natural language generation models, particularly for method name prediction, poses significant challenges. A robust metric must account for the versatility of method naming, considering both semantic and syntactic variations.…
Funding acknowledgments in scholarly publications provide large-scale trace data on organizations that support scientific research. We present a dataset for linking global science funding organizations to research publications by…
The use of children's drawings to examining their conceptual understanding has been proven to be an effective method, but there are two major problems with previous research: 1. The content of the drawings heavily relies on the task, and…
Advances in bio-technology have made available massive amounts of functional, structural and genomic data for many biological sequences. This increased availability of heterogeneous biological data has resulted in biological applications…
Generating rationales that justify scoring decisions has been a promising way to facilitate explainability in automated scoring systems. However, existing methods do not match the accuracy of classifier-based methods. Plus, the generated…
Determining spatial distributions of species and communities are key objectives of ecology and conservation. Joint species distribution models use multi-species detection-nondetection data to estimate species and community distributions.…
The ability of Large Language Models (LLMs) to perform reasoning tasks such as deduction has been widely investigated in recent years. Yet, their capacity to generate proofs-faithful, human-readable explanations of why conclusions…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
Decision trees are widely used for non-linear modeling, as they capture interactions between predictors while producing inherently interpretable models. Despite their popularity, performing inference on the non-linear fit remains largely…
Efficient and accurate bird sound classification is of important for ecology, habitat protection and scientific research, as it plays a central role in monitoring the distribution and abundance of species. However, prevailing methods…
The automatic disambiguation of word senses (i.e., the identification of which of the meanings is used in a given context for a word that has multiple meanings) is essential for such applications as machine translation and information…
Relational knowledge bases (KBs) are commonly used to represent world knowledge in machines. However, while advantageous for their high degree of precision and interpretability, KBs are usually organized according to manually-defined…
While information from the field of linguistic typology has the potential to improve performance on NLP tasks, reliable typological data is a prerequisite. Existing typological databases, including WALS and Grambank, suffer from…
Multilingual Alignment is an effective and representative paradigm to enhance LLMs' multilingual capabilities, which transfers the capabilities from the high-resource languages to the low-resource languages. Meanwhile, some research on…
Categories such as animal or furniture are acquired at an early age and play an important role in processing, organizing, and communicating world knowledge. Categories exist across cultures: they allow to efficiently represent the…
In this thesis, we present two approaches to a rigorous mathematical and algorithmic foundation of quantitative and statistical inference in constraint-based natural language processing. The first approach, called quantitative constraint…
Human explanations of natural language, rationales, form a tool to assess whether models learn a label for the right reasons or rely on dataset-specific shortcuts. Sufficiency is a common metric for estimating the informativeness of…
As large language models (LLMs) continue to advance, ensuring their alignment with human values becomes increasingly critical. Traditional alignment methods heavily rely on human feedback to fine-tune models. With the emergence of…