Graph-Theoretic Models for the Prediction of Molecular Measurements

Anna Niane; Prudence Djagba

Home/Archive/arXiv

arXiv · 2604.19840

Graph-Theoretic Models for the Prediction of Molecular Measurements

Anna Niane·Prudence Djagba

View original source ↗Read source document ↗Export metadata ↓

Abstract

Graph-theoretic approaches offer simplicity, interpretability, and low computational cost for molecular property prediction. Among these, the model proposed by Mukwembi and Nyabadza, based on the external activity $D(G)$ and internal activity $ζ(G)$ indices, achieved strong results on a small flavonoid dataset. However, its ability to generalize to larger and chemically diverse datasets has not been tested. This study evaluates the baseline $D(G)$-$ζ(G)$ polynomial model on five benchmark datasets from MoleculeNet, covering biological activity (BACE, 1,513 molecules), lipophilicity (LogP synthetic, 14,610 molecules; LogP experimental, 753 molecules), aqueous solubility (ESOL, 1,128 molecules), and hydration free energy (SAMPL, 642 molecules). The baseline model achieves an average $R^2 = 0.24$, confirming limited transferability. To address this, a systematic enhancement framework is proposed, progressively incorporating Ridge regularization, additional graph descriptors, physicochemical properties, ensemble learning with Gradient Boosting, Lasso feature selection, and a hybrid approach combining topological indices with Morgan fingerprints. The enhanced models raise the average best $R^2$ to 0.79, with individual improvements ranging from 165\% to 274\%. All improvements are statistically significant ($p < 0.001$). A direct comparison with a Graph Convolutional Network under identical experimental conditions shows that the enhanced classical models match or outperform deep learning on all five datasets. Comparison with the recent GNN+PGM hybrid of Djagba et al.\ further confirms competitiveness, with the enhanced models achieving the best results on two datasets and tying on one. The entire framework requires no GPU, trains in under five minutes, and uses only open-source tools, making it accessible for researchers in resource-limited settings.

Explore related subjects

cs.LG q-bio.QM

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Anna Niane, Prudence Djagba. 2026-04-21. Graph-Theoretic Models for the Prediction of Molecular Measurements. https://arxiv.org/abs/2604.19840

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Analysis of Regularized Learning in Banach Spaces for Linear-functional Data

This article delves into the study of the theory of regularized learning in Banach spaces for linear-functional data. It encompasses discussions on representer theorems, pseudo-approximation theorems, and convergence theorems. Regularized learning is designed to minimize regularized empirical risks over a Banach space. The empirical risks are calculated by utilizing training data and multi-loss functions. The input training data are composed of linear functionals in a predual space of the Banach space to capture discrete local information from multimodal data and multiscale models. Through the regularized learning, approximations of the exact solution to an unidentified or uncertain original problem are globally achieved. In the convergence theorems, the convergence of the approximate solutions to the exact solution is established through the utilization of the weak* topology of the Banach space. The theorems of regularized learning are utilized in the interpretation of classical machine learning, such as support vector machines and artificial neural networks.

cs.LG↗

arXiv2026

On Minimal Depth in Neural Networks

Understanding the relationship between the depth of a neural network and its representational capacity is a central problem in deep learning theory. In this work, we develop a geometric framework to analyze the expressivity of ReLU networks with the notion of depth complexity for convex polytopes. The depth of a polytope recursively quantifies the number of alternating convex hull and Minkowski sum operations required to construct it. This geometric perspective serves as a rigorous tool for deriving depth lower bounds and understanding the structural limits of deep neural architectures. We establish lower and upper bounds on the depth of polytopes, as well as tight bounds for classical families. These results yield two main consequences. First, we provide a purely geometric proof of the expressivity bound by Arora et al. (2018), confirming that $\lceil \log_2(n+1)\rceil$ hidden layers suffice to represent any continuous piecewise linear (CPWL) function. Second, we prove that, unlike general ReLU networks, convex polytopes do not admit a universal depth bound. Specifically, the depth of cyclic polytopes in dimensions $n \geq 4$ grows unboundedly with the number of vertices. This result implies that Input Convex Neural Networks (ICNNs) cannot represent all convex CPWL functions with a fixed depth, revealing a sharp separation in expressivity between ICNNs and standard ReLU networks.

cs.LG↗

arXiv2026

ELEMENT: Episodic and Lifelong Exploration via Maximum Entropy

Reinforcement learning agents depend on reward signals whose density is rarely under the designer's control, and when such signals are absent, an agent must generate its own drive to explore. State entropy maximization offers a principled objective for this, but existing methods break down at scale in two ways: the intrinsic reward vanishes once a state has been visited, discouraging revisits to the very gateways that lead onward, and estimating entropy over millions of accumulated observations becomes computationally prohibitive. We address both with Episodic and Lifelong Exploration via Maximum Entropy (ELEMENT), a multiscale intrinsically motivated framework for reward-free exploration that transfers to downstream tasks. ELEMENT couples lifelong entropy maximization with a complementary episodic term acting on a faster timescale. For the episodic term, we derive average episodic state entropy, an intrinsic reward that is the exact minimizer of a tractable upper bound on the reward-decomposition objective; for the lifelong term, we propose a $k$NN graph-based estimator that keeps entropy tractable without forgetting. ELEMENT consistently outperforms state-of-the-art intrinsic reward baselines on state coverage and unsupervised pre-training. Videos, code, and supplementary material: https://sites.google.com/view/element-rl.

cs.LG↗