Early detection and characterization of coronavirus disease (COVID-19), caused by SARS-CoV-2, remain critical for effective clinical response and public-health planning. The global availability of large-scale viral sequence data presents significant opportunities for computational analysis; however, existing approaches face notable limitations. Phylogenetic tree-based methods are computationally intensive and do not scale efficiently to today's multi-million-sequence datasets. Similarly, current embedding-based techniques often rely on aligned sequences or exhibit suboptimal predictive performance and high runtime costs, creating barriers to practical large-scale analysis. In this study, we focus on the most prevalent SARS-CoV-2 lineages associated with the spike protein region and introduce a scalable embedding method that leverages hashing to generate compact, low-dimensional representations of spike sequences. These embeddings are subsequently used to train a variety of machine learning models for supervised lineage classification. We conduct an extensive evaluation comparing our approach with multiple baseline and state-of-the-art biological sequence embedding methods across diverse metrics. Our results demonstrate that the proposed embeddings offer substantial improvements in efficiency, achieving up to 86.4\% classification accuracy while reducing embedding generation time by as much as 99.81\%. This highlights the method's potential as a fast, effective, and scalable solution for large-scale viral sequence analysis.

Traditional feature engineering approaches for molecular sequence classification suffer from sparsity issues and computational complexity, while deep learning models often underperform on tabular biological data. This paper introduces a novel topological approach that transforms molecular sequences into images by combining Chaos Game Representation (CGR) with Rips complex construction from algebraic topology. Our method maps sequence elements to 2D coordinates via CGR, computes pairwise distances, and constructs Rips complexes to capture both local structural and global topological features. We provide formal guarantees on representation uniqueness, topological stability, and information preservation. Extensive experiments on anticancer peptide datasets demonstrate superior performance over vector-based, sequence language models, and existing image-based methods, achieving 86.8\% and 94.5\% accuracy on breast and lung cancer datasets, respectively. The topological representation preserves critical sequence information while enabling effective utilization of vision-based deep learning architectures for molecular sequence analysis.

Reliable data-driven estimation of Shannon entropy from small data sets, where the number of examples is potentially smaller than the number of possible outcomes, is a critical matter in several applications. In this paper, we introduce a discrete entropy estimator, where we use the decomposability property in combination with estimations of the missing mass and the number of unseen outcomes to compensate for the negative bias induced by them. Experimental results show that the proposed method outperforms some classical estimators in undersampled regimes, and performs comparably with some well-established state-of-the-art estimators.

Hirschberg's algorithm (1975) reduces the space complexity for the longest common subsequence problem from $O(N^2)$ to $O(N)$ via recursive midpoint bisection on a grid dynamic program (DP). We show that the underlying idea generalizes to a broad class of dynamic programs with local dependencies on directed acyclic graphs (DP DAGs). Modeling a DP as deterministic time evolution over a topologically ordered DAG with frontier width $ω$ and bounded in-degree, and assuming a max-type semiring with deterministic tie breaking, we prove that in a standard offline random-access model any such DP admits deterministic traceback in space $O(ω\log T + (\log T)^{O(1)})$ cells over a fixed finite alphabet, where $T$ is the number of states. Our construction replaces backward dynamic programs by forward-only recomputation and organizes the time order into a height-compressed recursion tree whose nodes expose small "middle frontiers'' across which every optimal path must pass. The framework yields near-optimal traceback bounds for asymmetric and banded sequence alignment, one-dimensional recurrences, and dynamic-programming formulations on graphs of bounded pathwidth. We also show that an $Ω(ω)$ space term (in bits) is unavoidable in forward single-pass models and discuss conjectured $\sqrt{T}$-type barriers in streaming settings, supporting the view that space-efficient traceback is a structural property of width-bounded DP DAGs rather than a peculiarity of grid-based algorithms.

Spatially inhomogeneous magnetic fields offer a valuable, non-visual information source for positioning. Among systems leveraging this, magnetic field-based simultaneous localization and mapping (SLAM) systems are particularly attractive because they can provide positioning information and build a magnetic field map on the fly. Moreover, they have bounded error within mapped regions. However, state-of-the-art methods typically require low-drift odometry data provided by visual odometry or a wheel encoder, etc. This is because these systems need to minimize/reduce positioning errors while exploring, which happens when they are in unmapped regions. To address these limitations, this work proposes a loosely coupled and a tightly coupled inertial magnetic SLAM (IM-SLAM) system. The proposed systems use commonly available low-cost sensors: an inertial measurement unit (IMU), a magnetometer array, and a barometer. The use of non-visual data provides a significant advantage over visual-based systems, making it robust to low-visibility conditions. Both systems employ state-space representations, and magnetic field models on different scales. The difference lies in how they use a local and global magnetic field model. The loosely coupled system uses these models separately in two state-space models, while the tightly coupled system integrates them into one state-space model. Experiment results show that the tightly coupled IM-SLAM system achieves lower positioning errors than the loosely coupled system in most scenarios, with typical errors on the order of meters per 100 meters traveled. These results demonstrate the feasiblity of developing a full 3D IM-SLAM systems using low-cost sensors and the potential of applying these systems in emergency response scenarios such as mine/fire rescue.

Inverse medium scattering is an ill-posed, nonlinear wave-based imaging problem arising in medical imaging, remote sensing, and non-destructive testing. Machine learning (ML) methods offer increased inference speed and flexibility in capturing prior knowledge of imaging targets relative to classical optimization-based approaches; however, they perform poorly in regimes where the scattering behavior is highly nonlinear. A key limitation is that ML methods struggle to incorporate the physics governing the scattering process, which are typically inferred implicitly from the training data or loosely enforced via architectural design. In this paper, we present a method that endows a machine learning framework with explicit knowledge of problem physics, in the form of a differentiable solver representing the forward model. The proposed method progressively refines reconstructions of the scattering potential using measurements at increasing wave frequencies, following a classical strategy to stabilize recovery. Empirically, we find that our method provides high-quality reconstructions at a fraction of the computational or sampling costs of competing approaches.

General-purpose audio representations aim to map acoustically variable instances of the same event to nearby points, resolving content identity in a zero-shot setting. Unlike supervised classification benchmarks that measure adaptability via parameter updates, we introduce VocSim, a training-free benchmark probing the intrinsic geometric alignment of frozen embeddings. VocSim aggregates 125k single-source clips from 19 corpora spanning human speech, animal vocalizations, and environmental sounds. By restricting to single-source audio, we isolate content representation from the confound of source separation. We evaluate embeddings using Precision@k for local purity and the Global Separation Rate (GSR) for point-wise class separation. To calibrate GSR, we report lift over an empirical permutation baseline. Across diverse foundation models, a simple pipeline, frozen Whisper encoder features, time-frequency pooling, and label-free PCA, yields strong zero-shot performance. However, VocSim also uncovers a consistent generalization gap. On blind, low-resource speech, local retrieval drops sharply. While performance remains statistically distinguishable from chance, the absolute geometric structure collapses, indicating a failure to generalize to unseen phonotactics. As external validation, our top embeddings predict avian perceptual similarity, improve bioacoustic classification, and achieve state-of-the-art results on the HEAR benchmark. We posit that the intrinsic geometric quality measured here proxies utility in unlisted downstream applications. We release data, code, and a public leaderboard to standardize the evaluation of intrinsic audio geometry.

Learning the flows of hybrid systems that have both continuous and discrete time dynamics is challenging. The existing method learns the dynamics in each discrete mode, which suffers from the combination of mode switching and discontinuities in the flows. In this work, we propose CHyLL (Continuous Hybrid System Learning in Latent Space), which learns a continuous neural representation of a hybrid system without trajectory segmentation, event functions, or mode switching. The key insight of CHyLL is that the reset map glues the state space at the guard surface, reformulating the state space as a piecewise smooth quotient manifold where the flow becomes spatially continuous. Building upon these insights and the embedding theorems grounded in differential topology, CHyLL concurrently learns a singularity-free neural embedding in a higher-dimensional space and the continuous flow in it. We showcase that CHyLL can accurately predict the flow of hybrid systems with superior accuracy and identify the topological invariants of the hybrid systems. Finally, we apply CHyLL to the stochastic optimal control problem.

Abstract--Industrial automation with six-axis robotic arms is critical for many manufacturing tasks, including welding and additive manufacturing applications; however, many of these operations are functionally redundant due to the symmetrical tool axis, which effectively makes the operation a five-axis task. Exploiting this redundancy is crucial for achieving the desired workspace and dexterity required for the feasibility and optimisation of toolpath planning. Inverse kinematics algorithms can solve this in a fast, reactive framework, but these techniques are underutilised over the more computationally expensive offline planning methods. We propose a novel algorithm to solve functionally redundant inverse kinematics for robotic manipulation utilising a task space decomposition approach, the damped least-squares method and Halley's method to achieve fast and robust solutions with reduced joint motion. We evaluate our methodology in the case of toolpath optimisation in a cold spray coating application on a non-planar surface. The functionally redundant inverse kinematics algorithm can quickly solve motion plans that minimise joint motion, expanding the feasible operating space of the complex toolpath.

Large Language Models (LLMs) have demonstrated significant potential in democratizing access to information. However, in the domain of agriculture, general-purpose models frequently suffer from contextual hallucination, which provides non-factual advice or answers are scientifically sound in one region but disastrous in another due to variations in soil, climate, and local regulations. We introduce AgriRegion, a Retrieval-Augmented Generation (RAG) framework designed specifically for high-fidelity, region-aware agricultural advisory. Unlike standard RAG approaches that rely solely on semantic similarity, AgriRegion incorporates a geospatial metadata injection layer and a region-prioritized re-ranking mechanism. By restricting the knowledge base to verified local agricultural extension services and enforcing geo-spatial constraints during retrieval, AgriRegion ensures that the advice regarding planting schedules, pest control, and fertilization is locally accurate. We create a novel benchmark dataset, AgriRegion-Eval, which comprises 160 domain-specific questions across 12 agricultural subfields. Experiments demonstrate that AgriRegion reduces hallucinations by 10-20% compared to state-of-the-art LLMs systems and significantly improves trust scores according to a comprehensive evaluation.