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Other Quantitative Biology

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24 featured work(s)

preprint2026arXiv

SpecX: A Large-Scale Benchmark for Multi-Modal Spectroscopy and Cross-Paradigm Evaluation

Existing spectral benchmarks are limited in scale, modality alignment, and evaluation scope, and typically focus on either specialized models or multimodal language models (MLLMs). We introduce SpecX, a large-scale benchmark for multi-modal spectroscopy with cross-paradigm evaluation. SpecX contains 1.7M molecules with diverse spectral modalities, including NMR (1H, 13C, HSQC), IR, MS,UV,Raman and FL, and is organized into three tiers: a large-scale dataset for pretraining, an aligned multi-spectral subset for benchmarking, and a high-quality experimental subset for evaluation. SpecX supports a range of tasks such as molecular elucidation, spectrum simulation, and spectral understanding, and enables unified evaluation across both specialized spectral models and MLLMs. Experiments show that specialized models excel at signal-level modeling, while MLLMs exhibit strengths in high-level reasoning but lack precise spectral grounding. SpecX establishes a unified benchmark for spectral intelligence and highlights the need for spectrum-native foundation models.

preprint2026arXiv

Internally triggered retrospective learning in neural networks

Learning in artificial neural networks usually relies on continuous, externally driven weight updates, in which parameters are modified at every step in response to incoming data, error signals or reward feedback. In this setting, routine and informative inputs contribute similarly to parameter adjustment. We introduce a learning approach in which parameter updates are governed by internally generated events arising from the network own representational dynamics. During ongoing activity, synaptic interactions are accumulated as latent traces encoding recent coactivation patterns, without immediately modifying the underlying parameters. In parallel, an internal predictive process estimates the evolving latent state, while a scalar measure of discrepancy between predicted and observed states is continuously computed. When discrepancy exceeds an adaptive threshold derived from recent error statistics, a learning event is triggered, inducing a retrospective update selectively integrating past activity into the current configuration. We performed simulations using a minimal neural network exposed to structured sequential inputs with transient perturbations. We found that learning occurs through sparse, temporally localized events associated with increases in prediction error, leading to stepwise changes in synaptic efficacy and discrete transitions in latent state organization. By selectively reorganizing parameters in response to internally detected discrepancies, our episodic updating may reduce unnecessary parameter drift while preserving informative patterns. Potential applications include systems requiring selective adaptation to rare or informative inputs such as physiological, industrial or environmental monitoring, edge computing under limited energy budgets, autonomous systems operating in dynamic conditions and sequential computational data processing.

preprint2022arXiv

A new Standard DNA damage (SDD) data format

Our understanding of radiation induced cellular damage has greatly improved over the past decades. Despite this progress, there are still many obstacles to fully understanding how radiation interacts with biologically relevant cellular components to form observable endpoints. One hurdle is the difficulty faced by members of different research groups in directly comparing results. Multiple Monte Carlo codes have been developed to simulate damage induction at the DNA scale, while at the same time various groups have developed models that describe DNA repair processes with varying levels of detail. These repair models are intrinsically linked to the damage model employed in their development, making it difficult to disentangle systematic effects in either part of the modelling chain. The modelling chain typically consists of track structure Monte Carlo simulations of the physics interactions creating direct damages to the DNA; followed by simulations of the production and initial reactions of chemical species causing indirect damages. After the DNA damage induction, DNA repair models combine the simulated damage patterns with biological models to determine the biological consequences of the damage. We propose a new Standard data format for DNA Damage to unify the interface between the simulation of damage induction and the biological modelling of cell repair processes. Such a standard greatly facilitates inter model comparisons, providing an ideal environment to tease out model assumptions and identify persistent, underlying mechanisms. Through inter model comparisons, this unified standard has the potential to greatly advance our understanding of the underlying mechanisms of radiation induced DNA damage and the resulting observable biological effects.

preprint2022arXiv

Mobile Human Ad Hoc Networks: A Communication Engineering Viewpoint on Interhuman Airborne Pathogen Transmission

A number of transmission models for airborne pathogens transmission, as required to understand airborne infectious diseases such as COVID-19, have been proposed independently from each other, at different scales, and by researchers from various disciplines. We propose a communication engineering approach that blends different disciplines such as epidemiology, biology, medicine, and fluid dynamics. The aim is to present a unified framework using communication engineering, and to highlight future research directions for modeling the spread of infectious diseases through airborne transmission. We introduce the concept of mobile human ad hoc networks (MoHANETs), which exploits the similarity of airborne transmission-driven human groups with mobile ad hoc networks and uses molecular communication as the enabling paradigm. In the MoHANET architecture, a layered structure is employed where the infectious human emitting pathogen-laden droplets and the exposed human to these droplets are considered as the transmitter and receiver, respectively. Our proof-of-concept results, which we validated using empirical COVID-19 data, clearly demonstrate the ability of our MoHANET architecture to predict the dynamics of infectious diseases by considering the propagation of pathogen-laden droplets, their reception and mobility of humans.

preprint2026arXiv

Entropy-Dominated Temporal Vocal Dynamics as Digital Biomarkers for Depression Detection

Automated depression detection often relies on static aggregation of conversational signals, potentially obscuring clinically meaningful behavioral dynamics. We investigated whether entropy-driven temporal biomarkers improve depression detection beyond standard pooled features using the DAIC-WOZ corpus. Using 142 labeled participants, we reconstructed utterance-level acoustic trajectories and compared pooled temporal baselines, trajectory dynamics, Shannon entropy biomarkers, recurrence quantification, sample entropy, fractal complexity, and coupling biomarkers under leakage-aware validation. Static pooling achieved an AUC of 0.593, trajectory dynamics improved performance to 0.637, and entropy biomarkers produced the strongest statistically significant improvement over pooled baselines (AUC 0.646; nested cross-validated AUC 0.615; permutation p = 0.017). Entropy biomarkers outperformed recurrence, coupling, sample entropy, and fractalbased features, with several biomarkers stable across folds. These findings suggest depression-related signal may lie less in average acoustic levels than in entropy of conversational dynamics, supporting temporally informed digital phenotypes for mental-health assessment.

preprint2026arXiv

A Logistic Regression Model to Predict Malaria Severity in Children

One of the main causes of death around the globe is malaria. Researchers have sought to develop predictive models for malaria outbreaks based on meteorological data, climate data and the breeding cycle of Plasmodium, the causative agent of malaria. This study predicts the severity of malaria based on environmental and biological factors. A logistic regression model was developed in this study to predict the severity of malaria based on such factors as sickle cell disease, stagnant water, garbage dump, wet lawns, and the use of treated mosquito nets, with an 83.3% accuracy rate. The study was carried out in the Bosomtwe District of Ghana with 417 respondents. It was deduced that although children in the District are highly prone to malaria infection, the severity is very low. The study recommends that not just having a good sample size alone is important during machine learning model development, but also having a good sample representation of the various class labels is equally important.

preprint2022arXiv

Numerical investigation of Differential Biological Models via RBF collocation Method with Genetic Strategy

In this paper, we use Kansa method for solving the system of differential equations in the area of biology. One of the challenges in Kansa method is picking out an optimum value for Shape parameter in Radial Basis Function to achieve the best result of the method because there are not any available analytical approaches for obtaining optimum Shape parameter. For this reason, we design a genetic algorithm to detect a close optimum Shape parameter. The experimental results show that this strategy is efficient in the systems of differential models in biology such as HIV and Influenza. Furthermore, we prove that using Pseudo-Combination formula for crossover in genetic strategy leads to convergence in the nearly best selection of Shape parameter.

preprint2024arXiv

A how-to guide for code-sharing in biology

Computational biology continues to spread into new fields, becoming more accessible to researchers trained in the wet lab who are eager to take advantage of growing datasets, falling costs, and novel assays that present new opportunities for discovery even outside of the much-discussed developments in artificial intelligence. However, guidance for implementing these techniques is much easier to find than guidance for reporting their use, leaving biologists to guess which details and files are relevant. Here, we provide a set of recommendations for sharing code, with an eye toward guiding those who are comparatively new to applying open science principles to their computational work. Additionally, we review existing literature on the topic, summarize the most common tips, and evaluate the code-sharing policies of the most influential journals in biology, which occasionally encourage code-sharing but seldom require it. Taken together, we provide a user manual for biologists who seek to follow code-sharing best practices but are unsure where to start.

preprint2023arXiv

Many bioinformatics programming tasks can be automated with ChatGPT

Computer programming is a fundamental tool for life scientists, allowing them to carry out many essential research tasks. However, despite a variety of educational efforts, learning to write code can be a challenging endeavor for both researchers and students in life science disciplines. Recent advances in artificial intelligence have made it possible to translate human-language prompts to functional code, raising questions about whether these technologies can aid (or replace) life scientists' efforts to write code. Using 184 programming exercises from an introductory-bioinformatics course, we evaluated the extent to which one such model -- OpenAI's ChatGPT -- can successfully complete basic- to moderate-level programming tasks. On its first attempt, ChatGPT solved 139 (75.5%) of the exercises. For the remaining exercises, we provided natural-language feedback to the model, prompting it to try different approaches. Within 7 or fewer attempts, ChatGPT solved 179 (97.3%) of the exercises. These findings have important implications for life-sciences research and education. For many programming tasks, researchers no longer need to write code from scratch. Instead, machine-learning models may produce usable solutions. Instructors may need to adapt their pedagogical approaches and assessment techniques to account for these new capabilities that are available to the general public.

preprint2022arXiv

Approaches to the classification of complex systems: Words, texts, and more

The Chapter starts with introductory information about quantitative linguistics notions, like rank--frequency dependence, Zipf's law, frequency spectra, etc. Similarities in distributions of words in texts with level occupation in quantum ensembles hint at a superficial analogy with statistical physics. This enables one to define various parameters for texts based on this physical analogy, including "temperature", "chemical potential", entropy, and some others. Such parameters provide a set of variables to classify texts serving as an example of complex systems. Moreover, texts are perhaps the easiest complex systems to collect and analyze. Similar approaches can be developed to study, for instance, genomes due to well-known linguistic analogies. We consider a couple of approaches to define nucleotide sequences in mitochondrial DNAs and viral RNAs and demonstrate their possible application as an auxiliary tool for comparative analysis of genomes. Finally, we discuss entropy as one of the parameters, which can be easily computed from rank--frequency dependences. Being a discriminating parameter in some problems of classification of complex systems, entropy can be given a proper interpretation only in a limited class of problems. Its overall role and significance remain an open issue so far.

preprint2023arXiv

Translational Quantum Machine Intelligence for Modeling Tumor Dynamics in Oncology

Quantifying the dynamics of tumor burden reveals useful information about cancer evolution concerning treatment effects and drug resistance, which play a crucial role in advancing model-informed drug developments (MIDD) towards personalized medicine and precision oncology. The emergence of Quantum Machine Intelligence offers unparalleled insights into tumor dynamics via a quantum mechanics perspective. This paper introduces a novel hybrid quantum-classical neural architecture named $η-$Net that enables quantifying quantum dynamics of tumor burden concerning treatment effects. We evaluate our proposed neural solution on two major use cases, including cohort-specific and patient-specific modeling. In silico numerical results show a high capacity and expressivity of $η-$Net to the quantified biological problem. Moreover, the close connection to representation learning - the foundation for successes of modern AI, enables efficient transferability of empirical knowledge from relevant cohorts to targeted patients. Finally, we leverage Bayesian optimization to quantify the epistemic uncertainty of model predictions, paving the way for $η-$Net towards reliable AI in decision-making for clinical usages.

preprint2022arXiv

Experimental Evidence Supporting a New "Osmosis Law & Theory" Derived New Formula that Improves van't Hoff Osmotic Pressure Equation

Experimental data were used to support a new concept of osmotic force and a new osmotic law that can explain the osmotic process without the difficulties encountered with van't Hoff osmotic pressure theory. Derived new osmotic formula with curvilinear equation (via new osmotic law) overcomes the limitations and incompleteness of van't Hoff (linear) osmotic pressure equation, $π=(n/v)RT$, (for ideal dilute solution only). The application of this classical theory often resulted in contradiction regardless of miscellaneous explaining efforts. This is due to the lack of a scientific concept like "osmotic force" that we believe can elaborate the osmotic process. Via this new concept, the proposed new osmotic law and derived new osmotic pressure equation will greatly complete and improve the theoretical consistency within the scientific framework of osmosis.

preprint2022arXiv

Biophysical Sequence Analysis of Functional Differences of Piezo1 and Piezo2

Because of their large size and widespread mechanosensitive interactions the only recently discovered titled transmembrane proteins have attracted much attention. Here we present and discuss their hydropathic profiles using a new method of sequence analysis. We find large-scale similarities and differences not obtainable by conventional sequence or structural studies. These differences support the evolution-towards-criticality conjecture popular among physicists.

preprint2022arXiv

Global technology access in biolabs -- from DIY trend to an open source transformation

This article illustrates how open hardware solutions are implemented by researchers as a strategy to access technology for cutting-edge research. Specifically, it is discussed what kind of open technologies are most enabling in scientific environments characterized by economic and infrastructural constraints. It is demonstrated that do-it-yourself (DIY) technologies are already wide spread, in particular in countries with lower science funding, which in turn is the basis for the development of open technologies. Beyond financial accessibility, open hardware can be transformational to the technology access of laboratories through advantages in local production and direct knowledge transfer. Central drivers of the adoption of appropriate technologies in biolabs globally are open sharing, digital fabrication, local production, standard parts use, and detailed documentation.

preprint2021arXiv

Antibacterial and antibiofilm activities of a traditional herbal formula against respiratory infection causing bacteria

The plants, Althaea officinalis, Tilia cordata and Psidium guaja have been used traditionally to treat respiratory infection symptoms. Flowers of A. officinalis and leaves of T. cordata and P. guaja have been used to treat cough, sore throat, catarrh, oral and pharyngeal mucosa irritation. Therefore, this study was designed to examine the antibacterial and antibiofilm effects of these plants individually as well as in combination, as a formula against respiratory infections causing pathogens. The tested pathogens were Extended Spectrum Beta-Lactamase producing Escherichia coli (ESBL), Beta-Lactamase producing Escherichia coli (BL), Beta-Lactamase producing Klebsiella pneumoniae (BL), Beta-Lactamase producing Pseudomonas aeruginosa (BL), Enterobacter cloacae, and Beta-Lactamase producing Staphylococcus aureus (BL). The tested plants were extracted using ethanol and then fractionated using different polarity solvents (hexane, ethyl acetate and water). Disc diffusion and microdilution (Minimum Inhibitory Concentration) methods were used to evaluate the antibacterial activity while the antibiofilm activity was tested using crystal violet assay. The results showed that A. officinalis and T. cordata extracts and fractions exhibited weak antibacterial activity having MIC values ranged from 6.25 to 12.5 mg/mL. P. guaja exhibited moderate antibacterial activity with MIC values ranged from 6.25 to 1.56 mg/mL. Combination between these plants extracts and fractions in equal proportion provides stronger antibacterial (with MIC values ranged from 6.25 to 0.8 mg/mL) and antibiofilm activities (MBIC50 was 0.2 mg/mL). Therefore, this study provides a valuable scientific knowledge to support the use of plants in combination rather than individually.

preprint2022arXiv

Influence of different factors on survival of patients with colorectal cancer

Colorectal cancer refers to the cancer from the dentate line to the junction of rectosigmoid colon, which is one of the most common malignant tumors of the digestive tract. The treatment of colorectal cancer is controversial, so understanding the risk factors and survival factors of colorectal cancer is of great significance for the diagnosis of patients. This study sampled patients with colorectal cancer from the SEER database. The factors affecting the survival of colorectal cancer patients were analysed by combining principal component analysis and competitive risk model, and the survival time of patients was analysed by combining principal component analysis and linear regression. Finally, the data were predicted. The results show that principal component analysis can effectively reduce the number of variables, and the combination of competitive risk model and linear regression model can effectively analyse and predict the data.

preprint2022arXiv

Recommendations for extending the GFF3 specification for improved interoperability of genomic data

The GFF3 format is a common, flexible tab-delimited format representing the structure and function of genes or other mapped features (https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md). However, with increasing re-use of annotation data, this flexibility has become an obstacle for standardized downstream processing. Common software packages that export annotations in GFF3 format model the same data and metadata in different notations, which puts the burden on end-users to interpret the data model. The AgBioData consortium is a group of genomics, genetics and breeding databases and partners working towards shared practices and standards. Providing concrete guidelines for generating GFF3, and creating a standard representation of the most common biological data types would provide a major increase in efficiency for AgBioData databases and the genomics research community that use the GFF3 format in their daily operations. The AgBioData GFF3 working group has developed recommendations to solve common problems in the GFF3 format. We suggest improvements for each of the GFF3 fields, as well as the special cases of modeling functional annotations, and standard protein-coding genes. We welcome further discussion of these recommendations. We request the genomics and bioinformatics community to utilize the github repository (https://github.com/NAL-i5K/AgBioData_GFF3_recommendation) to provide feedback via issues or pull requests.

preprint2022arXiv

Machine Learning Characterization of Cancer Patients-Derived Extracellular Vesicles using Vibrational Spectroscopies

The early detection of cancer is a challenging problem in medicine. The blood sera of cancer patients are enriched with heterogeneous secretory lipid bound extracellular vesicles (EVs), which present a complex repertoire of information and biomarkers, representing their cell of origin, that are being currently studied in the field of liquid biopsy and cancer screening. Vibrational spectroscopies provide non-invasive approaches for the assessment of structural and biophysical properties in complex biological samples. In this pilot study, multiple Raman spectroscopy measurements were performed on the EVs extracted from the blood sera of 9 patients consisting of four different cancer subtypes (colorectal cancer, hepatocellular carcinoma, breast cancer and pancreatic cancer) and five healthy patients (controls). FTIR (Fourier Transform Infrared) spectroscopy measurements were performed as a complementary approach to Raman analysis, on two of the four cancer subtypes. The AdaBoost Random Forest Classifier, Decision Trees, and Support Vector Machines (SVM) distinguished the baseline corrected Raman spectra of cancer EVs from those of healthy controls (18 spectra) with a classification accuracy of above 90 percent when reduced to a spectral frequency range of 1800 to 1940 inverse cm and subjected to a 50:50 training: testing split. FTIR classification accuracy on 14 spectra showed an 80 percent classification accuracy. Our findings demonstrate that basic machine learning algorithms are powerful applied intelligence tools to distinguish the complex vibrational spectra of cancer patient EVs from those of healthy patients. These experimental methods hold promise as valid and efficient liquid biopsy for artificial intelligence-assisted early cancer screening.

preprint2022arXiv

Low-Order Nonlinear Animal Model of Glucose Dynamics for a Bihormonal Intraperitoneal Artificial Pancreas

Objective: The design of an Artificial Pancreas (AP) to regulate blood glucose levels requires reliable control methods. Model Predictive Control has emerged as a promising approach for glycemia control. However, model--based control methods require computationally simple and identifiable mathematical models that represent glucose dynamics accurately, which is challenging due to the complexity of glucose homeostasis. Methods: In this work, a simple model is deduced to estimate blood glucose concentration in subjects with Type 1 Diabetes Mellitus (T1DM). Novel features in the model are power--law kinetics for intraperitoneal insulin absorption and a separate glucagon sensitivity state. Profile likelihood and a method based on singular value decomposition of the sensitivity matrix are carried out to assess parameter identifiability and guide a model reduction for improving the identification of parameters. Results: A reduced model with 10 parameters is obtained and calibrated, showing good fit to experimental data from pigs where insulin and glucagon boluses were delivered in the intraperitoneal cavity. Conclusion: A simple model with power--law kinetics can accurately represent glucose dynamics submitted to intraperitoneal insulin and glucagon injections. The reduced model was found to exhibit local practical as well as structural identifiability. Importance: The proposed model facilitates intraperitoneal bi-hormonal model-based closed-loop control in animal trials.

preprint2022arXiv

COVID 19: Open source model for rapid reduction of R to below 1 in high R0 scenarios

We present an open source model that allows quantitative prediction of the effects of testing on the rate of spread of COVID-19 described by R, the reproduction number, and on the degree of quarantine, isolation and lockdown required to limit it. The paper uses the model to quantify the outcomes of different test types and regimes, and to identify strategies and tests that can reduce the rate of spread and R value by a factor of between 1.67 and 33.3, reducing it to between 60% and 3% of the initial value.

preprint2022arXiv

MITI Minimum Information guidelines for highly multiplexed tissue images

The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that guide data deposition, curation and release. We describe a Minimum Information about highly multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology.

preprint2022arXiv

Meta-analysis for Discovering Which Genes are Differentially Expressed in Neuroinflammation

Neuroinflammation is a significant aspect of many neurological diseases of Homo sapiens, and the genes that are differentially expressed in this process should be well understood to gather the nature of such diseases. We have conducted a meta-analysis (based on a combined adjusted P value and logFC scheme) of 6 multi-species (Homo sapiens, Mus musculus) datasets (available on GEO, short for Gene Expression Omnibus) obtained through microarray technology. Our analysis shows that the genes coding pleckstrin homology domain and galectin-9 proteins take part in neuroinflammation in microglia.

preprint2022arXiv

In vitro evaluation of the effect of Ceftiofur Sodium and of a new Gentamycin Sulfate formulation on the viability of Marek disease virus

The present study evaluated In vitro effect of gentamicin sulfate and ceftiofur sodium on the viability of the Marek's disease virus. The titer of cell associated turkey herpesvirus (HVT) vaccine was not appreciably reduced when incubated with 50 mg/ml of gentamicin sulfate or ceftiofur sodium. Statistic difference was not found between the number of plaqueforming units (PFU) of reconstituted vaccine associated with both antibiotics 0, 15, 30 and 60 minutes after reconstitution of vaccine. The antibiotics did not considerably alter the pH values. There was a significative decrease of the titer of all vaccinal solutions when they were inoculated 30 and 60 minutes after the reconstitution of the vaccine. Nevertheless, these titers are higher than the required titers to protectect against the Marek disease.

preprint2026arXiv

From Organization to Viability: A Multi-Level Analysis of Gait Dynamics Under Occlusal Constraint

Clinical interpretation often assumes that observable performance provides sufficient information about the organization of an adaptive system. However, similar observable performance may correspond to distinct latent organizations. This study extends a previous multi-level framework by introducing a fourth analytical level centered on longitudinal viability. Using an exploratory single-case design in a Parkinsonian patient, gait data were recorded with instrumented insoles under three occlusal conditions: neutral natural occlusion (ONL), a 2.5-degree increase in vertical dimension of occlusion (OC2.5), and a 3-degree increase in vertical dimension of occlusion (OC3). Two measurement sessions were conducted eleven weeks apart, during which the participant underwent a structured sensorimotor intervention. The vertical dimension of occlusion was considered as an experimentally varied constraint applied to an adaptive neuromechanical system. Although observable performance remained globally comparable across conditions, PCA-based latent-space analysis revealed differentiated longitudinal centroid displacements. OC3 exhibited the smallest displacement, ONL an intermediate displacement, and OC2.5 the largest displacement. This hierarchy supports the relevance of a Level 4 framework centered on viability, understood here as an exploratory proxy for a configuration's capacity to maintain lower longitudinal reorganization over time. These findings remain within-subject, exploratory, and non-causal. They do not establish a validated clinical threshold, causal occlusal effect, or therapeutic optimum. More generally, the work suggests that clinical relevance cannot be inferred solely from instantaneous performance or static latent structure, but may also depend on the capacity of a configuration to sustain a coherent trajectory over time.

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