Bacterial Colony Counting

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Biologically Informed Representation Learning for Robust Cross-Center Generalization of MALDI-TOF Mass Spectrometry
Aug 8, 2026Alejandro L. García-Navarro, Carlos Sevilla-Salcedo, Belén Rodríguez-Sánchez +1Bacterial Colony Counting Tandem Mass Spectra
Department of Signal Theory and Communications, Universidad Carlos III de Madrid, Leganés, 28911, Spain · Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, 28009 Spain · Clinical Microbiology and Infectious Diseases Department at Hospital General Universitario Gregorio Marañón, Madrid, 28007, Spain
Artificial Intelligence Can Match Domain Experts in Evidence Extraction and Critical Appraisal of Microbial Oncogenesis Research Publications
Aug 7, 2026Kaela Kokkas, Hairong Wang, Richard Klein +11Systematic Review Biomedical Text
Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa · School of Computer Science and Applied Mathematics, University of the Witwatersrand, Johannesburg, South Africa · Wits Machine Intelligence and Neural Discovery (MIND) Institute, University of the Witwatersrand, Johannesburg, South Africa +13
BioSecBench-Surveillance: A Verifiable Benchmark for AI Agents in Pathogen Genomic Surveillance
Jul 21, 2026Harmon Bhasin, Kevin Flyangolts, Dianzhuo Wang +9Bacterial Colony Counting Artificial Intelligence Agents
LatchBio, San Francisco, CA · Aclid, New York, NY
Stochastic Filtering for Quorum Sensing in Robot Swarms under Anonymous Communication
Jul 15, 2026Fabio Oddi, Andreagiovanni Reina, Vito TrianniSwarms Collaborative Sensing
DIAG, Sapienza University of Rome, Italy · ISTC, National Research Council, Rome, Italy · Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Germany +2
Screening of Biosecurity Features in Metagenomic Data with Evo 2 Probes
Jul 15, 2026Jeremy Guntoro, Alexander Dack, Dylan Danno +3Bacterial Colony Counting Screening
John Innes Centre · AIxBio Hackathon contestant · Department of Bioengineering, Imperial College London +1
CHM-Net: Center Heatmap-driven Macro-Micro Modeling Network for MRI-based Microbial Density Stratification
Jul 10, 2026Jiaming Liang, Haolin Chen, Tingting Li +7Bacterial Colony Counting Lesion
School of Computer Science and Engineering South China University of Technology Guangzhou, China · School of Future Technology South China University of Technology Guangzhou, China · Department of Medical Imaging Affiliated Cancer Hospital, Guangzhou Medical University Guangzhou, China
Structured Gaussian Processes for Uncertainty-Aware Classification of High-Dimensional, Small-Sampled Omics Data
Jul 2, 2026Yue Zhang, Nandini Amit Gadhia, Georgios Karagiannis +1Multi-Omic Integration Bacterial Colony Counting
Department of Mathematical Sciences Durham University Durham, United Kingdom · STFC Hartree Centre University of Liverpool Liverpool, United Kingdom · STFC Hartree Centre Daresbury, United Kingdom
Radial Interaction Tomography: Recognizing Non-Transitive Evolutionary Games from One Range-Expansion Image
Jul 1, 2026Faruk Alpay, Baris BasaranBifurcation Bacterial Colony Counting
Department of Computer Engineering, Bahçeşehir University, Istanbul, Türkiye
Are Tabular Foundation Models Robust to Realistic Query Distribution Shifts in Microbiome Data?
Jun 23, 2026Giulia Perciballi, Ahmad Fall, Federica Granese +2Tabular Foundation Models Bacterial Colony Counting
IRD, Sorbonne Université, Unité de Modélisation Mathématique et Informatique des Systèmes Complexes (UMMISCO), Paris, France · Inria, CNRS, I3S, Université Côte d’Azur, Valbonne, France · INSERM, Nutrition et Obésités; Approches Systémiques, NutriOmique, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
PHOEBI: An Open-World Benchmark for Bacterial Identification in Phase-Contrast Microscopy
Jun 22, 2026Aaditya Baranwal, Md Jahid Hasan, Shruti VyasBacterial Colony Counting Species Identification
University of Central Florida
Constrained hybrid modelling to predict microbial dynamics and organic matter turnover in soil systems
Jun 18, 2026Paul Collart, Juergen Gall, Andrea Schnepf +2Soil Bacterial Colony Counting
Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Germany · Institute of Crop Science and Resource Conservation, University of Bonn, Germany · Institute of Computer Science, University of Bonn, Germany +1
AURA: Active-Response Attribution under Treatment Ambiguity in Bacterial Cytological Profiling
Jun 15, 2026Kartik Jhawar, Mrunmayee Deshpande, Wilfried Moreira +2Bacterial Colony Counting Antimicrobial Peptide
Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore 636921 · School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798 · Institute for Functional Intelligent Materials, National University of Singapore, Singapore 117544
Seeing Below the Limit of Detection: A Censored-Poisson Bayesian Latent-Growth Change-Point Detector (the Span Detector) for Serial ctDNA in HR+/HER2- Metastatic Breast Cancer
Jun 10, 2026Aarchi Singh Thakur, Abhijoy SarkarChange-Point Detection Bacterial Colony Counting
Span AI
Knowledge-Inclusive Adaptive Physics-Informed Neural Network for Microbial Interaction Modelling
Jun 5, 2026Ravisha Rupasinghe, Rajith Vidanaarachchi, Asela Hevapathige +3Parametric Physics-Informed Neural Network Bacterial Colony Counting
AI, Optimisation and Pattern Recognition Lab, Department of Mechanical Engineering, University of Melbourne, Melbourne, Victoria, Australia · Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
Environment-Robust Representation Learning with Empirical Bayes
Jun 3, 2026Yuli Slavutsky, Matthew Shen, Bohan Wu +1Empirical Bayes Bayesian Inference
Department of Statistics Columbia University New York, NY 10027, USA · Departments of Statistics and Computer Science Columbia University New York, NY 10027, USA
iLoRA: Bayesian Low-Rank Adaptation with Latent Interaction Graphs for Microbiome Diagnosis
May 28, 2026Yang Song, Yixuan Zhang, Lingfa Meng +5Bacterial Colony Counting Bayesian Networks
Section of Health Data Science & AI, Department of Public Health, University of Copenhagen, Copenhagen, Denmark · University of Copenhagen, Copenhagen, Denmark · Rutgers University, New Brunswick, NJ, USA +1
TaxDistill: Improving Metagenomic Taxonomic Annotation via Distilled Genomic Foundation Models
May 22, 2026Rongye Ye, Lun Li, Zheng Luo +3Bacterial Colony Counting Genome-Wide Association Study
National Genomics Data Center, China National Center for Bioinformation, Beijing 100101, China · Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China · University of Chinese Academy of Sciences, Beijing 100049, China +1
SAM-Sode: Towards Faithful Explanations for Tiny Bacteria Detection
May 20, 2026Wanying Tan, Shuo Yan, Dazhi Huang +7Bacterial Colony Counting Interpretability
Shenzhen University, Shenzhen, China · The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China · The Hong Kong University of Science and Technology (Guangzhou), Guangzhou,2026 China +2
Do Biological Structural Guarantees Earn Their Complexity?
May 13, 2026Bogdan BanuBiological Bacterial Colony Counting
Set-Aggregated Genome Embeddings for Microbiome Abundance Prediction
May 12, 2026Younhun Kim, Georg K. Gerber, Travis E. GibsonBacterial Colony Counting Future Latent Representations
1Brigham and Women’s Hospital, Boston, MA, USA · 2Harvard Medical School, Boston, MA, USA
Automated high-frequency quantification of fish communities and biomass using computer vision
May 11, 2026Kota Ishikawa, Takuma Masui, Keita Koeda +3Fish Biomass
Graduate School of Life Sciences, Tohoku University, Sendai, Japan · Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), Tohoku University, Sendai, Japan · Graduate School of Science and Engineering, University of the Ryukyus, Okinawa, Japan +1
MicroFuse: Protein-to-Genome Expert Fusion for Microbial Operon Reasoning
May 9, 2026Seungik ChoBacterial Colony Counting Genome-Wide Association Study
Department of Physics and Astronomy, Rice University, Texas, USA.
Mining Negative Sequential Patterns to Improve Viral Genomic Feature Representation and Classification
Apr 28, 2026Wenxi Zhu, Wensheng Gan, Zhenlian QiSirus Genome-Wide Association Study
College of Information Science and Technology, Jinan University, Guangzhou 510632, China · College of Cyber Security, Jinan University, Guangzhou 510632, China · Guangdong Eco-Engineering Polytechnic, Guangzhou 510520, China
Learning to count small and clustered objects with application to bacterial colonies
Apr 21, 2026Minghua Zheng, Na Helian, Peter C. R. Lane +2Bacterial Colony Counting Microscopy
King’s College London, St Thomas Street, London, SE1 1UL, United Kingdom · University of Hertfordshire, College Lane, Hatfield, AL10 9AB, United Kingdom · Synoptics Ltd, Beacon House, Nuffield Road, Cambridge, CB4 1TF, United Kingdom
Investigation of cardinality classification for bacterial colony counting using explainable artificial intelligence
Apr 21, 2026Minghua Zheng, Na Helian, Peter C. R. Lane +2Bacterial Colony Counting Xai
King’s College London, St Thomas Street, London, SE1 1UL, United Kingdom · University of Hertfordshire, College Lane, Hatfield, AL10 9AB, United Kingdom · Synoptics Ltd, Beacon House, Nuffield Road, Cambridge, CB4 1TF, United Kingdom
What Makes a Bacterial Model a Good Reservoir Computer? Predicting Performance from Separability and Similarity
Apr 17, 2026Laura Alonso Bartolomé, Jean-Loup Faulon, Xavier HinautBacterial Colony Counting Reservoir Computing
MICALIS, Mnemosyne · University Paris Saclay, INRAE, AgroParisTech, MICALIS Institute, 78350 Jouy-en-Josas, France · Centre Inria de l’Universit´e de Bordeaux, France +4
Friend or Foe
Aug 29, 2025Oleksandr Cherednichenko, Josephine Solowiej-Wedderburn, Laura M. Carroll +1Bacterial Colony Counting Peers
Integrated Science Lab (IceLab), Department of Mathematics and Mathematical Statistics, Umeå University · Department of Clinical Microbiology, SciLifeLab, Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University
Hierarchical Sparse Bayesian Multitask Learning for Disease Prediction in Pooled Microbiome Studies
Feb 4, 2025Haonan Zhu, Andre R. Goncalves, Camilo Valdes +10Bacterial Colony Counting Bayesian Networks
Lawrence Livermore National Laboratory · Electrical and Computer Engineering, University of Michigan
When do cheap embeddings beat protein language models? A theoretically-grounded hashing sketch for biological sequence classification
Date pendingSarwan Ali, Taslim Murad, Imdadullah Khan +1Contextual Embeddings Locality-Sensitive Hashing
Columbia University, NY, USA · Institute of Business Administration, Karachi, Pakistan · Lahore University of Management Sciences, Lahore, Pakistan +1

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Biologically Informed Representation Learning for Robust Cross-Center Generalization of MALDI-TOF Mass Spectrometry

Alejandro L. García-Navarro, Carlos Sevilla-Salcedo, Belén Rodríguez-Sánchez, Vanessa Gómez-Verdejo

Department of Signal Theory and Communications, Universidad Carlos III de Madrid, Leganés, 28911, Spain · Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, 28009 Spain · Clinical Microbiology and Infectious Diseases Department at Hospital General Universitario Gregorio Marañón, Madrid, 28007, Spain

Bacterial Colony Counting Tandem Mass Spectra Transfer Learning Representation Learning Clinical Prediction

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Machine learning models for MALDI-TOF mass spectrometry have shown considerable promise for clinical microbiology tasks such as microbial identification and antimicrobial resistance prediction. However, their deployment across institutions remains limited by domain shift, as acquisition-specific variability often leads models to capture technical artifacts rather than transferable biological information. Existing representation learning approaches primarily address this problem through statistical domain alignment while largely overlooking the biological supervision naturally available in microbiology datasets. We introduce DALMA, a probabilistic representation learning framework that jointly models acquisition-specific variability and biological supervision to learn biologically structured latent representations. By combining domain-specific reconstruction with biologically guided representation learning, DALMA learns transferable representations that generalize across heterogeneous clinical centers without requiring institution-specific components at inference, enabling zero-shot deployment on previously unseen sites. We evaluate DALMA on a multi-center benchmark comprising seven datasets from three countries. DALMA consistently achieves state-of-the-art zero-shot microbial identification across two held-out clinical centers, while the learned representations also transfer effectively to antimicrobial resistance prediction. Furthermore, latent-space novelty estimation enables reliable selective prediction under previously unseen domain shifts. These results demonstrate that biologically informed representation learning provides an effective strategy for robust and transferable ML in clinical microbiology.

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