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8 papers in the last four weeks, against 1 the four weeks before. 0.1% of all new papers.

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Latest papers 20

Sep 24, 2026cs.CL

How Reproducible Are Evaluation Conclusions? A Self-Audit of LLM-Inferred Prompt Structure

Evaluations of LLM systems routinely average over small prompt sets and report models as a ranked table. We ask how much confidence such a table deserves, using LLM-based prompt-structure inference as the case study: eight open model variants across five families and 8B to 675B parameters, caching disabled, 293 raw intermediate representations persisted. The measured phenomenon is unstable to begin with. Identical calls do not reliably recover identical structure, with mean node-set Jaccard from 0.39 to 0.96 and 72% of prompt-model cells never node-set-perfect. Auditing the evaluation weakens its conclusions further, and this is our main contribution. Under a joint cluster bootstrap over prompts, only the bottom of the ranking is firm: the two least reproducible models hold rank in 99% and 86% of replicates, the middle four in 27% to 48%, and the top two in 68% each, so the table identifies the worst model reliably but does not reliably identify the best. Two equally defensible rules for merging repeated campaigns change four of eight rows and move the study-wide headline by 7 percentage points. Checking the inferred structure against ground-truth annotations shows reproducibility cannot be read as accuracy. And four of the eight endpoints were withdrawn within ten weeks of measurement, so the study as specified can no longer be run. Small-sample LLM evaluations can therefore look far more definitive than their evidence supports. We recommend reporting rank stability, per-cell provenance, executed sensitivity comparisons, raw per-run outputs, and a measurement date alongside any ranking.

Dipankar Sarkar

Skelf Research

Large Language Model Evaluation Reproducibility Prompt Engineering Model Auditing Virtual Cell Model-Based Bootstrap

Sep 23, 2026cs.LG

Discover, Falsify, Revise: Auditing Input-Use Claims from Source Code to Predictive Contribution in Agent-Discovered Cell Models

AI virtual cells aim to predict cellular responses to specified interventions, yet held-out predictive performance alone does not establish use of the supplied perturbation information. This prediction-claim gap matters in agentic model discovery, where language-model agents generate and revise predictors using score-based feedback. We introduce CELLAUDIT, which audits input-use claims by asking whether an input can enter the cited computation, whether fitted predictions depend on it, and whether that dependence improves prediction of observed response. On a paired morphology-transcriptomics perturbation benchmark (BBBC047), an agent-selected predictor attains a mean held-out Global Pearson correlation coefficient (PCC) of 0.3153 but remains invariant to compound replacement; a control-profile-only predictor reaches 0.3142. Source inspection identifies a compound-query pathway blocked by singleton key-value attention, and the invariance persists after refitting with disjoint control wells. In a stratified audit of 48 candidates across two linked tasks, 47 change predictions under compound replacement on both held-out folds, but only 20 show target-loss gains with intervals above zero on both folds. On BBBC047, falsification-guided revisions recover positive mean compound contributions while retaining gains over the control-profile-only baseline. In matched sci-Plex searches, audit-enriched feedback yields higher held-out performance and larger mean compound and dose contributions across five trajectories, although paired intervals span zero. Refitting fixed designs on an independently acquired cohort shows predictive generalization need not imply generalization of input-use claims: dose contribution persists, whereas support for compound identity does not. CELLAUDIT adds a falsification layer to agentic model discovery, moving from generate-score-revise toward discover-falsify-revise.

Mengran Li, Bo Li, Chengyang Zhang +3

Sun Yat-sen University · University of Macau · Sichuan University +3

Virtual Cell Model Auditing Agentic Evaluations Transcriptomics Falsehood Feedback+1

Sep 22, 2026cs.CV

Feed the Panel Dimensions, Not Verdicts: Rubric-Decomposed Fusion of Vision-Language Aesthetic Judges

Vision-language models (VLMs) are deployed as zero-shot judges of image aesthetics, and panels of several models are recommended, on thin evidence, as the way to make such judges reliable. On two human-rated datasets, EVA and PARA, we find that a panel of holistic judges never significantly beats its best member, whether the verdicts are averaged or fused by a learned combiner. What a panel is worth depends on what it is fed. We therefore have each model score each image on the five dimensions of a frozen, human-written rubric and fuse those scores, alongside each model's verdict, across model families with an out-of-fold combiner. The dimension scores measure what their labels claim: with the overall human score partialled out, a dimension prompt carries more attribute-specific information than the holistic prompt in 28 of 30 model-attribute cells. Fused, they beat the best single VLM in all ten three-family panels on EVA (against that best single model, +0.07 Spearman rho for the strongest trio and +0.10 for the pre-declared one, and +0.06 and +0.07 when averaged over twenty fold partitions; against the panel mean, the primary test gives +0.118 on its EVA design set), and on PARA they reach parity under Spearman rho and a small, non-significant loss under Kendall tau-b, where one model already captures 85% of the human noise ceiling. It is not a feature-count artefact: giving the same combiner an equal number of pure holistic columns, split from the same repetitions, does not reproduce it. The gain costs a few hundred labels, which do not transfer between datasets, and 4.8x the API calls on EVA; we report it with paired bootstraps and Kendall tau-b, alongside a failed pre-registration and the configurations that lost.

Amit Jadhav, Shaurya Beriwala, Beomjin Kim

Purdue University Fort Wayne

Aesthetics Multimodal Evaluation Judges Verdict Virtual Cell

Sep 22, 2026cs.AI

Math Reasoning in LLMs is Organized by Approach, Not Topic

Mathematical reasoning benchmarks are typically organized by topic, but language models may organize their internal computation by reusable reasoning approach instead. In this paper, we investigate whether open math-capable LLMs organize internally by topical sub-skill or by reasoning approach, and we present evidence that the approach is the key. We introduce a generation-replay protocol: a model first generates a solution, after which we replay the exact prompt-plus-generation trajectory and extract activation-importance signatures over the reasoning tokens. We cluster these signatures without supervision across eight models and five mathematical reasoning sources, then evaluate the recovered structure with structural, semantic, and intervention tests. Across all 40 model-source cells, the recovered clusters outperform matched-size random baselines. Two independent frontier-LLM judges find approach-level coherence in 77-82% of real clusters versus 6-11% in within-source controls, and topic-pure clusters usually receive labels finer than the topic itself. In approach-controlled prompting, changing the requested reasoning approach shifts cluster assignment in seven of eight model conditions, whereas paraphrases largely preserve it. These results indicate that math-capable LLMs organize internal mathematical computation by reasoning approach rather than benchmark topic. The implication is that topic-stratified benchmarks and topic-balanced training corpora can still miss the axis that matters: even deliberately topic-balanced corpora may remain imbalanced over reasoning approaches.

Sajad Goudarzi, Samaneh Zamanifard, Moloud Nasiri +1

Clemson University

Mathematical Reasoning Benchmarks Large Language Model Tool Use Text Corpora Virtual Cell

Sep 22, 2026cs.CL

Recognized but Not Produced: A Generation Benchmark for Culturally Specific Kinship Terms

Current literature evaluates large language models (LLMs) on multilingual kinship understanding using multiple choice benchmarks, treating it as a recognition problem. We instead prompt five open weight LLMs to generate kinship terms in three non Western languages (Hindi, Tamil, and Korean) across two communicative tasks and pair this with a matched option-supported selection baseline. On identical relation language cells, GPT OSS120B selects the correct term in 90.67% of 75 valid cells but produces an accepted term in 36.00% of the corresponding attempts; Llama 3.370B shows the same pattern (77.92% versus 24.24%). Since the four-option condition displays the candidate terms and does not require script production, the difference is interpreted as an evaluation format gap rather than direct proof that lexical knowledge is intact. On explicitly specified L3 prompts, accuracy varies sharply, from GLM-5.1 at 72.29% to Llama-3.370B at 24.24%. The paternal-lineage advantage is language specific; it is large in Hindi but weak or reversed in Korean, while Tamil shared-term pairs provide a control for measurement variation. These results show that culturally specific kinship generation remains difficult even when the relationship is explicitly stated and motivate generation-based evaluation alongside multiple-choice testing.

Sahil Pardasani, Madhusudan Singh

Blockchain Data Intelligence Lab The Pennsylvania State University University Park, PA, USA

Multilingual Multiple-Choice Questions Virtual Cell

Sep 15, 2026cs.AI

What You Can't See Is Still What You Learn: A Preregistered Sixty-Society Confirmation That Evidence Masking Drives Compositional Generalization

Restricting what a module can read may improve what a system learns to compute. We test this in a preregistered confirmation with sixty four-cell systems sharing a frozen language-model backbone and communicating through learned continuous packets. Five conditions vary evidence masking, ownership markers, and replacement of foreign evidence with neutral filler (task-irrelevant text of the same token length), across six initialization clusters, each with two data orders, on one fresh task world. With markers available in both regimes, masking improved accuracy on held-out two- and three-operation compositions by median paired differences of 0.846 and 0.859; all twelve pairs cleared the required margins, and the full preregistered behavioral criterion passed. The unmarked replication also passed. No marked global-visibility (G+) system passed the marker-following check, so the effect of usable role information remains unresolved. The filler condition yielded seven full generalizers, but its decomposition criteria were inconclusive. Packet interventions in all eighteen audited masked systems followed the predicted intermediate-value changes on eligible cases; these finite, success-conditioned audits do not establish mediation. The results confirm a large advantage of the tested masking regime, while leaving its finer attribution and generality open. Protocols, results, and checkpoints are public.

Narcis Marincat

Independent researcher.

Compositional Generalization Ablation Membership Inference Virtual Cell

Sep 12, 2026cs.AI

Portable Semantics, Private Dialects: Reuse and Negative Transfer in Latent Communication Between Language-Model Cells

In shared-genome language-model societies, restricted evidence visibility favors reusable, value-indexed latent packet interfaces, whereas the sole high-performing globally visible model in the parent study learned an episode-entangled code. This companion study asks whether independently trained societies share one packet language, where strict zero-shot transfer fails, and whether inherited interface state helps or harms later learning. First, a leakage-controlled causal interoperability audit over all 30 ordered pairs of six independently trained restricted societies -- under sealed held-out structure and a preregistered raw/orthogonal/linear/nonlinear alignment ladder -- shows the six semantically similar interfaces do not form one raw language: one same-initialization pair is exactly interoperable in both directions, a second shows asymmetric partial compatibility, and all 26 cross-initialization directions fail every frozen alignment rung. Second, within the tested decomposition and a single sealed source formulation, a source-span control localizes strict zero-shot failure to interpretation and execution of the new operator instructions. Third, in a matched adaptation factorial, the globally trained communication interface acts as a severe negative-transfer prior: reinitializing only the packet reader, writer, and mouth raises final depth-three accuracy from 0.169 to 0.857. Fourth, across two restricted checkpoints and two independently frozen target streams each, inherited interfaces never exceeded fresh-interface controls by the preregistered 0.10 margin. All primary conclusions are bounded to a near-transfer 17-state setting; the negative-transfer factorial concerns one globally visible parent-cohort checkpoint, while an appendix adds a post hoc tagged-global twin case study.

Narcis Marincat

Independent researcher.

Language Pairs Language Modeling Cross-Task Knowledge Transfer Dialects Virtual Cell Negative Results+2

Sep 1, 2026cs.AI

Consistency Without Alignment: Item-Sensitive Language Models Indistinguishable From Random

Item-sensitivity, defined as whether a model's choice depends on the specific input rather than on its own output prior, is widely reported as evidence of task competence. We show this evidence is necessary but not sufficient using a forced-choice signalling task abstracted from the board game Deception: Murder in Hong Kong. In this environment, the reference points against which a coordinate should be judged (a fit-maximising strategy, a posterior-maximising strategy, and uniform random selection) are all computable in closed form. Across seven language models, two model families, a post-training ablation, and three independent scoring rules, every one of 21 model-by-rule cells is reliably item-sensitive. Yet 8 of those 21 cells are not statistically distinguishable from a chooser that ignores the item and selects at random, and 5 score worse than random at describing the target. Item-sensitivity and distance from random correlate at only r = 0.30. We call this consistency without alignment and argue it generalises to any evaluation that relies on item-sensitivity, permutation consistency, or self-consistency without an independent reference for the measured quantity. We further find that a literal-similarity baseline with no pragmatics outperforms most tested language models, that adding a pragmatic layer over two baseline similarity sources moves choosers toward random rather than toward the Bayesian reference, and that a standard labelled multiple-choice format carries no measurable content signal here. All results represent the model side of a pre-registered instrument; a matched human condition is designed and piloted but not yet collected.

Cris Huynh

Independent researcher

Large Language Model Alignment Item Response Theory Language Modeling Deception Virtual Cell Bayesian

Aug 9, 2026cs.HC

Human-Guided Causal Knowledge Injection for Virtual Cells

Virtual cells employ machine learning models to simulate and predict cellular behaviors, serving as a critical computational framework for investigating health and disease. Injecting causal graphs into virtual cells can improve the interpretability, but such graphs are usually not available in real-world applications. Recently, many methods have been proposed to construct causal graphs from data, which group genes based on their similarities to form concepts and extract their causal relationships. However, since this automatic process is unsupervised, the causal graphs usually contain errors. In this paper, we propose a human-guided causal knowledge injection method for virtual cells. We developed a gene-similarity-aware causal graph visualization supported by a hybrid optimization algorithm to help explore both the causal relationships between concepts and the similarities between genes. Based on the exploration, we further developed a counterfactual analysis strategy supported by a counterfactual visualization and a causal path visualization to help validate and refine causal graphs. The effectiveness of our method is demonstrated through two real-world case studies, the extraction of scientifically meaningful causal insights, and positive feedback from domain experts.

Pengcheng Wang, Changjian Chen, Zhuo Tang +4

Causal Graph Virtual Cell Causal

Jul 29, 2026cs.CV

From Pixels to PCells: A Neurosymbolic Approach to Photonic Component Creation

We present PixCell, a neurosymbolic system in which multimodal agents convert a visually presented photonic component into a parametric program over a small domain-specific language (DSL) of geometric primitives. A system enabling deterministic visual verification renders evaluation asymmetrically cheaper than the generation attempt. While models using multi-seed sampling and iterative revision reach a mean best-turn IoU of only 0.416, multimodal agents through PixCell's interface and verifier consistently exceed 0.9 mean IoU, with scores reaching 0.974 and 0.955 across eight component targets while also satisfying source contracts. These results demonstrate that frontier multimodal agents can reliably understand and render executable parametric representations from visual targets. Using these live parameters, cross-stack studies on an interferometer reconstruct primitive programs that satisfy an 8.0 nm free spectral range target and the original footprint constraint on modeled 220-nm SOI, 400-nm SiN, and 400-nm TFLN stacks. PixCell further carries a paper-derived splitter from visual reconstruction through SOI full-wave simulation, producing symmetric propagation and balanced outputs. Finally, the same executable verifier supplies a training reward and dataset used to train a Qwen3.6-35B-A3B model with LoRA and GRPO without supervised demonstrations. On eight training-excluded paper figures, its mean champion IoU rises from 0.422 after eight initial attempts to 0.491 after three verifier-guided revision rounds. These results therefore establish a controlled framework for measuring, retargeting, and improving visual-to-parametric photonic component design.

Aadarsh Agarwal, Kenaish Al Qubaisi, Dirk Englund

Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

Nanophotonic Pixelloop Virtual Cell Multimodal Agents Reference-Guided Multimodal In-Context Verification Pixels+1

Jul 23, 2026cs.LG

Scaling Laws for Classical Machine Learning on Tabular Data: A Benchmark Study

Prior classical-ML learning-curve work fits power laws to tree, linear, and kernel models on tabular data, but at small scale: typically one curve, one team, a handful of cells. We present a distributed classroom-scale replication: 127 graduate students each ran a fixed protocol on 3 assigned datasets, drawn from 18 tabular classification and regression datasets and 6 model families (Boosting, Random Forest, SVM, Linear/Logistic, Ridge, Lasso), yielding 11,536 training runs and 1,648 fitted power-law curves of the form error(N) = a N^(-b) + c. Three findings. (1) Power laws fit: R^2 > 0.8 on 77.7% of cells, with tree ensembles dominating at full data (Boosting 50% of datasets, RandomForest 33%; linear models underperform on classification). (2) Approximate shared exponents within a model family: for 5 of 6 families, a single family-level exponent predicts each family's cross-dataset curves nearly as well as per-dataset exponents (R^2 gap < 0.011), though AIC favors the unconstrained fit and curve collapse is partial (32-58% of points within +/-0.5 dex). We frame this as approximate predictive compressibility, not dataset-independent universality; Lasso fails outright (negative control) and Ridge is fragile under leave-one-dataset-out. (3) Replicator-implementation variance: with random_state=42 fixed, independent re-implementations of the same protocol still differ by mean CV(b) = 0.144 on the fitted exponent -- not seed variance, but the spread induced by unconstrained parts of the protocol (preprocessing, encoding, missing-value handling). We release the aggregated curves, per-cell fits, and a practical data-requirement table for N* to reach target error 0.15.

Kaihua Ding

University of Pennsylvania

Tabular Learning Scaling Laws Mle-Bench Lite Tabular Data Virtual Cell

Jul 6, 2026cs.LG

Score Distributions, Not Cells: Evaluating Single-Cell Perturbations Under Class Overlap

Most classification problems assume the classes are roughly separable, so that an individual sample can usually be assigned to one class. Single-cell perturbation data violates this assumption: two perturbations can produce different populations of cells while overlapping so much that an individual cell could belong to either. Per-cell accuracy then measures this overlap rather than model quality. We see this on Tahoe-100M and the Virtual Cell Challenge, where a linear classifier, an MLP, and a Transformer all plateau near macro-F1 0.2-0.3 even though almost every pair of perturbations is statistically distinguishable. The fix is to score perturbations across the whole population rather than cell by cell. We average a classifier's per-cell probability vectors over all cells of a perturbation to form a population profile, then rank candidate perturbations by this profile; we call the resulting score the Classifier Discrimination Score (CDS). Taking the top-ranked class recovers the winning perturbation. It needs no retraining, costs linear time in the number of cells, and recovers near-perfect identification from the same weak models. CDS differs from the pseudobulk-based Perturbation Discrimination Score (PDS) used in recent benchmarks only in where the average is taken, raw gene expression for PDS versus a learned discriminative space for CDS, and identifies the true perturbation more reliably on both datasets, with the gap widening as cells grow scarce. Because a metric that misranks the ground truth will misrank the models scored against it, per-cell accuracy and raw-pseudobulk scores should be used with caution when comparing perturbation models.

Youssef Marrakchi, Davide D'Ascenzo, Sebastiano Cultrera di Montesano

Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA. · Department of Computer Science, University of Milan, Milan, Italy. · Department of Control and Computer Engineering, Politecnico di Torino, Torino, Italy. +1

Single-Cell Perturbation Prediction Cells Virtual Cell Classifier

Jul 5, 2026cs.LG

Geometry of Ordinal Representations in Language Models

Recent work showed that language models represent character counts on curved 1D manifolds, with attention heads performing geometric transformations to enable computation. We test whether this generalizes across four ordinal tasks (bracket depth, indentation, table position, numeric magnitude) in Gemma-2-2B, Gemma-2-9B, and Qwen3-4B. We find that 1D manifolds with place-cell feature tiling emerge for tasks where the ordinal variable is locally computable from token identity, while tasks requiring cross-position integration or semantic extraction produce higher-dimensional or incoherent representations. Geometric computation is architecture-dependent: Qwen3-4B shows substantially stronger twisting than Gemma models for indentation, and its twisters preserve ordinal order, unlike its numeric twisters. Activation patching confirms that the identified manifold subspaces concentrate task-relevant information, with manifold-direction ablation causing dramatically larger probe accuracy drops than random-direction controls.

Saksham Bassi, Sharvi Tomar

*Equal contribution

Virtual Cell Counting

Jun 28, 2026cs.CV

CellDETR: A Detection-Guided Framework for Scalable Cell Representation Learning from Histopathology Images

Recent advances in pathology foundation models have substantially improved patch and slide level representation learning from whole-slide images (WSIs).However, cell-level representations learning remain underexplored, limiting cell resolved interpretability, biological discovery, and clinical translation. We propose CellDETR, a detection-guided framework built on Deformable DETR for scalable cell representation learning from WSIs. By introducing location feature decoupling and box-constrained attention mechanism, CellDETR enables automated extraction of cell-level embeddings, and outperform existing state-of-the-art methods in supervised cell classification on PanNuke data. In addition, by incorporating contrastive learning design, we build a CellDETR-based pretraining model for scalable cell representation learning from unlabeled WSIs, which improves downstream cell classification performance. Furthermore, we show that after pretraining with Xenium spatial transcriptomics-derived cell annotations, CellDETR achieves accurate cross-dataset cell classification, demonstrating the transferability and biological relevance of the learned cell embeddings. Together, CellDETR provides a scalable route toward general cell-level representation learning framework for interpretable computational patholog

Shikang Zhang, Guojun Li, Yicong Mao +1

Zhejiang University of Technology · Tianjin University · Hangzhou Institute of Medicine, Chinese Academy of Sciences

Digital Pathology Whole-Slide Images Cells Virtual Cell

Jun 11, 2026q-bio.QM

OCOO-T : A Simple and Scalable Virtual Cell Model for Transcriptional Perturbation Response Prediction

Predicting single-cell transcriptional responses to genetic, chemical and cytokine perturbations is a fundamental challenge in computational biology and AI Virtual Cell (AIVC) modeling, with direct implications for drug discovery and the elucidation of gene regulatory networks. Existing approaches often rely on auxiliary cell-state encoders, hierarchical variational autoencoders, dedicated Transformer encoder-decoder modules, or gene-interaction priors to compress high-dimensional expression profiles into latent representations. While effective, these designs increase architectural complexity and may limit scalability and generalizability. This paper introduces OCOO-T, a minimalist flow-matching-based AIVC model for transcriptional perturbation response prediction. OCOO-T utilizes a vanilla Transformer stack that operates directly on continuous gene expression profiles and formulates perturbation response prediction as a continuous-time denoising process. Perturbation embeddings, dosage information, and cell-line/cell-type specificity are integrated through adaptive layer normalization and in-context tokens. Comprehensive evaluations on Tahoe100M, Replogle, and PBMC benchmarks demonstrate that OCOO-T achieves state-of-the-art performance across diverse perturbations and cell types while effectively scaling to long transcriptional profiles through patching and depatching of cellular contexts. By leveraging the simplicity of Transformer-based denoising for single-cell omics, OCOO-T provides an effective and scalable framework for in-silico cellular simulation.

Danning Jiang, Zheming An, Yalong Zhao +1

INFevo

Single-Cell Perturbation Prediction Single-Cell Rna Transcriptomics Virtual Cell

Jun 6, 2026cs.RO

Vision-Guided Dual-Arm Humanoid Robotic Disassembly of End-of-Life 18650 Lithium-ion Battery Packs

The growing volume of retired lithium-ion battery packs from electric vehicles and portable electronics calls for automated disassembly that is safe, flexible, and selective down to the individual cell. Existing robotic systems, however, mostly assume known pack poses, external fixtures, or specialised tooling, leaving fixture-free cell-level disassembly under pose uncertainty largely unsolved. This paper presents a vision-guided dual-arm pipeline that disassembles a 21-cell 18650 pack from an arbitrary initial pose using only general-purpose parallel-jaw grippers, RGB-D sensing, and a pre-trained grasp detector. Pose uncertainty is absorbed by a learn-and-filter perception stack with discrete look-and-move wrist-camera corrections, while a mid-task support transfer between the two arms extends the effective workspace without any external clamp. The pipeline achieves an 8/10 end-to-end success rate, a cell-localisation root-mean-square error of

2.4

,mm, and a mean cycle time of 6.0,minutes per pack, providing a practical, fixture-free building block for industrial battery recycling.

Yile Chen, Zhihao Liu, Xi Vincent Wang +1

KTH Royal Institute of Technology, Brinellvägen 8, 114 28, Stockholm, Sweden

Lithium-Ion Batteries Waste Disassembly Computer Vision Virtual Cell Uncertainty

Jun 4, 2026cs.AI

Towards World Models in Biomedical Research

A central goal of biomedicine is to understand, predict and ultimately control the dynamic mechanisms by which biological systems respond to perturbations, disease progression and therapeutic intervention. Although foundation models and large language models have accelerated biomedical data interpretation, most current systems remain focused on static pattern recognition rather than prospective simulation of biological futures. Here we propose biomedical world models as a paradigm for AI-driven discovery. These models learn latent representations of molecular, cellular, tissue and clinical states, together with intervention-conditioned dynamics that allow future trajectories to be simulated before actions are taken. We discuss how biomedical world models could function as data engines, environment simulators and scientific planning substrates across applications including virtual cells, organoids, virtual patients and surgical simulation. We outline the data infrastructure, evaluation benchmarks, safety constraints and governance frameworks required. Biomedical world models may provide a foundation for simulation-guided, closed-loop and experimentally actionable biomedical discovery.

Guangyu Wang, Jingkun Yue, Siqi Zhang +19

State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, China · Department of Engineering Science, University of Oxford, Oxford, United Kingdom · Institute of Medical Artificial Intelligence, South China Hospital, Medical School, Shenzhen University, Shenzhen, Guangdong, China +8

Biomedical World Models Virtual Cell Long-Horizon Inference

May 11, 2026cs.LG

AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents

Recent advances in machine learning and large-scale biological data collections have revived the prospect of building a virtual cell, a computational model of cellular behavior that could accelerate biological discovery. One of the most compelling promises of this vision is the ability to perform in silico phenotypic screens, in which a model predicts the effects of cellular perturbations in unseen biological contexts. This task combines heterogeneous textual inputs with diverse phenotypic outputs, making it particularly well-suited to LLMs and agentic systems. Yet, no standard benchmark currently exists for this task, as existing efforts focus on narrower molecular readouts that are only indirectly aligned with the phenotypic endpoints driving many real-world drug discovery workflows. In this work, we present AssayBench, a benchmark for phenotypic screen prediction, built from 1,920 publicly available CRISPR screens spanning five broad classes of cellular phenotypes. We formulate the screen prediction task as a gene rank prediction for each screen and introduce the adjusted nDCG, a continuous metric for comparing performance across heterogeneous assays. Our extensive evaluation shows that existing methods remain far from empirically estimated performance ceilings and zero-shot generalist LLMs outperform biology-specific LLMs and trainable baselines. Optimization techniques such as fine-tuning, ensembling, and prompt optimization can further improve LLM performance on this task. Overall, AssayBench offers a practical testbed for measuring progress toward in silico phenotypic screening and, more broadly, virtual cell models.

Edward De Brouwer, Carl Edwards, Alexander Wu +9

Genentech

Phenotypes Virtual Cell Drug Discovery Screening

May 8, 2026cs.LG

CellScientist: From Execution Feedback to Auditable Model-Revision Trajectories for Cellular Perturbation Prediction

Cellular perturbation-response modeling requires coordinated choices of representations, fusion mechanisms, objectives, and training procedures. Large language models (LLMs) can propose executable candidates, but unconstrained revision can produce invalid implementations, change task semantics, or discard useful components. We present CellScientist, a protocol-constrained workflow that converts execution and validation feedback into auditable model-revision trajectories. It records design states and outcomes, routes discrepancies to specific components, and applies local revisions under a fixed task contract. A matched-budget study fixes the candidate language, predictor, fitting, and evaluator: structured revision finds better held-out predictors at small budgets under two LLM backbones. Operational audits link history to fewer repeated proposals, contract checks to contained violations, and discrepancy routing to targeted repairs. Refits of two frozen designs on an independently acquired cohort evaluate external predictive utility. Open-workflow trajectories retain improvements, regressions, and failures, while transcriptomic and single-cell searches extend application to additional response spaces. CellScientist produces both a selected predictor and an inspectable record of its development. Project page: https://limengran98.github.io/CellScientist/.

Mengran Li, Bo Li, Jiaying Wang +7

Center for Artificial Intelligence and Robotics (CAIR), Hong Kong Institute of Science and Innovation (HKISI)

Virtual Cell Single-Cell Perturbation Prediction Heterogeneous Modeling Tools Scientific Agents Hypothesis Class Vehicle Routing Problem

Apr 21, 2026cs.AI

AblateCell: A Reproduce-then-Ablate Agent for Virtual Cell Repositories

Systematic ablations are essential to attribute performance gains in AI Virtual Cells, yet they are rarely performed because biological repositories are under-standardized and tightly coupled to domain-specific data and formats. While recent coding agents can translate ideas into implementations, they typically stop at producing code and lack a verifier that can reproduce strong baselines and rigorously test which components truly matter. We introduce AblateCell, a reproduce-then-ablate agent for virtual cell repositories that closes this verification gap. AblateCell first reproduces reported baselines end-to-end by auto-configuring environments, resolving dependency and data issues, and rerunning official evaluations while emitting verifiable artifacts. It then conducts closed-loop ablation by generating a graph of isolated repository mutations and adaptively selecting experiments under a reward that trades off performance impact and execution cost. Evaluated on three single-cell perturbation prediction repositories (CPA, GEARS, BioLORD), AblateCell achieves 88.9% (+29.9% to human expert) end-to-end workflow success and 93.3% (+53.3% to heuristic) accuracy in recovering ground-truth critical components. These results enable scalable, repository-grounded verification and attribution directly on biological codebases.

Xue Xia, Chengkai Yao, Mingyu Tsoi +10

Shanghai Artificial Intelligence Laboratory · The Hong Kong University of Science and Technology (Guangzhou) · University of California San Diego +4

Virtual Cell Cells Single-Cell Perturbation Prediction Reproducibility