Sarcopenia is a progressive loss of muscle mass and function linked to poor surgical outcomes such as prolonged hospital stays, impaired mobility, and increased mortality. Although it can be assessed through cross-sectional imaging by measuring skeletal muscle area (SMA), the process is time-consuming and adds to clinical workloads, limiting timely detection and management; however, this process could become more efficient and scalable with the assistance of artificial intelligence applications. This paper presents high-quality three-dimensional cross-sectional computed tomography (CT) images of patients with sarcopenia collected at the Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust. Expert clinicians manually annotated the SMA at the third lumbar vertebra, generating precise segmentation masks. We develop deep-learning models to measure SMA in CT images and automate this task. Our methodology employed transfer learning and self-supervised learning approaches using labelled and unlabeled CT scan datasets. While we developed qualitative assessment models for detecting sarcopenia, we observed that the quantitative assessment of SMA is more precise and informative. This approach also mitigates the issue of class imbalance and limited data availability. Our model predicted the SMA, on average, with an error of +-3 percentage points against the manually measured SMA. The average dice similarity coefficient of the predicted masks was 93%. Our results, therefore, show a pathway to full automation of sarcopenia assessment and detection.

Data from satellites or aerial vehicles are most of the times unlabelled. Annotating such data accurately is difficult, requires expertise, and is costly in terms of time. Even if Earth Observation (EO) data were correctly labelled, labels might change over time. Learning from unlabelled data within a semi-supervised learning framework for segmentation of aerial images is challenging. In this paper, we develop a new model for semantic segmentation of unlabelled images, the Non-annotated Earth Observation Semantic Segmentation (NEOS) model. NEOS performs domain adaptation as the target domain does not have ground truth semantic segmentation masks. The distribution inconsistencies between the target and source domains are due to differences in acquisition scenes, environment conditions, sensors, and times. Our model aligns the learned representations of the different domains to make them coincide. The evaluation results show that NEOS is successful and outperforms other models for semantic segmentation of unlabelled data.

Echocardiography (echo) is the first imaging modality used when assessing cardiac function. The measurement of functional biomarkers from echo relies upon the segmentation of cardiac structures and deep learning models have been proposed to automate the segmentation process. However, in order to translate these tools to widespread clinical use it is important that the segmentation models are robust to a wide variety of images (e.g. acquired from different scanners, by operators with different levels of expertise etc.). To achieve this level of robustness it is necessary that the models are trained with multiple diverse datasets. A significant challenge faced when training with multiple diverse datasets is the variation in label presence, i.e. the combined data are often partially-labelled. Adaptations of the cross entropy loss function have been proposed to deal with partially labelled data. In this paper we show that training naively with such a loss function and multiple diverse datasets can lead to a form of shortcut learning, where the model associates label presence with domain characteristics, leading to a drop in performance. To address this problem, we propose a novel label dropout scheme to break the link between domain characteristics and the presence or absence of labels. We demonstrate that label dropout improves echo segmentation Dice score by 62% and 25% on two cardiac structures when training using multiple diverse partially labelled datasets.

In this paper, we address an issue of finding explainable clusters of class-uniform data in labelled datasets. The issue falls into the domain of interpretable supervised clustering. Unlike traditional clustering, supervised clustering aims at forming clusters of labelled data with high probability densities. We are particularly interested in finding clusters of data of a given class and describing the clusters with the set of comprehensive rules. We propose an iterative method to extract high-density clusters with the help of decisiontree-based classifiers as the most intuitive learning method, and discuss the method of node selection to maximize quality of identified groups.

In this post I will go through the steps we took to create a human labelled dataset (i.e. Note that the other approach, and one we will talk about in another post, is to simply let a pre-trained tool do the work of labelling without any human intervention. But we thought that it would be worthwhile to try the human labelling out before seeing what the out-of-the-box results are. I used the photographs in the Claude William Jamson archive, kindly provided by Hull University Archives. This is a collection with a variety of content that lends itself to this kind of experiment.

Clustering in high dimension spaces is a difficult task; the usual distance metrics may no longer be appropriate under the curse of dimensionality. Indeed, the choice of the metric is crucial, and it is highly dependent on the dataset characteristics. However a single metric could be used to correctly perform clustering on multiple datasets of different domains. We propose to do so, providing a framework for learning a transferable metric. We show that we can learn a metric on a labelled dataset, then apply it to cluster a different dataset, using an embedding space that characterises a desired clustering in the generic sense. We learn and test such metrics on several datasets of variable complexity (synthetic, MNIST, SVHN, omniglot) and achieve results competitive with the state-of-the-art while using only a small number of labelled training datasets and shallow networks.

Despite the prevalence and many successes of deep learning applications in de novo molecular design, the problem of peptide generation targeting specific proteins remains unsolved. A main barrier for this is the scarcity of the high-quality training data. To tackle the issue, we propose a novel machine learning based peptide design architecture, called Latent Space Approximate Trajectory Collector (LSATC). It consists of a series of samplers on an optimization trajectory on a highly non-convex energy landscape that approximates the distributions of peptides with desired properties in a latent space. The process involves little human intervention and can be implemented in an end-to-end manner. We demonstrate the model by the design of peptide extensions targeting Beta-catenin, a key nuclear effector protein involved in canonical Wnt signalling. When compared with a random sampler, LSATC can sample peptides with $36\%$ lower binding scores in a $16$ times smaller interquartile range (IQR) and $284\%$ less hydrophobicity with a $1.4$ times smaller IQR. LSATC also largely outperforms other common generative models. Finally, we utilized a clustering algorithm to select 4 peptides from the 100 LSATC designed peptides for experimental validation. The result confirms that all the four peptides extended by LSATC show improved Beta-catenin binding by at least $20.0\%$, and two of the peptides show a $3$ fold increase in binding affinity as compared to the base peptide.

After writing this, someone asked me if there's a way to avoid to constantly pay OpenAI API and still use at scale any GPT-3-based NLP pipeline, trying to keep the same quality. Of course, if you have enough budget for your use case, a fine-tuned GPT-3 (which now turned to be the even more powerful GPT-3.5) may still be the best choice in terms of quality. Said that, I think there are strategies to use GPT-3 more wisely, save some money and still get good results. For ABSA, sentiment analysis or any other NLP text classification task, you may consider to redesign your pipeline leveraging few-shot text classification. Indeed, recently significant improvements have been made public on this kind of tasks.

Research in Natural Language Processing (NLP) has increasingly become important due to applications such as text classification, text mining, sentiment analysis, POS tagging, named entity recognition, textual entailment, and many others. This paper introduces several machine and deep learning methods with manual and automatic labelling for news classification in the Bangla language. We implemented several machine (ML) and deep learning (DL) algorithms. The ML algorithms are Logistic Regression (LR), Stochastic Gradient Descent (SGD), Support Vector Machine (SVM), Random Forest (RF), and K-Nearest Neighbour (KNN), used with Bag of Words (BoW), Term Frequency-Inverse Document Frequency (TF-IDF), and Doc2Vec embedding models. The DL algorithms are Long Short-Term Memory (LSTM), Bidirectional LSTM (BiLSTM), Gated Recurrent Unit (GRU), and Convolutional Neural Network (CNN), used with Word2vec, Glove, and FastText word embedding models. We develop automatic labelling methods using Latent Dirichlet Allocation (LDA) and investigate the performance of single-label and multi-label article classification methods. To investigate performance, we developed from scratch Potrika, the largest and the most extensive dataset for news classification in the Bangla language, comprising 185.51 million words and 12.57 million sentences contained in 664,880 news articles in eight distinct categories, curated from six popular online news portals in Bangladesh for the period 2014-2020. GRU and Fasttext with 91.83% achieve the highest accuracy for manually-labelled data. For the automatic labelling case, KNN and Doc2Vec at 57.72% and 75% achieve the highest accuracy for single-label and multi-label data, respectively. The methods developed in this paper are expected to advance research in Bangla and other languages.

Using deep learning techniques, anomalies in the paranasal sinus system can be detected automatically in MRI images and can be further analyzed and classified based on their volume, shape and other parameters like local contrast. However due to limited training data, traditional supervised learning methods often fail to generalize. Existing deep learning methods in paranasal anomaly classification have been used to diagnose at most one anomaly. In our work, we consider three anomalies. Specifically, we employ a 3D CNN to separate maxillary sinus volumes without anomalies from maxillary sinus volumes with anomalies. To learn robust representations from a small labelled dataset, we propose a novel learning paradigm that combines contrastive loss and cross-entropy loss. Particularly, we use a supervised contrastive loss that encourages embeddings of maxillary sinus volumes with and without anomaly to form two distinct clusters while the cross-entropy loss encourages the 3D CNN to maintain its discriminative ability. We report that optimising with both losses is advantageous over optimising with only one loss. We also find that our training strategy leads to label efficiency. With our method, a 3D CNN classifier achieves an AUROC of 0.85 while a 3D CNN classifier optimised with cross-entropy loss achieves an AUROC of 0.66.