Enhancing Generalized Few-Shot Semantic Segmentation via Effective Knowledge Transfer

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.

Incorporating Prior Knowledge in Deep Learning Models via Pathway Activity Autoencoders

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.

Multi-Omic Data Integration and Feature Selection for Survival-based Patient Stratification via Supervised Concrete Autoencoders

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