Sophia Tsoka

Pedro Henrique da Costa Avelar, Roman Laddach, Sophia Karagiannis et al.

Cancer is a complex disease with significant social and economic impact. Advancements in high-throughput molecular assays and the reduced cost for performing high-quality multi-omics measurements have fuelled insights through machine learning . Previous studies have shown promise on using multiple omic layers to predict survival and stratify cancer patients. In this paper, we developed a Supervised Autoencoder (SAE) model for survival-based multi-omic integration which improves upon previous work, and report a Concrete Supervised Autoencoder model (CSAE), which uses feature selection to jointly reconstruct the input features as well as predict survival. Our experiments show that our models outperform or are on par with some of the most commonly used baselines, while either providing a better survival separation (SAE) or being more interpretable (CSAE). We also perform a feature selection stability analysis on our models and notice that there is a power-law relationship with features which are commonly associated with survival. The code for this project is available at: https://github.com/phcavelar/coxae

Pedro Henrique da Costa Avelar, Min Wu, Sophia Tsoka

Motivation: Despite advances in the computational analysis of high-throughput molecular profiling assays (e.g. transcriptomics), a dichotomy exists between methods that are simple and interpretable, and ones that are complex but with lower degree of interpretability. Furthermore, very few methods deal with trying to translate interpretability in biologically relevant terms, such as known pathway cascades. Biological pathways reflecting signalling events or metabolic conversions are Small improvements or modifications of existing algorithms will generally not be suitable, unless novel biological results have been predicted and verified. Determining which pathways are implicated in disease and incorporating such pathway data as prior knowledge may enhance predictive modelling and personalised strategies for diagnosis, treatment and prevention of disease. Results: We propose a novel prior-knowledge-based deep auto-encoding framework, PAAE, together with its accompanying generative variant, PAVAE, for RNA-seq data in cancer. Through comprehensive comparisons among various learning models, we show that, despite having access to a smaller set of features, our PAAE and PAVAE models achieve better out-of-set reconstruction results compared to common methodologies. Furthermore, we compare our model with equivalent baselines on a classification task and show that they achieve better results than models which have access to the full input gene set. Another result is that using vanilla variational frameworks might negatively impact both reconstruction outputs as well as classification performance. Finally, our work directly contributes by providing comprehensive interpretability analyses on our models on top of improving prognostication for translational medicine.

Xinyue Chen, Miaojing Shi, Zijian Zhou et al.

Generalized few-shot semantic segmentation (GFSS) aims to segment objects of both base and novel classes, using sufficient samples of base classes and few samples of novel classes. Representative GFSS approaches typically employ a two-phase training scheme, involving base class pre-training followed by novel class fine-tuning, to learn the classifiers for base and novel classes respectively. Nevertheless, distribution gap exists between base and novel classes in this process. To narrow this gap, we exploit effective knowledge transfer from base to novel classes. First, a novel prototype modulation module is designed to modulate novel class prototypes by exploiting the correlations between base and novel classes. Second, a novel classifier calibration module is proposed to calibrate the weight distribution of the novel classifier according to that of the base classifier. Furthermore, existing GFSS approaches suffer from a lack of contextual information for novel classes due to their limited samples, we thereby introduce a context consistency learning scheme to transfer the contextual knowledge from base to novel classes. Extensive experiments on PASCAL-5$^i$ and COCO-20$^i$ demonstrate that our approach significantly enhances the state of the art in the GFSS setting. The code is available at: https://github.com/HHHHedy/GFSS-EKT.

Chengan Che, Chao Wang, Tom Vercauteren et al.

Traditional open-access datasets focusing on surgical procedures are often limited by their small size, typically consisting of fewer than 100 videos and less than 30 hours of footage, which leads to poor model generalization. To address this constraint, a new dataset called LEMON has been compiled using a novel aggregation pipeline that collects high-resolution videos from online sources. Featuring an extensive collection of over 4K surgical videos totaling 938 hours (85 million frames) of high-quality footage across multiple procedure types, LEMON offers a comprehensive resource surpassing existing alternatives in size and scope, including two novel downstream tasks. To demonstrate the effectiveness of this diverse dataset, we introduce LemonFM, a foundation model pretrained on LEMON using a novel self-supervised augmented knowledge distillation approach. LemonFM consistently outperforms existing surgical foundation models across four downstream tasks and six datasets, achieving significant gains in surgical phase recognition (+9.5pp, +9.4pp, and +8.4pp of Jaccard in AutoLaparo, M2CAI16, and Cholec80), surgical action recognition (+4.4pp of mAP in CholecT50), surgical tool presence detection (+5.3pp and +10.2pp of mAP in Cholec80 and GraSP), and surgical semantic segmentation (+8.3pp of mDice in CholecSeg8k). LEMON and LemonFM will serve as foundational resources for the research community and industry, accelerating progress in developing autonomous robotic surgery systems and ultimately contributing to safer and more accessible surgical care worldwide.

Chao Wang, Chengan Che, Xinyue Chen et al.

Counterfactual explanations (CFEs) are minimal and semantically meaningful modifications of the input of a model that alter the model predictions. They highlight the decisive features the model relies on, providing contrastive interpretations for classifiers. State-of-the-art visual counterfactual explanation methods are designed to explain image classifiers. The generation of CFEs for video classifiers remains largely underexplored. For the counterfactual videos to be useful, they have to be physically plausible, temporally coherent, and exhibit smooth motion trajectories. Existing CFE image-based methods, designed to explain image classifiers, lack the capacity to generate temporally coherent, smooth and physically plausible video CFEs. To address this, we propose Back To The Feature (BTTF), an optimization framework that generates video CFEs. Our method introduces two novel features, 1) an optimization scheme to retrieve the initial latent noise conditioned by the first frame of the input video, 2) a two-stage optimization strategy to enable the search for counterfactual videos in the vicinity of the input video. Both optimization processes are guided solely by the target classifier, ensuring the explanation is faithful. To accelerate convergence, we also introduce a progressive optimization strategy that incrementally increases the number of denoising steps. Extensive experiments on video datasets such as Shape-Moving (motion classification), MEAD (emotion classification), and NTU RGB+D (action classification) show that our BTTF effectively generates valid, visually similar and realistic counterfactual videos that provide concrete insights into the classifier's decision-making mechanism.

Chengan Che, Chao Wang, Xinyue Chen et al.

Procedural activities, ranging from routine cooking to complex surgical operations, are highly structured as a set of actions conducted in a specific temporal order. Despite their success on static images and short clips, current self-supervised learning methods often overlook the procedural nature that underpins such activities. We expose the lack of procedural awareness in current SSL methods with a motivating experiment: models pretrained on forward and time-reversed sequences produce highly similar features, confirming that their representations are blind to the underlying procedural order. To address this shortcoming, we propose PL-Stitch, a self-supervised framework that harnesses the inherent temporal order of video frames as a powerful supervisory signal. Our approach integrates two novel probabilistic objectives based on the Plackett-Luce (PL) model. The primary PL objective trains the model to sort sampled frames chronologically, compelling it to learn the global workflow progression. The secondary objective, a spatio-temporal jigsaw loss, complements the learning by capturing fine-grained, cross-frame object correlations. Our approach consistently achieves superior performance across five surgical and cooking benchmarks. Specifically, PL-Stitch yields significant gains in surgical phase recognition (e.g., +11.4 pp k-NN accuracy on Cholec80) and cooking action segmentation (e.g., +5.7 pp linear probing accuracy on Breakfast), demonstrating its effectiveness for procedural video representation learning.

Pedro Henrique da Costa Avelar, Min Wu, Sophia Tsoka

Motivation: Network-based analyses of omics data are widely used, and while many of these methods have been adapted to single-cell scenarios, they often remain memory- and space-intensive. As a result, they are better suited to batch data or smaller datasets. Furthermore, the application of network-based methods in multi-omics often relies on similarity-based networks, which lack structurally-discrete topologies. This limitation may reduce the effectiveness of graph-based methods that were initially designed for topologies with better defined structures. Results: We propose Subset-Contrastive multi-Omics Network Embedding (SCONE), a method that employs contrastive learning techniques on large datasets through a scalable subgraph contrastive approach. By exploiting the pairwise similarity basis of many network-based omics methods, we transformed this characteristic into a strength, developing an approach that aims to achieve scalable and effective analysis. Our method demonstrates synergistic omics integration for cell type clustering in single-cell data. Additionally, we evaluate its performance in a bulk multi-omics integration scenario, where SCONE performs comparable to the state-of-the-art despite utilising limited views of the original data. We anticipate that our findings will motivate further research into the use of subset contrastive methods for omics data.