Related papers: Constructing and Employing Tree Alignment Graphs f…
The precise formulation of derivation for tree-adjoining grammars has important ramifications for a wide variety of uses of the formalism, from syntactic analysis to semantic interpretation and statistical language modeling. We argue that…
Large Language Models (LLMs) have achieved remarkable success in natural language processing through strong semantic understanding and generation. However, their black-box nature limits structured and multi-hop reasoning. In contrast,…
In mathematical phylogenetics, the time-consistent galled trees provide a simple class of rooted binary network structures that can be used to represent a variety of different biological phenomena. We study the enumerative combinatorics of…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
The derivation trees of a tree adjoining grammar provide a first insight into the sentence semantics, and are thus prime targets for generation systems. We define a formalism, feature-based regular tree grammars, and a translation from…
We present a graph-based Tree Adjoining Grammar (TAG) parser that uses BiLSTMs, highway connections, and character-level CNNs. Our best end-to-end parser, which jointly performs supertagging, POS tagging, and parsing, outperforms the…
Tree adjoining grammars (TAGs) provide an ample tool to capture syntax of many Indian languages. Tamil represents a special challenge to computational formalisms as it has extensive agglutinative morphology and a comparatively difficult…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
To a given gene tree topology $G$ and species tree topology $S$ with leaves labeled bijectively from a fixed set $X$, one can associate a set of ancestral configurations, each of which encodes a set of gene lineages that can be found at a…
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
Constructing taxonomies from citation graphs is essential for organizing scientific knowledge, facilitating literature reviews, and identifying emerging research trends. However, manual taxonomy construction is labor-intensive,…
An important and well-studied problem in phylogenetics is to compute a \emph{consensus tree} so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively labeled by the same…
The formalism of synchronous tree-adjoining grammars, a variant of standard tree-adjoining grammars (TAG), was intended to allow the use of TAGs for language transduction in addition to language specification. In previous work, the…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
In this report, we present TAGLAS, an atlas of text-attributed graph (TAG) datasets and benchmarks. TAGs are graphs with node and edge features represented in text, which have recently gained wide applicability in training graph-language or…
We consider the problem of uniformly generating a spanning tree, of a connected undirected graph. This process is useful to compute statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
Semantic parsing is the task of producing structured meaning representations for natural language sentences. Recent research has pointed out that the commonly-used sequence-to-sequence (seq2seq) semantic parsers struggle to generalize…