Saman Halgamuge

Ravisha Rupasinghe, Rajith Vidanaarachchi, Asela Hevapathige et al.

Physics-Informed Neural Network (PINN) is a way of including knowledge in the form of equations in Machine Learning methods. Beyond equations, knowledge exists in other forms, such as text and network structure. While existing PINN-based approaches discover equation parameters from data, they rely solely on experimental measurements. We propose a new PINN framework that enriches parameter discovery by incorporating auxiliary knowledge sources. We instantiate our framework for microbiology, where generalised Lotka-Volterra (gLV) serves as a biological foundation for modelling microbial communities. We demonstrate that incorporating knowledge improves microbial community modelling. Our framework enriches the gLV parameters using peer-reviewed metagenomics literature, as text provides biological context on external influences that gLV alone cannot capture. We combine this knowledge with experimental measurements of microbial abundance using a data-driven integration approach. We integrate network-based structural knowledge by explicitly modelling microbial interactions. Our knowledge-inclusive framework infers microbial networks, revealing ecological insights. We validate these findings against ecological roles documented in the literature. We evaluate on real and simulated datasets spanning human- and plant-associated microbial communities. Our framework improves over the state-of-the-art by up to 53%, even without knowledge. Knowledge addition yields gains of up to 23% in Bray-Curtis Dissimilarity-based accuracy and 47% in $\mathrm{R}^2$.

Thiru Thillai Nadarasar Bahavan, Sachith Seneviratne, Saman Halgamuge

Deep Neural Network (DNN) classifiers suffer from poor calibration when their softmax outputs (predictive confidence) deviate from the empirical likelihoods. This manifests itself as either overconfident incorrect predictions or under-confident correct predictions. Label smoothing (LS) enhances model calibration by introducing entropy regularization during training through redistributing probability mass from the ground-truth label to the remaining classes. LS, including Margin-based LS (MbLS), have restrictive assumptions: they rely on predefined, uniform smoothing rules and only tackle overconfidence. In reality, samples exhibit diverse characteristics, such as difficulty/ambiguity, that interact with the evolving nature of the model being trained. In training, samples may have various degrees of under- or overconfidence. To overcome this, a mechanism that identifies the specific confidence state of each sample and determines the appropriate degree of smoothing in each training step is needed, tailoring the adjustment to the individual sample. We propose FedLAS: Feature-Modulated Bidirectional Label Smoothing, a plug-and-play algorithm for label smoothing-based losses. In FedLAS, we introduce a Feature Norm-based Confidence Indicator (NCI) to control smoothing and a Bidirectional Calibration Gating (BCG) module to detect both over and under-confidence. Our algorithm can be integrated with LS and MbLS based losses when applied to standard DNNs, enhancing performance. Extensive experiments on standard and fine-grained high-resolution vision benchmarks show that FedLAS consistently improves calibration compared to modern baselines, reducing Expected Calibration Error (ECE) and Adaptive ECE while maintaining Top-1 accuracy. Code: github.com/nadarasarbahavan/FEDLAS