Efficient Task Grouping Through Samplewise Optimisation Landscape Analysis

Shared training approaches, such as multi-task learning (MTL) and gradient-based meta-learning, are widely used in various machine learning applications, but they often suffer from negative transfer, leading to performance degradation in specific tasks. While several optimisation techniques have been developed to mitigate this issue for pre-selected task cohorts, identifying optimal task combinations for joint learning - known as task grouping - remains underexplored and computationally challenging due to the exponential growth in task combinations and the need for extensive training and evaluation cycles. This paper introduces an efficient task grouping framework designed to reduce these overwhelming computational demands of the existing methods. The proposed framework infers pairwise task similarities through a sample-wise optimisation landscape analysis, eliminating the need for the shared model training required to infer task similarities in existing methods. With task similarities acquired, a graph-based clustering algorithm is employed to pinpoint near-optimal task groups, providing an approximate yet efficient and effective solution to the originally NP-hard problem. Empirical assessments conducted on 8 different datasets highlight the effectiveness of the proposed framework, revealing a five-fold speed enhancement compared to previous state-of-the-art methods. Moreover, the framework consistently demonstrates comparable performance, confirming its remarkable efficiency and effectiveness in task grouping.

FE-Adapter: Adapting Image-based Emotion Classifiers to Videos

Utilizing large pre-trained models for specific tasks has yielded impressive results. However, fully fine-tuning these increasingly large models is becoming prohibitively resource-intensive. This has led to a focus on more parameter-efficient transfer learning, primarily within the same modality. But this approach has limitations, particularly in video understanding where suitable pre-trained models are less common. Addressing this, our study introduces a novel cross-modality transfer learning approach from images to videos, which we call parameter-efficient image-to-video transfer learning. We present the Facial-Emotion Adapter (FE-Adapter), designed for efficient fine-tuning in video tasks. This adapter allows pre-trained image models, which traditionally lack temporal processing capabilities, to analyze dynamic video content efficiently. Notably, it uses about 15 times fewer parameters than previous methods, while improving accuracy. Our experiments in video emotion recognition demonstrate that the FE-Adapter can match or even surpass existing fine-tuning and video emotion models in both performance and efficiency. This breakthrough highlights the potential for cross-modality approaches in enhancing the capabilities of AI models, particularly in fields like video emotion analysis where the demand for efficiency and accuracy is constantly rising.

CC-SAM: SAM with Cross-feature Attention and Context for Ultrasound Image Segmentation

The Segment Anything Model (SAM) has achieved remarkable successes in the realm of natural image segmentation, but its deployment in the medical imaging sphere has encountered challenges. Specifically, the model struggles with medical images that feature low contrast, faint boundaries, intricate morphologies, and small-sized objects. To address these challenges and enhance SAM's performance in the medical domain, we introduce a comprehensive modification. Firstly, we incorporate a frozen Convolutional Neural Network (CNN) branch as an image encoder, which synergizes with SAM's original Vision Transformer (ViT) encoder through a novel variational attention fusion module. This integration bolsters the model's capability to capture local spatial information, which is often paramount in medical imagery. Moreover, to further optimize SAM for medical imaging, we introduce feature and position adapters within the ViT branch, refining the encoder's representations. We see that compared to current prompting strategies to fine-tune SAM for ultrasound medical segmentation, the use of text descriptions that serve as text prompts for SAM helps significantly improve the performance. Leveraging ChatGPT's natural language understanding capabilities, we generate prompts that offer contextual information and guidance to SAM, enabling it to better understand the nuances of ultrasound medical images and improve its segmentation accuracy. Our method, in its entirety, represents a significant stride towards making universal image segmentation models more adaptable and efficient in the medical domain.

Masks and Manuscripts: Advancing Medical Pre-training with End-to-End Masking and Narrative Structuring

Contemporary medical contrastive learning faces challenges from inconsistent semantics and sample pair morphology, leading to dispersed and converging semantic shifts. The variability in text reports, due to multiple authors, complicates semantic consistency. To tackle these issues, we propose a two-step approach. Initially, text reports are converted into a standardized triplet format, laying the groundwork for our novel concept of ``observations'' and ``verdicts''. This approach refines the {Entity, Position, Exist} triplet into binary questions, guiding towards a clear ``verdict''. We also innovate in visual pre-training with a Meijering-based masking, focusing on features representative of medical images' local context. By integrating this with our text conversion method, our model advances cross-modal representation in a multimodal contrastive learning framework, setting new benchmarks in medical image analysis.

Rapid Biomedical Research Classification: The Pandemic PACT Advanced Categorisation Engine

This paper introduces the Pandemic PACT Advanced Categorisation Engine (PPACE) along with its associated dataset. PPACE is a fine-tuned model developed to automatically classify research abstracts from funded biomedical projects according to WHO-aligned research priorities. This task is crucial for monitoring research trends and identifying gaps in global health preparedness and response. Our approach builds on human-annotated projects, which are allocated one or more categories from a predefined list. A large language model is then used to generate `rationales' explaining the reasoning behind these annotations. This augmented data, comprising expert annotations and rationales, is subsequently used to fine-tune a smaller, more efficient model. Developed as part of the Pandemic PACT project, which aims to track and analyse research funding and clinical evidence for a wide range of diseases with outbreak potential, PPACE supports informed decision-making by research funders, policymakers, and independent researchers. We introduce and release both the trained model and the instruction-based dataset used for its training. Our evaluation shows that PPACE significantly outperforms its baselines. The release of PPACE and its associated dataset offers valuable resources for researchers in multilabel biomedical document classification and supports advancements in aligning biomedical research with key global health priorities.

SpikeLLM: Scaling up Spiking Neural Network to Large Language Models via Saliency-based Spiking

The recent advancements in large language models (LLMs) with billions of parameters have significantly boosted their performance across various real-world applications. However, the inference processes for these models require substantial energy and computational resources, presenting considerable deployment challenges. In contrast, human brains, which contain approximately 86 billion biological neurons, exhibit significantly greater energy efficiency compared to LLMs with a similar number of parameters. Inspired by this, we redesign 7 to 70 billion parameter LLMs using bio-plausible spiking mechanisms, emulating the efficient behavior of the human brain. We propose the first spiking large language model as recent LLMs termed SpikeLLM. Coupled with the proposed model, a novel spike-driven quantization framework named Optimal Brain Spiking is introduced to reduce the energy cost and accelerate inference speed via two essential approaches: first (second)-order differentiation-based salient channel detection, and per-channel salient outlier expansion with Generalized Integrate-and-Fire neurons. Our proposed spike-driven quantization can plug in main streams of quantization training methods. In the OmniQuant pipeline, SpikeLLM significantly reduces 25.51% WikiText2 perplexity and improves 3.08% average accuracy of 6 zero-shot datasets on a LLAMA2-7B 4A4W model. In the GPTQ pipeline, SpikeLLM realizes a sparse ternary quantization, which achieves additive in all linear layers. Compared with PB-LLM with similar operations, SpikeLLM also exceeds significantly. We will release our code on GitHub.

Computation-Efficient Semi-Supervised Learning for ECG-based Cardiovascular Diseases Detection

Label scarcity problem is the main challenge that hinders the wide application of deep learning systems in automatic cardiovascular diseases (CVDs) detection using electrocardiography (ECG). Tuning pre-trained models alleviates this problem by transferring knowledge learned from large datasets to downstream small datasets. However, bottlenecks in computational efficiency and CVDs detection performance limit its clinical applications. It is difficult to improve the detection performance without significantly sacrificing model computational efficiency. Here, we propose a computation-efficient semi-supervised learning paradigm (FastECG) for robust and computation-efficient CVDs detection using ECG. It enables a robust adaptation of pre-trained models on downstream datasets with limited supervision and high computational efficiency. First, a random-deactivation technique is developed to achieve robust and fast low-rank adaptation of pre-trained weights. Subsequently, we propose a one-shot rank allocation module to determine the optimal ranks for the update matrices of the pre-trained weights. Finally, a lightweight semi-supervised learning pipeline is introduced to enhance model performance by leveraging labeled and unlabeled data with high computational efficiency. Extensive experiments on four downstream ECG datasets demonstrate that FastECG not only outperforms the state-of-the-art methods in multi-label CVDs detection but also consumes fewer GPU footprints, training time, and parameter storage space. As such, this paradigm provides an effective solution for achieving high computational efficiency and robust detection performance in the clinical applications of pre-trained models under limited supervision.

Sample Selection Bias in Machine Learning for Healthcare

While machine learning algorithms hold promise for personalised medicine, their clinical adoption remains limited. One critical factor contributing to this restraint is sample selection bias (SSB) which refers to the study population being less representative of the target population, leading to biased and potentially harmful decisions. Despite being well-known in the literature, SSB remains scarcely studied in machine learning for healthcare. Moreover, the existing techniques try to correct the bias by balancing distributions between the study and the target populations, which may result in a loss of predictive performance. To address these problems, our study illustrates the potential risks associated with SSB by examining SSB's impact on the performance of machine learning algorithms. Most importantly, we propose a new research direction for addressing SSB, based on the target population identification rather than the bias correction. Specifically, we propose two independent networks (T-Net) and a multitasking network (MT-Net) for addressing SSB, where one network/task identifies the target subpopulation which is representative of the study population and the second makes predictions for the identified subpopulation. Our empirical results with synthetic and semi-synthetic datasets highlight that SSB can lead to a large drop in the performance of an algorithm for the target population as compared with the study population, as well as a substantial difference in the performance for the target subpopulations that are representative of the selected and the non-selected patients from the study population. Furthermore, our proposed techniques demonstrate robustness across various settings, including different dataset sizes, event rates, and selection rates, outperforming the existing bias correction techniques.

Large Language Models in Healthcare: A Comprehensive Benchmark

The adoption of large language models (LLMs) to assist clinicians has attracted remarkable attention. Existing works mainly adopt the close-ended question-answering task with answer options for evaluation. However, in real clinical settings, many clinical decisions, such as treatment recommendations, involve answering open-ended questions without pre-set options. Meanwhile, existing studies mainly use accuracy to assess model performance. In this paper, we comprehensively benchmark diverse LLMs in healthcare, to clearly understand their strengths and weaknesses. Our benchmark contains seven tasks and thirteen datasets across medical language generation, understanding, and reasoning. We conduct a detailed evaluation of the existing sixteen LLMs in healthcare under both zero-shot and few-shot (i.e., 1,3,5-shot) learning settings. We report the results on five metrics (i.e. matching, faithfulness, comprehensiveness, generalizability, and robustness) that are critical in achieving trust from clinical users. We further invite medical experts to conduct human evaluation.

Exploring the Effectiveness of Instruction Tuning in Biomedical Language Processing

Large Language Models (LLMs), particularly those similar to ChatGPT, have significantly influenced the field of Natural Language Processing (NLP). While these models excel in general language tasks, their performance in domain-specific downstream tasks such as biomedical and clinical Named Entity Recognition (NER), Relation Extraction (RE), and Medical Natural Language Inference (NLI) is still evolving. In this context, our study investigates the potential of instruction tuning for biomedical language processing, applying this technique to two general LLMs of substantial scale. We present a comprehensive, instruction-based model trained on a dataset that consists of approximately $200,000$ instruction-focused samples. This dataset represents a carefully curated compilation of existing data, meticulously adapted and reformatted to align with the specific requirements of our instruction-based tasks. This initiative represents an important step in utilising such models to achieve results on par with specialised encoder-only models like BioBERT and BioClinicalBERT for various classical biomedical NLP tasks. Our work includes an analysis of the dataset's composition and its impact on model performance, providing insights into the intricacies of instruction tuning. By sharing our codes, models, and the distinctively assembled instruction-based dataset, we seek to encourage ongoing research and development in this area.