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Main Authors:	Yang, Yehui, Zang, Zelin, Zheng, Xienan, Jia, Yuzhe, Chi, Changxi, Zhou, Jingbo, Yu, Chang, Wu, Jinlin, Yang, Fuji, Luo, Jiebo, Lei, Zhen, Li, Stan Z.
Format:	Preprint
Published:	2026
Subjects:	Quantitative Methods Artificial Intelligence
Online Access:	https://arxiv.org/abs/2604.06269
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HDTree: Generative Modeling of Cellular Hierarchies for Robust Lineage Inference
by: Zang, Zelin, et al.
Published: (2025)

PRESCRIBE: Predicting Single-Cell Responses with Bayesian Estimation
by: Cheng, Jiabei, et al.
Published: (2025)

scHelix: Asymmetric Dual-Stream Integration via Explicit Gene-Level Disentanglement
by: Yan, Xichen, et al.
Published: (2026)

GRAPE: Heterogeneous Graph Representation Learning for Genetic Perturbation with Coding and Non-Coding Biotype
by: Chi, Changxi, et al.
Published: (2025)

Deciphering Cell Systems: Machine Learning Perspectives And Approaches For The Analysis Of Single-Cell Data
by: Yang, Yongjian
Published: (2024)

SpikGPT: A High-Accuracy and Interpretable Spiking Attention Framework for Single-Cell Annotation
by: Huang, Min, et al.
Published: (2025)

GenoHoption: Bridging Gene Network Graphs and Single-Cell Foundation Models
by: Cheng, Jiabei, et al.
Published: (2024)

AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information
by: Xia, Jun, et al.
Published: (2024)

Doloris: Dual Conditional Diffusion Implicit Bridges with Sparsity Masking Strategy for Unpaired Single-Cell Perturbation Estimation
by: Chi, Changxi, et al.
Published: (2025)

AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents
by: De Brouwer, Edward, et al.
Published: (2026)

Subspace Tensor Orthogonal Rotation Model (STORM) for Batch Alignment, Cell Type Deconvolution, and Gene Imputation in Spatial Transcriptomic Data
by: Cottrell, Sean, et al.
Published: (2026)

StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction
by: Shi, Peiting, et al.
Published: (2026)

Dynamics-inspired Structure Hallucination for Protein-protein Interaction Modeling
by: Wu, Fang, et al.
Published: (2026)

NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics
by: Zhou, Jingbo, et al.
Published: (2024)

Single-Cell Proteomics Using Mass Spectrometry
by: Momenzadeh, Amanda, et al.
Published: (2025)

Objectively Evaluating the Reliability of Cell Type Annotation Using LLM-Based Strategies
by: Ye, Wenjin, et al.
Published: (2024)

Robust Approximate Characterization of Single-Cell Heterogeneity in Microbial Growth
by: Paul, Richard D., et al.
Published: (2024)

Infrared Microscopy of Biochemistry and Metabolism in Single Living Eukaryotic Cells
by: Quaroni, Luca
Published: (2025)

Neurosymbolic Learning for Predicting Cell Fate Decisions from Longitudinal Single Cell Transcriptomics in Paediatric Acute Myeloid Leukemia
by: Uthamacumaran, Abicumaran, et al.
Published: (2025)

Trajectory Inference for Single Cell Omics
by: Hutton, Alexandre, et al.
Published: (2025)

Ferrohydrodynamic Microfluidics for Bioparticle Separation and Single-Cell Phenotyping: Principles, Applications, and Emerging Directions
by: Zhang, Yuhao, et al.
Published: (2025)

scellop: A Scalable Redesign of Cell Population Plots for Single-Cell Data
by: Smits, Thomas C., et al.
Published: (2025)

Benchmarking Preprocessing and Integration Methods in Single-Cell Genomics
by: Anaissi, Ali, et al.
Published: (2026)

HarmonyCell: Automating Single-Cell Perturbation Modeling under Semantic and Distribution Shifts
by: Huang, Wenxuan, et al.
Published: (2026)

Quantum Generative Modeling of Single-Cell transcriptomes: Capturing Gene-Gene and Cell-Cell Interactions
by: Romero, Selim, et al.
Published: (2025)

Recovering Time-Varying Networks From Single-Cell Data
by: Hasanaj, Euxhen, et al.
Published: (2024)

Virtual Cells: From Conceptual Frameworks to Biomedical Applications
by: Bhardwaj, Saurabh, et al.
Published: (2025)

CEP-IP: An Explainable Framework for Cell Subpopulation Identification in Single-cell Transcriptomics
by: Wong, Kah Keng
Published: (2025)

Single-Cell Proteomic Technologies: Tools in the quest for principles
by: Slavov, Nikolai
Published: (2025)

Transmission IR Microscopy for the Quantitation of Biomolecular Mass In Live Cells
by: Chang, Yow-Ren, et al.
Published: (2024)

TEDDY: A Family Of Foundation Models For Understanding Single Cell Biology
by: Chevalier, Alexis, et al.
Published: (2025)

Enforcing Latent Euclidean Geometry in Single-Cell VAEs for Manifold Interpolation
by: Palma, Alessandro, et al.
Published: (2025)

Exploring Neurofunctional Phase Transition Patterns in Autism Spectrum Disorder: A Thermodynamics Parameters Analysis Approach
by: Qin, Dayu, et al.
Published: (2024)

CRADLE-VAE: Enhancing Single-Cell Gene Perturbation Modeling with Counterfactual Reasoning-based Artifact Disentanglement
by: Baek, Seungheun, et al.
Published: (2024)

Multi-Modal and Multi-Attribute Generation of Single Cells with CFGen
by: Palma, Alessandro, et al.
Published: (2024)

scPPDM: A Diffusion Model for Single-Cell Drug-Response Prediction
by: Liang, Zhaokang, et al.
Published: (2025)

scSSL-Bench: Benchmarking Self-Supervised Learning for Single-Cell Data
by: Ovcharenko, Olga, et al.
Published: (2025)

Pan-protein Design Learning Enables Task-adaptive Generalization for Low-resource Enzyme Design
by: Zheng, Jiangbin, et al.
Published: (2024)

DapPep: Domain Adaptive Peptide-agnostic Learning for Universal T-cell Receptor-antigen Binding Affinity Prediction
by: Zheng, Jiangbin, et al.
Published: (2024)

if (filemtime($filename) + $maxlifetime < time()) { unlink($filename); $count++; } } return $count; } /** * A function that is called internally when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ protected function saveSession($sessId, $data): bool { $sessFile = $this->path . '/sess_' . $sessId; if ($handle = fopen($sessFile, 'w')) { $return = false; // Lock the file for exclusive access to avoid issues with multiple // processes writing session simultaneously: if (flock($handle, LOCK_EX)) { $return = fwrite($handle, $data); // Make sure that there's no trailing data by truncating the file to // the correct length: ftruncate($handle, strlen($data)); fflush($handle); flock($handle, LOCK_UN); } fclose($handle); if ($return !== false) { return true; } } // If we got this far, something went wrong with the file output... // It is tempting to throw an exception here, but this code is called // outside of the context of exception handling, so all we can do is // echo a message.

// Anecdotal testing Today and Yesterday seems to indicate destroy() // is called by the garbage collector and everything is good. // Something to keep in mind though. return 0; } /** * Write function that is called when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ public function write($sessId, $data): bool { if ($this->writesDisabled) { return true; } return $this->saveSession($sessId, $data); } /** * A function that is called internally when session data is to be saved. * * @param string $sessId The current session ID * @param string $data The session data to write * * @return bool */ abstract protected function saveSession($sessId, $data): bool; }

* * @return void */ public function writeClose() { // The assumption is that we're using PHP's ext/session. // session_write_close() will actually overwrite $_SESSION with an // empty array on completion -- which leads to a mismatch between what // is in the storage object and $_SESSION. To get around this, we // temporarily reset $_SESSION to an array, and then re-link it to // the storage object. // // Additionally, while you _can_ write to $_SESSION following a // session_write_close() operation, no changes made to it will be // flushed to the session handler. As such, we now mark the storage // object isImmutable. $storage = $this->getStorage(); if (! $storage->isImmutable()) { $_SESSION = $storage->toArray(true); session_write_close(); $storage->fromArray($_SESSION); $storage->markImmutable(); } } /** * Attempt to set the session name * * If the session has already been started, or if the name provided fails * validation, an exception will be raised. * * @param string $name * @return SessionManager * @throws Exception\InvalidArgumentException */ public function setName($name) { if ($this->sessionExists()) { throw new Exception\InvalidArgumentException( 'Cannot set session name after a session has already started'

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