Pedro Avelar

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.

Pedro Henrique da Costa Avelar, Anderson R. Tavares, Luís C. Lamb

Superpixel-based image classification has traditionally leveraged graph neural networks (GNNs) for processing irregular image representations. Recent advances in computer vision, driven by Vision Transformers (ViTs), have introduced new paradigms in self-attentional models, surpassing convolutional neural networks (CNNs) in various tasks. However, a synergistic connection between GNNs, superpixels, and transformers remains unexplored. In this work, we propose Superpixel Transformers (SPT), a novel framework that unifies superpixel-based image classification and ViTs. SPT generalizes the Superpixel Image Classification with Graph Attention Networks (SICGAT) model and ViT to support arbitrary superpixel-based chunking strategies, connectivity graphs, and positional encodings. We introduce refinements including a multidimensional sine-cosine positional encoding and an enriched patch data structure that fully incorporates superpixel shape and color information. By testing SPT across datasets such as CIFAR10, FashionMNIST, and Imagenette, with various superpixel generation and graph connectivity strategies, we demonstrate that SPT achieves superior performance compared to previous superpixel-based GNN methods and remains competitive with ViTs. Notably, our approach addresses the limitations of SICGAT, such as information loss during pixel aggregation, and shows how constrained graph connectivity can enhance ViT performance. SPT bridges the gap between superpixel-based and transformer models, opening avenues for cross-domain generalization and future innovations in hybrid attentional frameworks, and showing that an image can also be worth $16\times16$ superpixels.

Rafael B. Audibert, Henrique Lemos, Pedro Avelar et al.

Artificial Intelligence is now recognized as a general-purpose technology with ample impact on human life. This work aims at understanding the evolution of AI and, in particular Machine learning, from the perspective of researchers' contributions to the field. In order to do so, we present several measures allowing the analyses of AI and machine learning researchers' impact, influence, and leadership over the last decades. This work also contributes, to a certain extent, to shed new light on the history and evolution of AI by exploring the dynamics involved in the field's evolution by looking at papers published at the flagship AI and machine learning conferences since the first International Joint Conference on Artificial Intelligence (IJCAI) held in 1969. AI development and evolution have led to increasing research output, reflected in the number of articles published over the last sixty years. We construct comprehensive citation collaboration and paper-author datasets and compute corresponding centrality measures to carry out our analyses. These analyses allow a better understanding of how AI has reached its current state of affairs in research. Throughout the process, we correlate these datasets with the work of the ACM Turing Award winners and the so-called two AI winters the field has gone through. We also look at self-citation trends and new authors' behaviors. Finally, we present a novel way to infer the country of affiliation of a paper from its organization. Therefore, this work provides a deep analysis of Artificial Intelligence history from information gathered and analysed from large technical venues datasets and suggests novel insights that can contribute to understanding and measuring AI's evolution.

Pedro Henrique da Costa Avelar, Le Ou-Yang, Min Wu et al.

Integrating complex, multi-omics data presents significant challenges. Existing approaches often face a trade-off between model interpretability and representational capacity, with most either relying on post-hoc interpretation or use linear models that may overlook complex interactions. We report Pathway Activity Autoencoders for the multi-omics setting, which embed prior knowledge via pathway-informed architectural constraints, fostering interpretability, while preserving representational power. Our multi-omic framework is applied in the context of breast cancer and is evaluated in survival prediction and subtype classification with results indicating a positive effect of integration. We conduct analysis of individual omics layer impact on end-task performance, revealing that gene, protein, and microRNA expression layers provide the strongest contribution. Repeatability studies indicate that, while dropout improves model robustness and consistency, excessive regularisation can reduce predictive performance. Finally, visualizations of the learned feature space illustrate the framework's intrinsic transparency and clinical relevance. The results underscore the value of multi-omic integration and delineate the impact of individual omics layers, establishing practical guidelines for integration within our framework. Overall, our pathway activity autoencoder frameworks yield superior latent representations that are biologically meaningful and are directly translatable into clinically relevant insights.

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.

Marcio Nicolau, Anderson R. Tavares, Zhiwei Zhang et al.

Computational learning theory states that many classes of boolean formulas are learnable in polynomial time. This paper addresses the understudied subject of how, in practice, such formulas can be learned by deep neural networks. Specifically, we analyze boolean formulas associated with model-sampling benchmarks, combinatorial optimization problems, and random 3-CNFs with varying degrees of constrainedness. Our experiments indicate that: (i) neural learning generalizes better than pure rule-based systems and pure symbolic approach; (ii) relatively small and shallow neural networks are very good approximators of formulas associated with combinatorial optimization problems; (iii) smaller formulas seem harder to learn, possibly due to the fewer positive (satisfying) examples available; and (iv) interestingly, underconstrained 3-CNF formulas are more challenging to learn than overconstrained ones. Such findings pave the way for a better understanding, construction, and use of interpretable neurosymbolic AI methods.

Henrique Lemos, Pedro Avelar, Marcelo Prates et al.

The recent developments and growing interest in neural-symbolic models has shown that hybrid approaches can offer richer models for Artificial Intelligence. The integration of effective relational learning and reasoning methods is one of the key challenges in this direction, as neural learning and symbolic reasoning offer complementary characteristics that can benefit the development of AI systems. Relational labelling or link prediction on knowledge graphs has become one of the main problems in deep learning-based natural language processing research. Moreover, other fields which make use of neural-symbolic techniques may also benefit from such research endeavours. There have been several efforts towards the identification of missing facts from existing ones in knowledge graphs. Two lines of research try and predict knowledge relations between two entities by considering all known facts connecting them or several paths of facts connecting them. We propose a neural-symbolic graph neural network which applies learning over all the paths by feeding the model with the embedding of the minimal subset of the knowledge graph containing such paths. By learning to produce representations for entities and facts corresponding to word embeddings, we show how the model can be trained end-to-end to decode these representations and infer relations between entities in a multitask approach. Our contribution is two-fold: a neural-symbolic methodology leverages the resolution of relational inference in large graphs, and we also demonstrate that such neural-symbolic model is shown more effective than path-based approaches

Henrique Lemos, Marcelo Prates, Pedro Avelar et al.

Deep learning has consistently defied state-of-the-art techniques in many fields over the last decade. However, we are just beginning to understand the capabilities of neural learning in symbolic domains. Deep learning architectures that employ parameter sharing over graphs can produce models which can be trained on complex properties of relational data. These include highly relevant NP-Complete problems, such as SAT and TSP. In this work, we showcase how Graph Neural Networks (GNN) can be engineered -- with a very simple architecture -- to solve the fundamental combinatorial problem of graph colouring. Our results show that the model, which achieves high accuracy upon training on random instances, is able to generalise to graph distributions different from those seen at training time. Further, it performs better than the Neurosat, Tabucol and greedy baselines for some distributions. In addition, we show how vertex embeddings can be clustered in multidimensional spaces to yield constructive solutions even though our model is only trained as a binary classifier. In summary, our results contribute to shorten the gap in our understanding of the algorithms learned by GNNs, as well as hoarding empirical evidence for their capability on hard combinatorial problems. Our results thus contribute to the standing challenge of integrating robust learning and symbolic reasoning in Deep Learning systems.

Pedro H. C. Avelar, Henrique Lemos, Marcelo O. R. Prates et al.

The application of deep learning to symbolic domains remains an active research endeavour. Graph neural networks (GNN), consisting of trained neural modules which can be arranged in different topologies at run time, are sound alternatives to tackle relational problems which lend themselves to graph representations. In this paper, we show that GNNs are capable of multitask learning, which can be naturally enforced by training the model to refine a single set of multidimensional embeddings $\in \mathbb{R}^d$ and decode them into multiple outputs by connecting MLPs at the end of the pipeline. We demonstrate the multitask learning capability of the model in the relevant relational problem of estimating network centrality measures, focusing primarily on producing rankings based on these measures, i.e. is vertex $v_1$ more central than vertex $v_2$ given centrality $c$?. We then show that a GNN can be trained to develop a \emph{lingua franca} of vertex embeddings from which all relevant information about any of the trained centrality measures can be decoded. The proposed model achieves $89\%$ accuracy on a test dataset of random instances with up to 128 vertices and is shown to generalise to larger problem sizes. The model is also shown to obtain reasonable accuracy on a dataset of real world instances with up to 4k vertices, vastly surpassing the sizes of the largest instances with which the model was trained ($n=128$). Finally, we believe that our contributions attest to the potential of GNNs in symbolic domains in general and in relational learning in particular.