Related papers: GBNL: Graded Betti Number Learning of Complex Biol…
Artificial intelligence-assisted drug design is revolutionizing the pharmaceutical industry. Effective molecular features are crucial for accurate machine learning predictions, and advanced mathematics plays a key role in designing these…
We introduce several new quantum algorithms for estimating homological invariants, specifically Betti numbers and persistent Betti numbers, of a simplicial complex given via a structured classical input. At the core of our algorithm lies…
Topological data analysis (TDA) has emerged as an effective approach in data science, with its key technique, persistent homology, rooted in algebraic topology. Although alternative approaches based on differential topology, geometric…
Recent years have witnessed a fast growth in mathematical artificial intelligence (AI). One of the most successful mathematical AI approaches is topological data analysis (TDA) via persistent homology (PH) that provides explainable AI (xAI)…
Biomolecular structure comparison not only reveals evolutionary relationships, but also sheds light on biological functional properties. However, traditional definitions of structure or sequence similarity always involve superposition or…
The Betti tables of a multigraded module encode the grades at which there is an algebraic change in the module. Multigraded modules show up in many areas of pure and applied mathematics, and in particular in topological data analysis, where…
Topological Data Analysis (TDA), a relatively new field of data analysis, has proved very useful in a variety of applications. The main persistence tool from TDA is persistent homology in which data structure is examined at many scales.…
Persistent homology is a powerful mathematical tool that summarizes useful information about the shape of data allowing one to detect persistent topological features while one adjusts the resolution. However, the computation of such…
Understanding how protein mutations affect protein-nucleic acid binding is critical for unraveling disease mechanisms and advancing therapies. Current experimental approaches are laborious, and computational methods remain limited in…
We study how the topology of feature embedding space changes as it passes through the layers of a well-trained deep neural network (DNN) through Betti numbers. Motivated by existing studies using simplicial complexes on shallow fully…
Meta-learning offers a principled framework leveraging \emph{task-invariant} priors from related tasks, with which \emph{task-specific} models can be fine-tuned on downstream tasks, even with limited data records. Gradient-based…
There is heightened interest in quantum algorithms for Topological Data Analysis (TDA) as it is a powerful tool for data analysis, but it can get highly computationally expensive. Even though there are different propositions and…
Topological data analysis (TDA) is a fast-growing field that utilizes advanced tools from topology to analyze large-scale data. A central problem in topological data analysis is estimating the so-called Betti numbers of the underlying…
Topological invariants of a dataset, such as the number of holes that survive from one length scale to another (persistent Betti numbers) can be used to analyze and classify data in machine learning applications. We present an improved…
Topological data analysis (TDA) is an emergent field of data analysis. The critical step of TDA is computing the persistent Betti numbers. Existing classical algorithms for TDA are limited if we want to learn from high-dimensional…
Binding energy is a fundamental thermodynamic property that governs molecular interactions, playing a crucial role in fields such as healthcare and the natural sciences. It is particularly relevant in drug development, vaccine design, and…
Prediction of protein-ligand (PL) binding affinity remains the key to drug discovery. Popular approaches in recent years involve graph neural networks (GNNs), which are used to learn the topology and geometry of PL complexes. However, GNNs…
Accurate prediction of residue-level pKa values is essential for understanding protein function, stability, and reactivity. While existing resources such as DeepKaDB and CpHMD-derived datasets provide valuable training data, their…
Topological data analysis (TDA) is a rapidly growing area that applies techniques from algebraic topology to extract robust features from large-scale data. A key task in TDA is the estimation of (normalized) Betti numbers, which capture…
Generalized linear mixed models (GLMM) encompass large class of statistical models, with a vast range of applications areas. GLMM extends the linear mixed models allowing for different types of response variable. Three most common data…