Matthew Choi

Marawan Elbatel, Mohamed Ghonim, Jiaji Mao et al.

Automated segmentation of liver lesions on non-contrast computed tomography (NCCT) is clinically important but fundamentally challenging, particularly in low-resource settings across Africa and Asia where contrast agents are frequently unavailable. Progress has been limited by the absence of annotated NCCT benchmarks. Here we describe the TriALS challenge for automated liver lesion segmentation under contrast-limited conditions, supported by a multi-centre dataset of 150 cases with four-phase CT acquisitions (600 volumes) from Egyptian and Chinese institutions. Algorithms were evaluated on 70 cases from three institutions, including an independent external cohort. The top-performing method achieved a mean venous-phase Dice of 0.754, consistent with human-level performance, yet dropped to 0.57 on NCCT. On external validation, the leading method outperformed off-the-shelf models by up to 28% in Dice on NCCT. Algorithm performance was most strongly predicted by training data scale and pre-training strategy. A cross-year comparison exposed a persistent perceptual barrier on NCCT that scaling pre-training alone cannot overcome. Data, annotations, and code are available at https://github.com/xmed-lab/TriALS.

Naixu Guo, Zhan Yu, Matthew Choi et al.

Powerful generative artificial intelligence from large language models (LLMs) harnesses extensive computational resources for inference. In this work, we investigate the transformer architecture, a key component of these models, under the lens of fault-tolerant quantum computing. We develop quantum subroutines to construct the building blocks in the transformer, including the self-attention, residual connection with layer normalization, and feed-forward network. As an important subroutine, we show how to efficiently implement the Hadamard product and element-wise functions of matrices on quantum computers. Our algorithm prepares an amplitude encoding of the transformer output, which can be measured for prediction or use in the next layer. We find that the matrix norm of the input sequence plays a dominant role in the quantum complexity. With numerical experiments on open-source LLMs, including for bio-informatics applications, we demonstrate the potential of a quantum speedup for transformer inference in practical regimes.

Matthew Choi, Muhammad Adil Asif, John Willes et al.

With the growth of large language models, now incorporating billions of parameters, the hardware prerequisites for their training and deployment have seen a corresponding increase. Although existing tools facilitate model parallelization and distributed training, deeper model interactions, crucial for interpretability and responsible AI techniques, still demand thorough knowledge of distributed computing. This often hinders contributions from researchers with machine learning expertise but limited distributed computing background. Addressing this challenge, we present FlexModel, a software package providing a streamlined interface for engaging with models distributed across multi-GPU and multi-node configurations. The library is compatible with existing model distribution libraries and encapsulates PyTorch models. It exposes user-registerable HookFunctions to facilitate straightforward interaction with distributed model internals, bridging the gap between distributed and single-device model paradigms. Primarily, FlexModel enhances accessibility by democratizing model interactions and promotes more inclusive research in the domain of large-scale neural networks. The package is found at https://github.com/VectorInstitute/flex_model.

Ruiyu Wang, Matthew Choi

Lexical Semantic Change Detection stands out as one of the few areas where Large Language Models (LLMs) have not been extensively involved. Traditional methods like PPMI, and SGNS remain prevalent in research, alongside newer BERT-based approaches. Despite the comprehensive coverage of various natural language processing domains by LLMs, there is a notable scarcity of literature concerning their application in this specific realm. In this work, we seek to bridge this gap by introducing LLMs into the domain of Lexical Semantic Change Detection. Our work presents novel prompting solutions and a comprehensive evaluation that spans all three generations of language models, contributing to the exploration of LLMs in this research area.

Matthew Choi, Daniel Flam-Shepherd, Thi Ha Kyaw et al.

The core objective of machine-assisted scientific discovery is to learn physical laws from experimental data without prior knowledge of the systems in question. In the area of quantum physics, making progress towards these goals is significantly more challenging due to the curse of dimensionality as well as the counter-intuitive nature of quantum mechanics. Here, we present the QNODE, a latent neural ODE trained on expectation values of closed and open quantum systems dynamics. It can learn to generate such measurement data and extrapolate outside of its training region that satisfies the von Neumann and time-local Lindblad master equations for closed and open quantum systems respectively in an unsupervised means. Furthermore, the QNODE rediscovers quantum mechanical laws such as the Heisenberg's uncertainty principle in a data-driven way, without any constraint or guidance. Additionally, we show that trajectories that are generated from the QNODE that are close in its latent space have similar quantum dynamics while preserving the physics of the training system.