Daily Papers

This study introduces a novel knowledge enhanced tokenisation mechanism, K-Tokeniser, for clinical text processing. Technically, at initialisation stage, K-Tokeniser populates global representations of tokens based on semantic types of domain concepts (such as drugs or diseases) from either a domain ontology like Unified Medical Language System or the training data of the task related corpus. At training or inference stage, sentence level localised context will be utilised for choosing the optimal global token representation to realise the semantic-based tokenisation. To avoid pretraining using the new tokeniser, an embedding initialisation approach is proposed to generate representations for new tokens. Using three transformer-based language models, a comprehensive set of experiments are conducted on four real-world datasets for evaluating K-Tokeniser in a wide range of clinical text analytics tasks including clinical concept and relation extraction, automated clinical coding, clinical phenotype identification, and clinical research article classification. Overall, our models demonstrate consistent improvements over their counterparts in all tasks. In particular, substantial improvements are observed in the automated clinical coding task with 13\% increase on Micro F_1 score. Furthermore, K-Tokeniser also shows significant capacities in facilitating quicker converge of language models. Specifically, using K-Tokeniser, the language models would only require 50\% of the training data to achieve the best performance of the baseline tokeniser using all training data in the concept extraction task and less than 20\% of the data for the automated coding task. It is worth mentioning that all these improvements require no pre-training process, making the approach generalisable.

Recent dynamic tokenisation methods operate directly on bytes and pool their latent representations into patches. This bears similarities to computational models of word segmentation that determine lexical boundaries using spikes in an autoregressive model's prediction error. Inspired by this connection, we explore whether grouping predictable bytes - rather than pooling their representations - can yield a useful fixed subword vocabulary. We propose a new information-driven subword tokeniser, ByteSpan, that uses an external byte-level LM during training to identify contiguous predictable byte sequences and group them into subwords. Experiments show that ByteSpan yields efficient vocabularies with higher morphological alignment scores than BPE for English. Multilingual experiments show similar compression and R\'enyi efficiency for 25 languages.

Modelling the complex spatiotemporal patterns of large-scale brain dynamics is crucial for neuroscience, but traditional methods fail to capture the rich structure in modalities such as magnetoencephalography (MEG). Recent advances in deep learning have enabled significant progress in other domains, such as language and vision, by using foundation models at scale. Here, we introduce MEG-GPT, a transformer based foundation model that uses time-attention and next time-point prediction. To facilitate this, we also introduce a novel data-driven tokeniser for continuous MEG data, which preserves the high temporal resolution of continuous MEG signals without lossy transformations. We trained MEG-GPT on tokenised brain region time-courses extracted from a large-scale MEG dataset (N=612, eyes-closed rest, Cam-CAN data), and show that the learnt model can generate data with realistic spatio-spectral properties, including transient events and population variability. Critically, it performs well in downstream decoding tasks, improving downstream supervised prediction task, showing improved zero-shot generalisation across sessions (improving accuracy from 0.54 to 0.59) and subjects (improving accuracy from 0.41 to 0.49) compared to a baseline methods. Furthermore, we show the model can be efficiently fine-tuned on a smaller labelled dataset to boost performance in cross-subject decoding scenarios. This work establishes a powerful foundation model for electrophysiological data, paving the way for applications in computational neuroscience and neural decoding.