相关论文: Principal Component Analysis as a Sanity Check for…
Retrieval Augmented Generation or RAG is the most popular pattern for modern Large Language Model or LLM applications. RAG involves taking a user query and finding relevant paragraphs of context in a large corpus typically captured in a…
The ability to compositionally map language to referents, relations, and actions is an essential component of language understanding. The recent gSCAN dataset (Ruis et al. 2020, NeurIPS) is an inspiring attempt to assess the capacity of…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
Statistical analysis is the tool of choice to turn data into information, and then information into empirical knowledge. To be valid, the process that goes from data to knowledge should be supported by detailed, rigorous guidelines, which…
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…
In high-dimensional prediction problems, where the number of features may greatly exceed the number of training instances, fully Bayesian approach with a sparsifying prior is known to produce good results but is computationally challenging.…
Lack of repeatability and generalisability are two significant threats to continuing scientific development in Natural Language Processing. Language models and learning methods are so complex that scientific conference papers no longer…
Bayesian networks faithfully represent the symmetric conditional independences existing between the components of a random vector. Staged trees are an extension of Bayesian networks for categorical random vectors whose graph represents…
Principal component analysis (PCA) is a tool to capture factors that explain variation in data. Across domains, data are now collected across multiple contexts (for example, individuals with different diseases, cells of different types, or…
We use the persistent homology method of topological data analysis and dimensional analysis techniques to study data of syntactic structures of world languages. We analyze relations between syntactic parameters in terms of dimensionality,…
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…
Tree-based priors for probability distributions are usually specified using a predetermined, data-independent collection of candidate recursive partitions of the sample space. To characterize an unknown target density in detail over the…
Principal Component Analysis (PCA) is one of the most used tools for extracting low-dimensional representations of data, in particular for time series. Performances are known to strongly depend on the quality (amount of noise) and the…
The diagnosis of cyber-physical systems aims to detect faulty behaviour, its root cause and a mitigation or even prevention policy. Therefore, diagnosis relies on a representation of the system's functional and faulty behaviour combined…
This paper presents a fundamental algorithm for parsing natural language sentences into dependency trees. Unlike phrase-structure (constituency) parsers, this algorithm operates one word at a time, attaching each word as soon as it can be…
We demonstrate the effectiveness of multilingual learning for unsupervised part-of-speech tagging. The central assumption of our work is that by combining cues from multiple languages, the structure of each becomes more apparent. We…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
Genetic sequence data of pathogens are increasingly used to investigate transmission dynamics in both endemic diseases and disease outbreaks; such research can aid in development of appropriate interventions and in design of studies to…