Daily Papers

Conventional transformer inference engines are request-driven, paying an O(n) prefill cost on every query. In streaming workloads, where data arrives continuously and queries probe an ever-growing context, this cost is prohibitive. We introduce a data-driven computational model centred on stateful sessions: a persistent KV cache advanced incrementally as new data arrives, so prefill is moved off the critical path and query latency becomes O(|q|), independent of accumulated context size. Building on this, Flash Queries reclaim idle GPU cycles between data arrivals to pre-evaluate registered questions and return cached answers before the user asks, a pattern that is structurally impossible in stateless engines because they discard intermediate state between requests. A multi-tenant continuous-batching scheduler with cell-budget admission and prefix-aware grouped prefill lets dozens of stateful sessions coexist on a single GPU while preserving full quadratic self-attention. On streaming market-data benchmarks the reference implementation achieves up to 5.9x speedup over conventional inference engines (vLLM, SGLang, TensorRT-LLM, llama.cpp), holding query latency constant as accumulated context grows.

Test-time scaling has become a dominant paradigm for improving LLM agent reliability, yet current approaches treat compute as an abundant resource, allowing agents to exhaust token and tool budgets on redundant steps or dead-end trajectories. Existing budget-aware methods either require expensive fine-tuning or rely on coarse, trajectory-level heuristics that cannot intervene mid-execution. We propose the Budget-Aware Value Tree (BAVT), a training-free inference-time framework that models multi-hop reasoning as a dynamic search tree guided by step-level value estimation within a single LLM backbone. Another key innovation is a budget-conditioned node selection mechanism that uses the remaining resource ratio as a natural scaling exponent over node values, providing a principled, parameter-free transition from broad exploration to greedy exploitation as the budget depletes. To combat the well-known overconfidence of LLM self-evaluation, BAVT employs a residual value predictor that scores relative progress rather than absolute state quality, enabling reliable pruning of uninformative or redundant tool calls. We further provide a theoretical convergence guarantee, proving that BAVT reaches a terminal answer with probability at least 1-ε under an explicit finite budget bound. Extensive evaluations on four multi-hop QA benchmarks across two model families demonstrate that BAVT consistently outperforms parallel sampling baselines. Most notably, BAVT under strict low-budget constraints surpasses baseline performance at 4times the resource allocation, establishing that intelligent budget management fundamentally outperforms brute-force compute scaling.

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.

Modeling cellular states and predicting their responses to perturbations are central challenges in computational biology and the development of virtual cells. Existing foundation models for single-cell transcriptomics provide powerful static representations, but they do not explicitly model the distribution of cellular states for generative simulation. Here, we introduce Lingshu-Cell, a masked discrete diffusion model that learns transcriptomic state distributions and supports conditional simulation under perturbation. By operating directly in a discrete token space that is compatible with the sparse, non-sequential nature of single-cell transcriptomic data, Lingshu-Cell captures complex transcriptome-wide expression dependencies across approximately 18,000 genes without relying on prior gene selection, such as filtering by high variability or ranking by expression level. Across diverse tissues and species, Lingshu-Cell accurately reproduces transcriptomic distributions, marker-gene expression patterns and cell-subtype proportions, demonstrating its ability to capture complex cellular heterogeneity. Moreover, by jointly embedding cell type or donor identity with perturbation, Lingshu-Cell can predict whole-transcriptome expression changes for novel combinations of identity and perturbation. It achieves leading performance on the Virtual Cell Challenge H1 genetic perturbation benchmark and in predicting cytokine-induced responses in human PBMCs. Together, these results establish Lingshu-Cell as a flexible cellular world model for in silico simulation of cell states and perturbation responses, laying the foundation for a new paradigm in biological discovery and perturbation screening.

Memory is increasingly central to Large Language Model (LLM) agents operating beyond a single context window, yet most existing systems rely on offline, query-agnostic memory construction that can be inefficient and may discard query-critical information. Although runtime memory utilization is a natural alternative, prior work often incurs substantial overhead and offers limited explicit control over the performance-cost trade-off. In this work, we present BudgetMem, a runtime agent memory framework for explicit, query-aware performance-cost control. BudgetMem structures memory processing as a set of memory modules, each offered in three budget tiers (i.e., Low/Mid/High). A lightweight router performs budget-tier routing across modules to balance task performance and memory construction cost, which is implemented as a compact neural policy trained with reinforcement learning. Using BudgetMem as a unified testbed, we study three complementary strategies for realizing budget tiers: implementation (method complexity), reasoning (inference behavior), and capacity (module model size). Across LoCoMo, LongMemEval, and HotpotQA, BudgetMem surpasses strong baselines when performance is prioritized (i.e., high-budget setting), and delivers better accuracy-cost frontiers under tighter budgets. Moreover, our analysis disentangles the strengths and weaknesses of different tiering strategies, clarifying when each axis delivers the most favorable trade-offs under varying budget regimes.

Cell type annotation is a key task in analyzing the heterogeneity of single-cell RNA sequencing data. Although recent foundation models automate this process, they typically annotate cells independently, without considering batch-level cellular context or providing explanatory reasoning. In contrast, human experts often annotate distinct cell types for different cell clusters based on their domain knowledge. To mimic this workflow, we introduce the CellPuzzles task, where the objective is to assign unique cell types to a batch of cells. This benchmark spans diverse tissues, diseases, and donor conditions, and requires reasoning across the batch-level cellular context to ensure label uniqueness. We find that off-the-shelf large language models (LLMs) struggle on CellPuzzles, with the best baseline (OpenAI's o1) achieving only 19.0% batch-level accuracy. To fill this gap, we propose Cell-o1, a 7B LLM trained via supervised fine-tuning on distilled reasoning traces, followed by reinforcement learning with batch-level rewards. Cell-o1 achieves state-of-the-art performance, outperforming o1 by over 73% and generalizing well across contexts. Further analysis of training dynamics and reasoning behaviors provides insights into batch-level annotation performance and emergent expert-like reasoning. Code and data are available at https://github.com/ncbi-nlp/cell-o1.

This paper presents advancements in automated early-stage prediction of the success of reprogramming human induced pluripotent stem cells (iPSCs) as a potential source for regenerative cell therapies.The minuscule success rate of iPSC-reprogramming of around 0.01% to 0.1% makes it labor-intensive, time-consuming, and exorbitantly expensive to generate a stable iPSC line. Since that requires culturing of millions of cells and intense biological scrutiny of multiple clones to identify a single optimal clone. The ability to reliably predict which cells are likely to establish as an optimal iPSC line at an early stage of pluripotency would therefore be ground-breaking in rendering this a practical and cost-effective approach to personalized medicine. Temporal information about changes in cellular appearance over time is crucial for predicting its future growth outcomes. In order to generate this data, we first performed continuous time-lapse imaging of iPSCs in culture using an ultra-high resolution microscope. We then annotated the locations and identities of cells in late-stage images where reliable manual identification is possible. Next, we propagated these labels backwards in time using a semi-automated tracking system to obtain labels for early stages of growth. Finally, we used this data to train deep neural networks to perform automatic cell segmentation and classification. Our code and data are available at https://github.com/abhineet123/ipsc_prediction.

Single-cell RNA sequencing (scRNA-seq) data analysis is crucial for biological research, as it enables the precise characterization of cellular heterogeneity. However, manual manipulation of various tools to achieve desired outcomes can be labor-intensive for researchers. To address this, we introduce CellAgent (http://cell.agent4science.cn/), an LLM-driven multi-agent framework, specifically designed for the automatic processing and execution of scRNA-seq data analysis tasks, providing high-quality results with no human intervention. Firstly, to adapt general LLMs to the biological field, CellAgent constructs LLM-driven biological expert roles - planner, executor, and evaluator - each with specific responsibilities. Then, CellAgent introduces a hierarchical decision-making mechanism to coordinate these biological experts, effectively driving the planning and step-by-step execution of complex data analysis tasks. Furthermore, we propose a self-iterative optimization mechanism, enabling CellAgent to autonomously evaluate and optimize solutions, thereby guaranteeing output quality. We evaluate CellAgent on a comprehensive benchmark dataset encompassing dozens of tissues and hundreds of distinct cell types. Evaluation results consistently show that CellAgent effectively identifies the most suitable tools and hyperparameters for single-cell analysis tasks, achieving optimal performance. This automated framework dramatically reduces the workload for science data analyses, bringing us into the "Agent for Science" era.

Single-cell transcriptomics enabled the study of cellular heterogeneity in response to perturbations at the resolution of individual cells. However, scaling high-throughput screens (HTSs) to measure cellular responses for many drugs remains a challenge due to technical limitations and, more importantly, the cost of such multiplexed experiments. Thus, transferring information from routinely performed bulk RNA HTS is required to enrich single-cell data meaningfully. We introduce chemCPA, a new encoder-decoder architecture to study the perturbational effects of unseen drugs. We combine the model with an architecture surgery for transfer learning and demonstrate how training on existing bulk RNA HTS datasets can improve generalisation performance. Better generalisation reduces the need for extensive and costly screens at single-cell resolution. We envision that our proposed method will facilitate more efficient experiment designs through its ability to generate in-silico hypotheses, ultimately accelerating drug discovery.

Large language models (LLMs) are increasingly applied in scientific research, offering new capabilities for knowledge discovery and reasoning. In single-cell biology, however, evaluation practices for both general and specialized LLMs remain inadequate: existing benchmarks are fragmented across tasks, adopt formats such as multiple-choice classification that diverge from real-world usage, and rely on metrics lacking interpretability and biological grounding. We present SC-ARENA, a natural language evaluation framework tailored to single-cell foundation models. SC-ARENA formalizes a virtual cell abstraction that unifies evaluation targets by representing both intrinsic attributes and gene-level interactions. Within this paradigm, we define five natural language tasks (cell type annotation, captioning, generation, perturbation prediction, and scientific QA) that probe core reasoning capabilities in cellular biology. To overcome the limitations of brittle string-matching metrics, we introduce knowledge-augmented evaluation, which incorporates external ontologies, marker databases, and scientific literature to support biologically faithful and interpretable judgments. Experiments and analysis across both general-purpose and domain-specialized LLMs demonstrate that (i) under the Virtual Cell unified evaluation paradigm, current models achieve uneven performance on biologically complex tasks, particularly those demanding mechanistic or causal understanding; and (ii) our knowledge-augmented evaluation framework ensures biological correctness, provides interpretable, evidence-grounded rationales, and achieves high discriminative capacity, overcoming the brittleness and opacity of conventional metrics. SC-Arena thus provides a unified and interpretable framework for assessing LLMs in single-cell biology, pointing toward the development of biology-aligned, generalizable foundation models.

The expanding computational costs and limited resources underscore the critical need for budgeted-iteration training, which aims to achieve optimal learning within predetermined iteration budgets.While learning rate schedules fundamentally govern the performance of different networks and tasks, particularly in budgeted-iteration scenarios, their design remains largely heuristic, lacking theoretical foundations.In addition, the optimal learning rate schedule requires extensive trial-and-error selection, making the training process inefficient.In this work, we propose the Unified Budget-Aware (UBA) schedule, a theoretically grounded learning rate schedule that consistently outperforms commonly-used schedules among diverse architectures and tasks under different constrained training budgets.First, we bridge the gap by constructing a novel training budget-aware optimization framework, which explicitly accounts for the robustness to landscape curvature variations.From this framework, we derive the UBA schedule, controlled by a single hyper-parameter varphi that provides a trade-off between flexibility and simplicity, eliminating the need for per-network numerical optimization. Moreover, we establish a theoretical connection between varphi and the condition number, adding interpretation and justification to our approach. Besides, we prove the convergence for different values of varphi.We offer practical guidelines for its selection via theoretical analysis and empirical results.xtensive experimental results show that UBA consistently surpasses the commonly-used schedules across diverse vision and language tasks, spanning network architectures (e.g., ResNet, OLMo) and scales, under different training-iteration budgets.

Single-cell RNA-seq (scRNA-seq) enables atlas-scale profiling of complex tissues, revealing rare lineages and transient states. Yet, assigning biologically valid cell identities remains a bottleneck because markers are tissue- and state-dependent, and novel states lack references. We present CellMaster, an AI agent that mimics expert practice for zero-shot cell-type annotation. Unlike existing automated tools, CellMaster leverages LLM-encoded knowledge (e.g., GPT-4o) to perform on-the-fly annotation with interpretable rationales, without pre-training or fixed marker databases. Across 9 datasets spanning 8 tissues, CellMaster improved accuracy by 7.1% over best-performing baselines (including CellTypist and scTab) in automatic mode. With human-in-the-loop refinement, this advantage increased to 18.6%, with a 22.1% gain on subtype populations. The system demonstrates particular strength in rare and novel cell states where baselines often fail. Source code and the web application are available at https://github.com/AnonymousGym/CellMaster{https://github.com/AnonymousGym/CellMaster}.

Motivated by the operational problems in click and collect systems, such as curbside pickup programs, we study a joint admission control and capacity allocation problem. We consider a system where arriving customers have preferred service delivery times and gauge the service quality based on the service provider's ability to complete the service as close as possible to the preferred time. Customers can be of different priority classes, and their priority may increase as they wait longer in the queue. The service provider can reject customers upon their arrival if the system is overloaded or outsource the service (alternatively work overtime) when the capacity is not enough. The service provider's goal is to find the minimum-cost admission and capacity allocation policy to dynamically decide when to serve and whom to serve. We model this problem as a Markov Decision Process. Our structural results partially characterize a set of suboptimal solutions, and we develop solution methods using these results. We also develop a problem-specific approximation method that is based on state aggregation to overcome the computational challenges. We present extensive computational results and discuss the impact of problem parameters on the optimal policy.