Deciphering Fingerprints of 3D Molecular Surfaces for Accurate Epitope Prediction

arXiv:2606.23830v1 Announce Type: new Abstract: Molecular surfaces encode the geometric and physicochemical patterns that determine antibody-antigen recognition, central to epitope prediction. However, existing methods rely on sequences or backbone structures and struggle to capture discontinuous, surface-driven epitopes. This study presents SurfBind, a surface-centric learning framework for epitope prediction that operates directly on molecular surface representations. SurfBind integrates geome

Generating in the Limit with Infinitely Many Hallucinations

arXiv:2606.28354v1 Announce Type: new Abstract: The classic paradigm of language identification in the limit models learning as a game between an adversary, who reveals strings from an unknown target language, and a learner tasked with identifying that language. The recently introduced framework of language generation in the limit shifted the objective to better reflect modern language modeling, requiring the learner to produce valid, unseen strings from the target language. Related work highlig

Extracting Knowledge from an Arabic-English Machine-Readable Dictionary Using Information Extraction

arXiv:2606.28457v1 Announce Type: new Abstract: Natural language processing (NLP) applications need large and rich amount of linguistic knowledge. Furthermore, electronic language sources such as dictionaries, encyclopedia, and corpora became available. So, automatic methods are emerged to extract lexical information from those sources to overcome the knowledge acquisition bottleneck. We presented a method to automatically extract lexical information from a machine-readable version of the Arabic

Developmental Trajectories of Situation Modeling and Mentalizing in Transformer Language Models

arXiv:2606.28524v1 Announce Type: new Abstract: Recent work suggests that Large Language Models (LLMs) are sensitive to the belief states of agents described by text, as measured by the false belief task (FBT), yet persistent concerns of construct validity remain. We adopt a **developmental perspective**, tracing the pattern of mental state reasoning behavior -- and likely **preconditions** for this behavior -- across multiple training stages in the Olmo2 and Pythia language model suites. We fin

Deciphering Fingerprints of 3D Molecular Surfaces for Accurate Epitope Prediction

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Generating in the Limit with Infinitely Many Hallucinations

Extracting Knowledge from an Arabic-English Machine-Readable Dictionary Using Information Extraction

Developmental Trajectories of Situation Modeling and Mentalizing in Transformer Language Models