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Aug 31

Sort & Slice: A Simple and Superior Alternative to Hash-Based Folding for Extended-Connectivity Fingerprints

Extended-connectivity fingerprints (ECFPs) are a ubiquitous tool in current cheminformatics and molecular machine learning, and one of the most prevalent molecular feature extraction techniques used for chemical prediction. Atom features learned by graph neural networks can be aggregated to compound-level representations using a large spectrum of graph pooling methods; in contrast, sets of detected ECFP substructures are by default transformed into bit vectors using only a simple hash-based folding procedure. We introduce a general mathematical framework for the vectorisation of structural fingerprints via a formal operation called substructure pooling that encompasses hash-based folding, algorithmic substructure-selection, and a wide variety of other potential techniques. We go on to describe Sort & Slice, an easy-to-implement and bit-collision-free alternative to hash-based folding for the pooling of ECFP substructures. Sort & Slice first sorts ECFP substructures according to their relative prevalence in a given set of training compounds and then slices away all but the L most frequent substructures which are subsequently used to generate a binary fingerprint of desired length, L. We computationally compare the performance of hash-based folding, Sort & Slice, and two advanced supervised substructure-selection schemes (filtering and mutual-information maximisation) for ECFP-based molecular property prediction. Our results indicate that, despite its technical simplicity, Sort & Slice robustly (and at times substantially) outperforms traditional hash-based folding as well as the other investigated methods across prediction tasks, data splitting techniques, machine-learning models and ECFP hyperparameters. We thus recommend that Sort & Slice canonically replace hash-based folding as the default substructure-pooling technique to vectorise ECFPs for supervised molecular machine learning.

  • 4 authors
·
Mar 10, 2024

Natural Language Processing: A Comprehensive Practical Guide from Tokenisation to RLHF

This preprint presents a systematic, research-oriented practicum that guides the reader through the entire modern NLP pipeline --- from tokenisation and vectorisation to fine tuning of large language models, retrieval augmented generation, reinforcement learning from human feedback, prompt engineering, model compression, and multimodal systems. Seventeen hands-on sessions combine concise theory with detailed implementation plans, formalised evaluation metrics, and transparent assessment criteria. The work is not a conventional textbook: it is designed as a reproducible research artefact where every session requires publishing code, models, and reports in public repositories. All experiments are conducted on a single evolving corpus, and the work advocates open weight models over commercial APIs, with special attention to the Hugging Face ecosystem. The material is enriched by original research on low resource languages, incorporating linguistic resources for Tajik and Tatar --- subword tokenisers, embeddings, lexical databases, and transliteration benchmarks --- demonstrating how modern NLP can be adapted to data scarce environments. The practicum also covers advanced topics including AI agents, multi-agent systems, LLMOps, and efficient inference, preparing students for both research and industrial deployment. Designed for senior undergraduates, graduate students, and practising developers seeking to implement, compare, and deploy methods from classical ML to state of the art multimodal and agent-based systems.

  • 1 authors
·
Aug 12