23 papers · ranked by Valyu relevance
Łukasz Dębowski
We revisit the problem of minimal local grammar-based coding. In this setting, the local grammar encoder encodes grammars symbol by symbol, whereas the minimal grammar transform minimizes the grammar length in a preset class of grammars as given by the length of local grammar encoding. It has been known that such…
Peter Heringer, Daniel Doerr
Pangenome graphs offer a compact and comprehensive representation of genomic diversity, improving tasks such as variant calling, genotyping, and other downstream analyses. Although the underlying graph structures scale sublinearly with the number of haplotypes, the widely used GFA file format suffers from rapidly…
Sean Deyo, Veit Elser
We introduce the logical grammar emdebbing (LGE), a model inspired by pregroup grammars and categorial grammars to enable unsupervised inference of lexical categories and syntactic rules from a corpus of text. LGE produces comprehensible output summarizing its inferences, has a completely transparent process for…
Xiang Hu, Haitao Mi, Liang Li, Gerard de Melo
Chart-based models have shown great potential in unsupervised grammar induction, running recursively and hierarchically, but requiring O(n 3 ) time-complexity. The Recursive Transformer based on Differentiable Trees (R2D2) makes it possible to scale to large language model pretraining even with a complex tree encoder…
Rahul Varki, Travis Gagie, Christina Boucher
Among grammar-based compression techniques, RePair is a notable offline encoding scheme known for its simplicity and powerful combinatorial properties, producing compact grammars by repeatedly replacing the most frequent adjacent pairs of symbols, known as bigrams. However, RePair’s memory usage scales poorly with…
Emily Cheng, Francesca Franzon
patterning Authors: ['Emily Cheng' 'Francesca Franzon'] Grammatical features such as number and gender serve two central functions in human languages. While they encode salient semantic attributes like numerosity and animacy, they also offload sentence processing cost by predictably linking words together via…
Lucas Y. Tian, Daniel J. Hanuska, Kedar Garzón Gupta, Yue Liu + 3 more
Humans and other animals can solve new problems, even on the first attempt. This capacity to generate novel problem-solving behavior has been hypothesized to depend on brain mechanisms for recombining units of knowledge using systems of procedural rules, or grammars. Yet, whether and how the brain represents and…
Richard Apodaca
Despite its widespread use, Simplified Molecular Input Line Entry System (SMILES) remains underspecified. The lack of a detailed specification encourages improvisation by software developers, complicates data standardization efforts, and undermines extension development. Balsa, a reformulation of SMILES, addresses…
Johannes T. Margraf, Zachary W. Ulissi, Yousung Jung, Karsten Reuter
The discovery of new catalytically active materi- als is one of the holy grails of computational chemistry as it has the potential to accelerate the adoption of renewable energy sources and reduce the energy consumption of chemical industry. Indeed, heterogeneous catalysts are essential for the production of synthetic…
Subhankar Roy, Dilip Kumar Maity, Anirban Mukhopadhyay
Deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) sequence compressors for novel species frequently face challenges when processing wide-scale raw, FASTA, or multi-FASTA structured data. For years, molecular sequence databases have favored the widely used general-purpose Gzip and Zstd compressors. The absence of…
Lin Sun, Sanjay G Manohar
Syntax is a central organizing component of human language but few models explain how it may be implemented in neurons. We combined two rapid synaptic rules to demonstrate how neurons can implement a simple grammar without accounting for the hierarchical property of syntax. Words bind to syntactic roles (e.g. “dog” as…
Tangina Sultana, Young-Koo Lee, Wookey Lee
The explosive volume of semantic data published in the Resource Description Framework (RDF) data model demands efficient management and compression with better compression ratio and runtime. Although extensive work has been carried out for compressing the RDF datasets, they do not perform well in all dimensions.…
Justin Kim, Rahul Varki, Marco Oliva, Christina Boucher
The RePair compression algorithm produces a context-free grammar by iteratively substituting the most frequently occurring pair of consecutive symbols with a new symbol until all consecutive pairs of symbols appear only once in the compressed text. It is widely used in the settings of bioinformatics, machine learning…
Olga Zamaraeva, Carlos Gómez‐Rodríguez
We present the latest version of the Spanish Resource Grammar (SRG), a grammar of Spanish implemented in the HPSG formalism. Such grammars encode a complex set of hypotheses about syntax making them a resource for empirical testing of linguistic theory. They also encode a strict notion of grammaticality which makes…
Sean Deyo, Veit Elser
We implement a divide-and-concur iterative projection approach to context-free grammar inference. Unlike most state-of-the-art models of natural language processing, our method requires a relatively small number of discrete parameters, making the inferred grammar directly interpretable — one can read off from a…
Saibo Geng, Martin Josifoski, Maxime Peyrard, Robert West
Despite their impressive performance, large language models (LMs) still struggle with reliably generating complex output structures when not finetuned to follow the required output format exactly. To address this issue, grammarconstrained decoding (GCD) can be used to control the generation of LMs, guaranteeing that…
Zijian Liang, Kai Niu, Jin Xu, Ping Zhang + 1 more
Recent semantic communication methods explore effective ways to expand the communication paradigm and improve the performance of communication systems. Nonetheless, a common problem with these methods is that the essence of semantics is not explicitly pointed out and directly utilized. A new epistemology suggests that…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
Lanzhi Cheng, Peiyun Ben, Yuchen Qiao
As one of the most widely used languages in the world, English plays a vital role in the communication between China and the world. However, grammar learning in English is a difficult and long process for English learners. Especially in English writing, English learners will inevitably make various grammatical writing…
Morgan Thomas, Mazen Ahmad, Gary Tresadern, Gianni de Fabritiis
SMILES-based generative models are amongst the most robust and successful recent methods used to augment drug design. They are typically used for complete de novo generation, however, scaffold decoration and fragment linking applications are sometimes desirable which requires a different architecture, a different…
Authors not listed
Deep generative models are transforming early-stage drug discovery, yet most current approaches are not well suited for realistic, small-data settings and often rely on simplified molecular representations such as linear strings, overlooking the inherent graph-based structure of molecules. To address this, we first…
Navya Tyagi, Naima Vahab, Sonika Tyagi
Integrating genomics with diverse data modalities has the potential to revolutionize personalized medicine. However, this integration poses significant challenges due to the fundamental differences in data types and structures. The vast size of the genome necessitates transformation into a condensed representation…
Marius Welzel, Peter Michael Schwarz, Hannah F. Löchel, Tolganay Kabdullayeva + 4 more
'Tolganay Kabdullayeva' 'Sandra Clemens' 'Anke Becker' 'Bernd Freisleben' 'Dominik Heider'] The extensive information capacity of DNA, coupled with decreasing costs for DNA synthesis and sequencing, makes DNA an attractive alternative to traditional data storage. The processes of writing, storing, and reading DNA…