Undoubtedly breast cancer identifies itself as one of the most widespread and terrifying cancers across the globe. Millions of women are getting affected each year from it. Breast cancer remains the major one for being the reason of largest number of demise of women. In the recent time of research, Medical Image Computing and Processing has been playing a significant role for detecting and classifying breast cancers from ultrasound images and mammograms, along with the celestial touch of deep neural networks. In this research, we focused mostly on our rigorous implementations and iterative result analysis of different cutting-edge modified versions of EfficientNet architectures namely EfficientNet-V1 (b0-b7) and EfficientNet-V2 (b0-b3) with ultrasound image, named as CEIMVEN. We utilized transfer learning approach here for using the pre-trained models of EfficientNet versions. We activated the hyper-parameter tuning procedures, added fully connected layers, discarded the unprecedented outliers and recorded the accuracy results from our custom modified EfficientNet architectures. Our deep learning model training approach was related to both identifying the cancer affected areas with region of interest (ROI) techniques and multiple classifications (benign, malignant and normal). The approximate testing accuracies we got from the modified versions of EfficientNet-V1 (b0- 99.15%, b1- 98.58%, b2- 98.43%, b3- 98.01%, b4- 98.86%, b5- 97.72%, b6- 97.72%, b7- 98.72%) and EfficientNet-V2 (b0- 99.29%, b1- 99.01%, b2- 98.72%, b3- 99.43%) are showing very bright future and strong potentials of deep learning approach for the successful detection and classification of breast cancers from the ultrasound images at a very early stage.
Population health surveys are an important tool to effectively allocate limited resources in low resource communities. In such an environment, surveys are often done by local population with pen and paper. Data thus collected is difficult to tabulate and analyze. We conducted a series of interviews and experiments in the Philippines to assess if mobile forms can be a viable and more efficient survey method. We first conducted pilot interviews and found 60% of the local surveyors actually preferred mobile forms over paper. We then built a software that can generate mobile forms that are easy to use, capable of working offline, and able to track key metrics such as time to complete questions. Our mobile form was field tested in three locations in the Philippines with 33 surveyors collecting health survey responses from 266 subjects. The percentage of surveyors preferring mobile forms increased to 76% after just using the form a few times. The results demonstrate our mobile form is a viable method to conduct large scale population health surveys in a low resource environment.
MET protein overexpression is a targetable event in non-small cell lung cancer (NSCLC) and is the subject of active drug development. Challenges in identifying patients for these therapies include lack of access to validated testing, such as standardized immunohistochemistry (IHC) assessment, and consumption of valuable tissue for a single gene/protein assay. Development of pre-screening algorithms using routinely available digitized hematoxylin and eosin (H&E)-stained slides to predict MET overexpression could promote testing for those who will benefit most. While assessment of MET expression using IHC is currently not routinely performed in NSCLC, next-generation sequencing is common and in some cases includes RNA expression panel testing. In this work, we leveraged a large database of matched H&E slides and RNA expression data to train a weakly supervised model to predict MET RNA overexpression directly from H&E images. This model was evaluated on an independent holdout test set of 300 over-expressed and 289 normal patients, demonstrating an ROC-AUC of 0.70 (95th percentile interval: 0.66 - 0.74) with stable performance characteristics across different patient clinical variables and robust to synthetic noise on the test set. These results suggest that H&E-based predictive models could be useful to prioritize patients for confirmatory testing of MET protein or MET gene expression status.
Human feedback is increasingly used to steer the behaviours of Large Language Models (LLMs). However, it is unclear how to collect and incorporate feedback in a way that is efficient, effective and unbiased, especially for highly subjective human preferences and values. In this paper, we survey existing approaches for learning from human feedback, drawing on 95 papers primarily from the ACL and arXiv repositories.First, we summarise the past, pre-LLM trends for integrating human feedback into language models. Second, we give an overview of present techniques and practices, as well as the motivations for using feedback; conceptual frameworks for defining values and preferences; and how feedback is collected and from whom. Finally, we encourage a better future of feedback learning in LLMs by raising five unresolved conceptual and practical challenges.
Biomarker detection is an indispensable part in the diagnosis and treatment of low-grade glioma (LGG). However, current LGG biomarker detection methods rely on expensive and complex molecular genetic testing, for which professionals are required to analyze the results, and intra-rater variability is often reported. To overcome these challenges, we propose an interpretable deep learning pipeline, a Multi-Biomarker Histomorphology Discoverer (Multi-Beholder) model based on the multiple instance learning (MIL) framework, to predict the status of five biomarkers in LGG using only hematoxylin and eosin-stained whole slide images and slide-level biomarker status labels. Specifically, by incorporating the one-class classification into the MIL framework, accurate instance pseudo-labeling is realized for instance-level supervision, which greatly complements the slide-level labels and improves the biomarker prediction performance. Multi-Beholder demonstrates superior prediction performance and generalizability for five LGG biomarkers (AUROC=0.6469-0.9735) in two cohorts (n=607) with diverse races and scanning protocols. Moreover, the excellent interpretability of Multi-Beholder allows for discovering the quantitative and qualitative correlations between biomarker status and histomorphology characteristics. Our pipeline not only provides a novel approach for biomarker prediction, enhancing the applicability of molecular treatments for LGG patients but also facilitates the discovery of new mechanisms in molecular functionality and LGG progression.
Large Language Models (LLMs) have shown promise in medical question answering by achieving passing scores in standardised exams and have been suggested as tools for supporting healthcare workers. Deploying LLMs into such a high-risk context requires a clear understanding of the limitations of these models. With the rapid development and release of new LLMs, it is especially valuable to identify patterns which exist across models and may, therefore, continue to appear in newer versions. In this paper, we evaluate a wide range of popular LLMs on their knowledge of medical questions in order to better understand their properties as a group. From this comparison, we provide preliminary observations and raise open questions for further research.
Prostate cancer (PCa) is a severe disease among men globally. It is important to identify PCa early and make a precise diagnosis for effective treatment. For PCa diagnosis, Multi-parametric magnetic resonance imaging (mpMRI) emerged as an invaluable imaging modality that offers a precise anatomical view of the prostate gland and its tissue structure. Deep learning (DL) models can enhance existing clinical systems and improve patient care by locating regions of interest for physicians. Recently, DL techniques have been employed to develop a pipeline for segmenting and classifying different cancer types. These studies show that DL can be used to increase diagnostic precision and give objective results without variability. This work uses well-known DL models for the classification and segmentation of mpMRI images to detect PCa. Our implementation involves four pipelines; Semantic DeepSegNet with ResNet50, DeepSegNet with recurrent neural network (RNN), U-Net with RNN, and U-Net with a long short-term memory (LSTM). Each segmentation model is paired with a different classifier to evaluate the performance using different metrics. The results of our experiments show that the pipeline that uses the combination of U-Net and the LSTM model outperforms all other combinations, excelling in both segmentation and classification tasks.
The visual examination of tissue biopsy sections is fundamental for cancer diagnosis, with pathologists analyzing sections at multiple magnifications to discern tumor cells and their subtypes. However, existing attention-based multiple instance learning (MIL) models, used for analyzing Whole Slide Images (WSIs) in cancer diagnostics, often overlook the contextual information of tumor and neighboring tiles, leading to misclassifications. To address this, we propose the Context-Aware Multiple Instance Learning (CAMIL) architecture. CAMIL incorporates neighbor-constrained attention to consider dependencies among tiles within a WSI and integrates contextual constraints as prior knowledge into the MIL model. We evaluated CAMIL on subtyping non-small cell lung cancer (TCGA-NSCLC) and detecting lymph node (CAMELYON16) metastasis, achieving test AUCs of 0.959\% and 0.975\%, respectively, outperforming other state-of-the-art methods. Additionally, CAMIL enhances model interpretability by identifying regions of high diagnostic value.
Deep neural networks (DNNs) are successful in many computer vision tasks. However, the most accurate DNNs require millions of parameters and operations, making them energy, computation and memory intensive. This impedes the deployment of large DNNs in low-power devices with limited compute resources. Recent research improves DNN models by reducing the memory requirement, energy consumption, and number of operations without significantly decreasing the accuracy. This paper surveys the progress of low-power deep learning and computer vision, specifically in regards to inference, and discusses the methods for compacting and accelerating DNN models. The techniques can be divided into four major categories: (1) parameter quantization and pruning, (2) compressed convolutional filters and matrix factorization, (3) network architecture search, and (4) knowledge distillation. We analyze the accuracy, advantages, disadvantages, and potential solutions to the problems with the techniques in each category. We also discuss new evaluation metrics as a guideline for future research.
Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translational research. In recent years, deep neural networks have achieved significant success in named entity recognition and many other Natural Language Processing (NLP) tasks. Most of these algorithms are trained end to end, and can automatically learn features from large scale labeled datasets. However, these data-driven methods typically lack the capability of processing rare or unseen entities. Previous statistical methods and feature engineering practice have demonstrated that human knowledge can provide valuable information for handling rare and unseen cases. In this paper, we address the problem by incorporating dictionaries into deep neural networks for the Chinese CNER task. Two different architectures that extend the Bi-directional Long Short-Term Memory (Bi-LSTM) neural network and five different feature representation schemes are proposed to handle the task. Computational results on the CCKS-2017 Task 2 benchmark dataset show that the proposed method achieves the highly competitive performance compared with the state-of-the-art deep learning methods.
ASR (automatic speech recognition) systems like Siri, Alexa, Google Voice or Cortana has become quite popular recently. One of the key techniques enabling the practical use of such systems in people's daily life is deep learning. Though deep learning in computer vision is known to be vulnerable to adversarial perturbations, little is known whether such perturbations are still valid on the practical speech recognition. In this paper, we not only demonstrate such attacks can happen in reality, but also show that the attacks can be systematically conducted. To minimize users' attention, we choose to embed the voice commands into a song, called CommandSong. In this way, the song carrying the command can spread through radio, TV or even any media player installed in the portable devices like smartphones, potentially impacting millions of users in long distance. In particular, we overcome two major challenges: minimizing the revision of a song in the process of embedding commands, and letting the CommandSong spread through the air without losing the voice "command". Our evaluation demonstrates that we can craft random songs to "carry" any commands and the modify is extremely difficult to be noticed. Specially, the physical attack that we play the CommandSongs over the air and record them can success with 94 percentage.