Semi-supervised medical image segmentation (SSMIS) has been demonstrated the potential to mitigate the issue of limited medical labeled data. However, confirmation and cognitive biases may affect the prevalent teacher-student based SSMIS methods due to erroneous pseudo-labels. To tackle this challenge, we improve the mean teacher approach and propose the Students Discrepancy-Informed Correction Learning (SDCL) framework that includes two students and one non-trainable teacher, which utilizes the segmentation difference between the two students to guide the self-correcting learning. The essence of SDCL is to identify the areas of segmentation discrepancy as the potential bias areas, and then encourage the model to review the correct cognition and rectify their own biases in these areas. To facilitate the bias correction learning with continuous review and rectification, two correction loss functions are employed to minimize the correct segmentation voxel distance and maximize the erroneous segmentation voxel entropy. We conducted experiments on three public medical image datasets: two 3D datasets (CT and MRI) and one 2D dataset (MRI). The results show that our SDCL surpasses the current State-of-the-Art (SOTA) methods by 2.57\%, 3.04\%, and 2.34\% in the Dice score on the Pancreas, LA, and ACDC datasets, respectively. In addition, the accuracy of our method is very close to the fully supervised method on the ACDC dataset, and even exceeds the fully supervised method on the Pancreas and LA dataset. (Code available at \url{//github.com/pascalcpp/SDCL}).
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Antepartum Cardiotocography (CTG) is vital for fetal health monitoring, but traditional methods like the Dawes-Redman system are often limited by high inter-observer variability, leading to inconsistent interpretations and potential misdiagnoses. This paper introduces PatchCTG, a transformer-based model specifically designed for CTG analysis, employing patch-based tokenisation, instance normalisation and channel-independent processing to capture essential local and global temporal dependencies within CTG signals. PatchCTG was evaluated on the Oxford Maternity (OXMAT) dataset, comprising over 20,000 CTG traces across diverse clinical outcomes after applying the inclusion and exclusion criteria. With extensive hyperparameter optimisation, PatchCTG achieved an AUC of 77%, with specificity of 88% and sensitivity of 57% at Youden's index threshold, demonstrating adaptability to various clinical needs. Testing across varying temporal thresholds showed robust predictive performance, particularly with finetuning on data closer to delivery, achieving a sensitivity of 52% and specificity of 88% for near-delivery cases. These findings suggest the potential of PatchCTG to enhance clinical decision-making in antepartum care by providing a reliable, objective tool for fetal health assessment. The source code is available at //github.com/jaleedkhan/PatchCTG.
Fine-grained classification of whole slide images (WSIs) is essential in precision oncology, enabling precise cancer diagnosis and personalized treatment strategies. The core of this task involves distinguishing subtle morphological variations within the same broad category of gigapixel-resolution images, which presents a significant challenge. While the multi-instance learning (MIL) paradigm alleviates the computational burden of WSIs, existing MIL methods often overlook hierarchical label correlations, treating fine-grained classification as a flat multi-class classification task. To overcome these limitations, we introduce a novel hierarchical multi-instance learning (HMIL) framework. By facilitating on the hierarchical alignment of inherent relationships between different hierarchy of labels at instance and bag level, our approach provides a more structured and informative learning process. Specifically, HMIL incorporates a class-wise attention mechanism that aligns hierarchical information at both the instance and bag levels. Furthermore, we introduce supervised contrastive learning to enhance the discriminative capability for fine-grained classification and a curriculum-based dynamic weighting module to adaptively balance the hierarchical feature during training. Extensive experiments on our large-scale cytology cervical cancer (CCC) dataset and two public histology datasets, BRACS and PANDA, demonstrate the state-of-the-art class-wise and overall performance of our HMIL framework. Our source code is available at //github.com/ChengJin-git/HMIL.
The emergence of large language models (LLMs) relies heavily on distributed training strategies, among which pipeline parallelism plays a crucial role. As LLMs' training sequence length extends to 32k or even 128k, the current pipeline parallel methods face severe bottlenecks, including high memory footprints and substantial pipeline bubbles, greatly hindering model scalability and training throughput. To enhance memory efficiency and training throughput, in this work, we introduce an efficient sequence-level one-forward-one-backward (1F1B) pipeline scheduling method tailored for training LLMs on long sequences named Seq1F1B. Seq1F1B decomposes batch-level schedulable units into finer sequence-level units, reducing bubble size and memory footprint. Considering that Seq1F1B may produce slight extra bubbles if sequences are split evenly, we design a computation-wise strategy to partition input sequences and mitigate this side effect. Compared to competitive pipeline baseline methods such as Megatron 1F1B pipeline parallelism, our method achieves higher training throughput with less memory footprint. Notably, Seq1F1B efficiently trains a LLM with 30B parameters on sequences up to 64k using 64 NVIDIA A100 GPUs without recomputation strategies, a feat unachievable with existing methods. Our source code is based on Megatron-LM, and now is avaiable at: //github.com/MayDomine/Seq1F1B.git.
An efficient data structure is fundamental to meeting the growing demands in dynamic graph processing. However, the dual requirements for graph computation efficiency (with contiguous structures) and graph update efficiency (with linked list-like structures) present a conflict in the design principles of graph structures. After experimental studies of existing state-of-the-art dynamic graph structures, we observe that the overhead of cache misses accounts for a major portion of the graph computation time. This paper presents GastCoCo, a system with graph storage and coroutine-based prefetch co-design. By employing software prefetching via stackless coroutines and introducing a prefetch-friendly data structure CBList, GastCoCo significantly alleviates the performance degradation caused by cache misses. Our results show that GastCoCo outperforms state-of-the-art graph storage systems by 1.3x - 180x in graph updates and 1.4x - 41.1x in graph computation.
As large language models become increasingly prevalent in the financial sector, there is a pressing need for a standardized method to comprehensively assess their performance. However, existing finance benchmarks often suffer from limited language and task coverage, as well as challenges such as low-quality datasets and inadequate adaptability for LLM evaluation. To address these limitations, we propose "Golden Touchstone", the first comprehensive bilingual benchmark for financial LLMs, which incorporates representative datasets from both Chinese and English across eight core financial NLP tasks. Developed from extensive open source data collection and industry-specific demands, this benchmark includes a variety of financial tasks aimed at thoroughly assessing models' language understanding and generation capabilities. Through comparative analysis of major models on the benchmark, such as GPT-4o Llama3, FinGPT and FinMA, we reveal their strengths and limitations in processing complex financial information. Additionally, we open-sourced Touchstone-GPT, a financial LLM trained through continual pre-training and financial instruction tuning, which demonstrates strong performance on the bilingual benchmark but still has limitations in specific tasks.This research not only provides the financial large language models with a practical evaluation tool but also guides the development and optimization of future research. The source code for Golden Touchstone and model weight of Touchstone-GPT have been made publicly available at \url{//github.com/IDEA-FinAI/Golden-Touchstone}, contributing to the ongoing evolution of FinLLMs and fostering further research in this critical area.
Large language models (LLMs) represent a groundbreaking advancement in the domain of natural language processing due to their impressive reasoning abilities. Recently, there has been considerable interest in increasing the context lengths for these models to enhance their applicability to complex tasks. However, at long context lengths and large batch sizes, the key-value (KV) cache, which stores the attention keys and values, emerges as the new bottleneck in memory usage during inference. To address this, we propose Eigen Attention, which performs the attention operation in a low-rank space, thereby reducing the KV cache memory overhead. Our proposed approach is orthogonal to existing KV cache compression techniques and can be used synergistically with them. Through extensive experiments over OPT, MPT, and Llama model families, we demonstrate that Eigen Attention results in up to 40% reduction in KV cache sizes and up to 60% reduction in attention operation latency with minimal drop in performance. Code is available at //github.com/UtkarshSaxena1/EigenAttn.
In the realm of medical image segmentation, both CNN-based and Transformer-based models have been extensively explored. However, CNNs exhibit limitations in long-range modeling capabilities, whereas Transformers are hampered by their quadratic computational complexity. Recently, State Space Models (SSMs), exemplified by Mamba, have emerged as a promising approach. They not only excel in modeling long-range interactions but also maintain a linear computational complexity. In this paper, leveraging state space models, we propose a U-shape architecture model for medical image segmentation, named Vision Mamba UNet (VM-UNet). Specifically, the Visual State Space (VSS) block is introduced as the foundation block to capture extensive contextual information, and an asymmetrical encoder-decoder structure is constructed with fewer convolution layers to save calculation cost. We conduct comprehensive experiments on the ISIC17, ISIC18, and Synapse datasets, and the results indicate that VM-UNet performs competitively in medical image segmentation tasks. To our best knowledge, this is the first medical image segmentation model constructed based on the pure SSM-based model. We aim to establish a baseline and provide valuable insights for the future development of more efficient and effective SSM-based segmentation systems. Our code is available at //github.com/JCruan519/VM-UNet.
Self-supervised learning methods are gaining increasing traction in computer vision due to their recent success in reducing the gap with supervised learning. In natural language processing (NLP) self-supervised learning and transformers are already the methods of choice. The recent literature suggests that the transformers are becoming increasingly popular also in computer vision. So far, the vision transformers have been shown to work well when pretrained either using a large scale supervised data or with some kind of co-supervision, e.g. in terms of teacher network. These supervised pretrained vision transformers achieve very good results in downstream tasks with minimal changes. In this work we investigate the merits of self-supervised learning for pretraining image/vision transformers and then using them for downstream classification tasks. We propose Self-supervised vIsion Transformers (SiT) and discuss several self-supervised training mechanisms to obtain a pretext model. The architectural flexibility of SiT allows us to use it as an autoencoder and work with multiple self-supervised tasks seamlessly. We show that a pretrained SiT can be finetuned for a downstream classification task on small scale datasets, consisting of a few thousand images rather than several millions. The proposed approach is evaluated on standard datasets using common protocols. The results demonstrate the strength of the transformers and their suitability for self-supervised learning. We outperformed existing self-supervised learning methods by large margin. We also observed that SiT is good for few shot learning and also showed that it is learning useful representation by simply training a linear classifier on top of the learned features from SiT. Pretraining, finetuning, and evaluation codes will be available under: //github.com/Sara-Ahmed/SiT.
We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.
The cross-domain recommendation technique is an effective way of alleviating the data sparsity in recommender systems by leveraging the knowledge from relevant domains. Transfer learning is a class of algorithms underlying these techniques. In this paper, we propose a novel transfer learning approach for cross-domain recommendation by using neural networks as the base model. We assume that hidden layers in two base networks are connected by cross mappings, leading to the collaborative cross networks (CoNet). CoNet enables dual knowledge transfer across domains by introducing cross connections from one base network to another and vice versa. CoNet is achieved in multi-layer feedforward networks by adding dual connections and joint loss functions, which can be trained efficiently by back-propagation. The proposed model is evaluated on two real-world datasets and it outperforms baseline models by relative improvements of 3.56\% in MRR and 8.94\% in NDCG, respectively.
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