Pancreatic ductal adenocarcinoma (PDAC) presents a critical global health challenge, and early detection is crucial for improving the 5-year survival rate. Recent medical imaging and computational algorithm advances offer potential solutions for early diagnosis. Deep learning, particularly in the form of convolutional neural networks (CNNs), has demonstrated success in medical image analysis tasks, including classification and segmentation. However, the limited availability of clinical data for training purposes continues to provide a significant obstacle. Data augmentation, generative adversarial networks (GANs), and cross-validation are potential techniques to address this limitation and improve model performance, but effective solutions are still rare for 3D PDAC, where contrast is especially poor owing to the high heterogeneity in both tumor and background tissues. In this study, we developed a new GAN-based model, named 3DGAUnet, for generating realistic 3D CT images of PDAC tumors and pancreatic tissue, which can generate the interslice connection data that the existing 2D CT image synthesis models lack. Our innovation is to develop a 3D U-Net architecture for the generator to improve shape and texture learning for PDAC tumors and pancreatic tissue. Our approach offers a promising path to tackle the urgent requirement for creative and synergistic methods to combat PDAC. The development of this GAN-based model has the potential to alleviate data scarcity issues, elevate the quality of synthesized data, and thereby facilitate the progression of deep learning models to enhance the accuracy and early detection of PDAC tumors, which could profoundly impact patient outcomes. Furthermore, this model has the potential to be adapted to other types of solid tumors, hence making significant contributions to the field of medical imaging in terms of image processing models.
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Empirical studies have widely demonstrated that neural networks are highly sensitive to small, adversarial perturbations of the input. The worst-case robustness against these so-called adversarial examples can be quantified by the Lipschitz constant of the neural network. In this paper, we study upper and lower bounds for the Lipschitz constant of random ReLU neural networks. Specifically, we assume that the weights and biases follow a generalization of the He initialization, where general symmetric distributions for the biases are permitted. For shallow neural networks, we characterize the Lipschitz constant up to an absolute numerical constant. For deep networks with fixed depth and sufficiently large width, our established upper bound is larger than the lower bound by a factor that is logarithmic in the width.
We provide quantitative evidence suggesting social learning in sperm whales across socio-cultural boundaries, using acoustic data from the Pacific and Atlantic Oceans. Traditionally, sperm whale populations are categorized into clans based on their vocal repertoire: the rhythmically patterned click sequences (codas) that they use. Among these codas, identity codas function as symbolic markers for each clan, accounting for 35-60% of codas they produce. We introduce a computational method to model whale speech, which encodes rhythmic micro-variations within codas, capturing their vocal style. We find that vocal style-clans closely align with repertoire-clans. However, contrary to vocal repertoire, we show that sympatry increases vocal style similarity between clans for non-identity codas, i.e. most codas, suggesting social learning across cultural boundaries. More broadly, this subcoda structure model offers a framework for comparing communication systems in other species, with potential implications for deeper understanding of vocal and cultural transmission within animal societies.
Antibody-drug conjugate (ADC) has revolutionized the field of cancer treatment in the era of precision medicine due to their ability to precisely target cancer cells and release highly effective drug. Nevertheless, the realization of rational design of ADC is very difficult because the relationship between their structures and activities is difficult to understand. In the present study, we introduce a unified deep learning framework called ADCNet to help design potential ADCs. The ADCNet highly integrates the protein representation learning language model ESM-2 and small-molecule representation learning language model FG-BERT models to achieve activity prediction through learning meaningful features from antigen and antibody protein sequences of ADC, SMILES strings of linker and payload, and drug-antibody ratio (DAR) value. Based on a carefully designed and manually tailored ADC data set, extensive evaluation results reveal that ADCNet performs best on the test set compared to baseline machine learning models across all evaluation metrics. For example, it achieves an average prediction accuracy of 87.12%, a balanced accuracy of 0.8689, and an area under receiver operating characteristic curve of 0.9293 on the test set. In addition, cross-validation, ablation experiments, and external independent testing results further prove the stability, advancement, and robustness of the ADCNet architecture. For the convenience of the community, we develop the first online platform (//ADCNet.idruglab.cn) for the prediction of ADCs activity based on the optimal ADCNet model, and the source code is publicly available at //github.com/idrugLab/ADCNet.
Large language models (LLMs) have shown their potential in biomedical fields. However, how the public uses them for healthcare purposes such as medical Q\&A, self-diagnosis, and daily healthcare information seeking is under-investigated. In this paper, we adopt a mixed-methods approach, including surveys (N=167) and interviews (N=17) to investigate how and why the public uses LLMs for healthcare. LLMs as a healthcare tool have gained popularity, and are often used in combination with other information channels such as search engines and online health communities to optimize information quality. LLMs provide more accurate information and a more convenient interaction/service model compared to traditional channels. LLMs also do a better job of reducing misinformation, especially in daily healthcare questions. Doctors using LLMs for diagnosis is less acceptable than for auxiliary work such as writing medical records. Based on the findings, we reflect on the ethical and effective use of LLMs for healthcare and propose future research directions.
With the growing popularity of dialogue agents based on large language models (LLMs), urgent attention has been drawn to finding ways to ensure their behaviour is ethical and appropriate. These are largely interpreted in terms of the 'HHH' criteria: making outputs more helpful and honest, and avoiding harmful (biased, toxic, or inaccurate) statements. Whilst this semantic focus is useful from the perspective of viewing LLM agents as mere mediums for information, it fails to account for pragmatic factors that can make the same utterance seem more or less offensive or tactless in different social situations. We propose an approach to ethics that is more centred on relational and situational factors, exploring what it means for a system, as a social actor, to treat an individual respectfully in a (series of) interaction(s). Our work anticipates a set of largely unexplored risks at the level of situated interaction, and offers practical suggestions to help LLM technologies behave as 'good' social actors and treat people respectfully.
Reinforcement learning can solve decision-making problems and train an agent to behave in an environment according to a predesigned reward function. However, such an approach becomes very problematic if the reward is too sparse and so the agent does not come across the reward during the environmental exploration. The solution to such a problem may be to equip the agent with an intrinsic motivation that will provide informed exploration during which the agent is likely to also encounter external reward. Novelty detection is one of the promising branches of intrinsic motivation research. We present Self-supervised Network Distillation (SND), a class of intrinsic motivation algorithms based on the distillation error as a novelty indicator, where the predictor model and the target model are both trained. We adapted three existing self-supervised methods for this purpose and experimentally tested them on a set of ten environments that are considered difficult to explore. The results show that our approach achieves faster growth and higher external reward for the same training time compared to the baseline models, which implies improved exploration in a very sparse reward environment. In addition, the analytical methods we applied provide valuable explanatory insights into our proposed models.
With growing concerns surrounding privacy and regulatory compliance, the concept of machine unlearning has gained prominence, aiming to selectively forget or erase specific learned information from a trained model. In response to this critical need, we introduce a novel approach called Attack-and-Reset for Unlearning (ARU). This algorithm leverages meticulously crafted adversarial noise to generate a parameter mask, effectively resetting certain parameters and rendering them unlearnable. ARU outperforms current state-of-the-art results on two facial machine-unlearning benchmark datasets, MUFAC and MUCAC. In particular, we present the steps involved in attacking and masking that strategically filter and re-initialize network parameters biased towards the forget set. Our work represents a significant advancement in rendering data unexploitable to deep learning models through parameter re-initialization, achieved by harnessing adversarial noise to craft a mask.
The coronavirus pandemic (COVID-19) is probably the most disruptive global health disaster in recent history. It negatively impacted the whole world and virtually brought the global economy to a standstill. However, as the virus was spreading, infecting people and claiming thousands of lives so was the spread and propagation of fake news, misinformation and disinformation about the event. These included the spread of unconfirmed health advice and remedies on social media. In this paper, false information about the pandemic is identified using a content-based approach and metadata curated from messages posted to online social networks. A content-based approach combined with metadata as well as an initial feature analysis is used and then several supervised learning models are tested for identifying and predicting misleading posts. Our approach shows up to 93% accuracy in the detection of fake news related posts about the COVID-19 pandemic
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.
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