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Jan 6

Infusing clinical knowledge into tokenisers for language models

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.

  • 10 authors
·
Jun 20, 2024

Discovery and recovery of crystalline materials with property-conditioned transformers

Generative models have recently shown great promise for accelerating the design and discovery of new functional materials. Conditional generation enhances this capacity by allowing inverse design, where specific desired properties can be requested during the generation process. However, conditioning of transformer-based approaches, in particular, is constrained by discrete tokenisation schemes and the risk of catastrophic forgetting during fine-tuning. This work introduces CrystaLLM-π (property injection), a conditional autoregressive framework that integrates continuous property representations directly into the transformer's attention mechanism. Two architectures, Property-Key-Value (PKV) Prefix attention and PKV Residual attention, are presented. These methods bypass inefficient sequence-level tokenisation and preserve foundational knowledge from unsupervised pre-training on Crystallographic Information Files (CIFs) as textual input. We establish the efficacy of these mechanisms through systematic robustness studies and evaluate the framework's versatility across two distinct tasks. First, for structure recovery, the model processes high-dimensional, heterogeneous X-ray diffraction patterns, achieving structural accuracy competitive with specialised models and demonstrating applications to experimental structure recovery and polymorph differentiation. Second, for materials discovery, the model is fine-tuned on a specialised photovoltaic dataset to generate novel, stable candidates validated by Density Functional Theory (DFT). It implicitly learns to target optimal band gap regions for high photovoltaic efficiency, demonstrating a capability to map complex structure-property relationships. CrystaLLM-π provides a unified, flexible, and computationally efficient framework for inverse materials design.

  • 8 authors
·
Nov 26, 2025

Foundation Models for Music: A Survey

In recent years, foundation models (FMs) such as large language models (LLMs) and latent diffusion models (LDMs) have profoundly impacted diverse sectors, including music. This comprehensive review examines state-of-the-art (SOTA) pre-trained models and foundation models in music, spanning from representation learning, generative learning and multimodal learning. We first contextualise the significance of music in various industries and trace the evolution of AI in music. By delineating the modalities targeted by foundation models, we discover many of the music representations are underexplored in FM development. Then, emphasis is placed on the lack of versatility of previous methods on diverse music applications, along with the potential of FMs in music understanding, generation and medical application. By comprehensively exploring the details of the model pre-training paradigm, architectural choices, tokenisation, finetuning methodologies and controllability, we emphasise the important topics that should have been well explored, like instruction tuning and in-context learning, scaling law and emergent ability, as well as long-sequence modelling etc. A dedicated section presents insights into music agents, accompanied by a thorough analysis of datasets and evaluations essential for pre-training and downstream tasks. Finally, by underscoring the vital importance of ethical considerations, we advocate that following research on FM for music should focus more on such issues as interpretability, transparency, human responsibility, and copyright issues. The paper offers insights into future challenges and trends on FMs for music, aiming to shape the trajectory of human-AI collaboration in the music realm.

  • 43 authors
·
Aug 26, 2024 2

Large Language and Text-to-3D Models for Engineering Design Optimization

The current advances in generative AI for learning large neural network models with the capability to produce essays, images, music and even 3D assets from text prompts create opportunities for a manifold of disciplines. In the present paper, we study the potential of deep text-to-3D models in the engineering domain, with focus on the chances and challenges when integrating and interacting with 3D assets in computational simulation-based design optimization. In contrast to traditional design optimization of 3D geometries that often searches for the optimum designs using numerical representations, such as B-Spline surface or deformation parameters in vehicle aerodynamic optimization, natural language challenges the optimization framework by requiring a different interpretation of variation operators while at the same time may ease and motivate the human user interaction. Here, we propose and realize a fully automated evolutionary design optimization framework using Shap-E, a recently published text-to-3D asset network by OpenAI, in the context of aerodynamic vehicle optimization. For representing text prompts in the evolutionary optimization, we evaluate (a) a bag-of-words approach based on prompt templates and Wordnet samples, and (b) a tokenisation approach based on prompt templates and the byte pair encoding method from GPT4. Our main findings from the optimizations indicate that, first, it is important to ensure that the designs generated from prompts are within the object class of application, i.e. diverse and novel designs need to be realistic, and, second, that more research is required to develop methods where the strength of text prompt variations and the resulting variations of the 3D designs share causal relations to some degree to improve the optimization.

  • 3 authors
·
Jul 3, 2023