Learning Latent Dynamical Causal Processes for Single-Cell Perturbation Prediction

Single-cell perturbation prediction aims to infer how cells respond to unseen interventions and to achieve out-of-distribution (OOD) generalization, providing a computational route to understanding how perturbations reshape cellular programs over time. Existing machine learning methods have made important progress, but typically capture only one side of the response. Latent causal approaches seek mechanisms that support generalization and interpretation, yet often treat perturbation effects as static outcomes. Temporal models describe how gene expression changes across time, but usually do not explicitly recover the latent causal generative mechanisms driving these changes. In practice, perturbation effects are both latent and dynamical: interventions act through unobserved cellular programs, whose states evolve over time and give rise to observed expression profiles. Motivated by this view, we propose a latent dynamical causal generative model for single-cell perturbation data that jointly captures latent cellular programs, perturbation-conditioned mechanisms, and temporal evolution. We further provide an identifiability analysis showing that, under suitable conditions, the latent causal variables are recoverable up to standard equivalence classes. Guided by this analysis, we develop CITE-VAE, a learning framework for recovering latent cellular programs and their perturbation-driven dynamics from single-cell sequencing data. Experiments on Causal-3DIdent validate the theoretical results and the effectiveness of the proposed method in controlled settings. Additional experiments on real-world CRISPR-based single-cell perturbation data show improved generalization to unseen perturbations compared with state-of-the-art baselines, highlighting the practical robustness of our approach.

S2Aligner: Pair-Efficient and Transferable Pre-Training for Sparse Text-Attributed Graphs

Pre-training on text-attributed graphs (TAGs) is central to building transferable graph foundation models, where LLM-as-Aligner methods align graph and text representations through the semantic knowledge of large language models. However, these methods usually assume that node texts provide sufficient and reliable supervision, an assumption often violated in real-world sparse TAGs. When textual anchors are missing, noisy, or uneven across domains, graph structures must be aligned with weak semantic evidence, leading to unreliable structure-semantics correspondence and sparsity-induced transfer bias. This paper presents S2Aligner, a sparsity-aware and structure-enhanced LLM-as-Aligner framework for graph-text pre-training on sparse TAGs. The key idea is to decouple semantic alignment from structural modeling, allowing topology-aware signals to enhance alignment without contaminating the shared semantic space. Specifically, S2Aligner decomposes graph-text representations into semantic and structural components, uses structure-oriented reconstruction with consistency control to inject reliable topology cues into text representations, and suppresses inconsistent structural signals under textual sparsity. Moreover, S2Aligner introduces sparsity-aware cross-domain risk balancing, which calibrates domain risks through a global-domain density ratio and downweights unreliable sparse samples via graph reliability estimation. Theoretical analysis shows that this objective reduces cross-domain generalization gaps by controlling domain risk discrepancy. Extensive experiments across diverse graph domains, sparsity levels, and downstream tasks demonstrate that S2Aligner consistently outperforms existing baselines.

What Makes a Representation Good for Single-Cell Perturbation Prediction?

Single-cell perturbation modeling is fundamental for understanding and predicting cellular responses to genetic perturbations. However, existing approaches, from causal representation learning to foundation models, often struggle with an overlooked challenge: gene expression is dominated by perturbation-invariant information, while perturbation-specific signals are intrinsically sparse. As a result, learned representations either entangle invariant and perturbation-specific information, leading to spurious and non-generalizable predictors, or suppress perturbation-specific signals altogether, rendering them ineffective for prediction. To address this, we propose PerturbedVAE, a general framework designed to resolve this signal imbalance. The framework explicitly separates perturbation-specific information from dominant invariant structure and recovers causal representations to effectively utilize such information for prediction. We further provide an identifiability analysis that characterizes the conditions under which sparse perturbation effects can be reliably recovered, thereby clarifying how the framework can be concretely specified under such conditions. Empirically, PerturbedVAE achieves state-of-the-art performance on a widely used benchmark across multiple evaluation settings, yielding significant gains on out-of-distribution combinatorial predictions and uncovering interpretable perturbation-response programs.

WisdomInterrogatory (LuWen): An Open-Source Legal Large Language Model Technical Report

Large language models have demonstrated remarkable capabilities across a wide range of natural language processing tasks, yet their application in the legal domain remains challenging due to the specialized terminology, complex reasoning requirements, and rapidly evolving legal knowledge involved. In this paper, we present WisdomInterrogatory (LuWen), an open-source Chinese legal language model built upon the Baichuan foundation model through three key techniques: continual pre-training on a large-scale legal corpus, supervised fine-tuning with carefully curated legal instruction data, and retrieval-augmented generation integrated with a comprehensive legal knowledge base. We evaluate LuWen on five representative legal tasks spanning both prediction and generation settings, including legal judgment prediction, judicial examination, legal text summarization, law article question answering, and judicial decision reasoning. Experimental results show that LuWen outperforms several strong baselines, demonstrating the effectiveness of our approach in adapting general-purpose language models to the legal domain.

Luwen Technical Report

Large language models have demonstrated remarkable capabilities across a wide range of natural language processing tasks, yet their application in the legal domain remains challenging due to the specialized terminology, complex reasoning requirements, and rapidly evolving legal knowledge involved. In this paper, we present Luwen, an open-source Chinese legal language model built upon the Baichuan foundation model through three key techniques: continual pre-training on a large-scale legal corpus, supervised fine-tuning with carefully curated legal instruction data, and retrieval-augmented generation integrated with a comprehensive legal knowledge base. We evaluate Luwen on five representative legal tasks spanning both prediction and generation settings, including legal judgment prediction, judicial examination, legal text summarization, law article question answering, and judicial decision reasoning. Experimental results show that Luwen outperforms several strong baselines, demonstrating the effectiveness of our approach in adapting general-purpose language models to the legal domain.

How Far Are We? Systematic Evaluation of LLMs vs. Human Experts in Mathematical Contest in Modeling

Large language models (LLMs) have achieved strong performance on reasoning benchmarks, yet their ability to solve real-world problems requiring end-to-end workflows remains unclear. Mathematical modeling competitions provide a stringent testbed for evaluating such end-to-end problem-solving capability. We propose a problem-oriented, stage-wise evaluation framework that assesses LLM performance across modeling stages using expert-verified criteria. We validate the framework's reliability by comparing automatic scores with independent human expert judgments on problems from the China Postgraduate Mathematical Contest in Modeling, demonstrating substantially stronger alignment than existing evaluation schemes. Using this framework, we reveal a comprehension-execution gap in state-of-the-art LLMs: while they perform well in early stages such as problem identification and formulation, they exhibit persistent deficiencies in execution-oriented stages including model solving, code implementation, and result analysis. These gaps persist even with increased model scale. We further trace these failures to insufficient specification, missing verification, and lack of validation, with errors propagating across stages without correction. Our findings suggest that bridging this gap requires approaches beyond model scaling, offering insights for applying LLMs to complex real-world problem solving.

HIFICL: High-Fidelity In-Context Learning for Multimodal Tasks

In-Context Learning (ICL) is a significant paradigm for Large Multimodal Models (LMMs), using a few in-context demonstrations (ICDs) for new task adaptation. However, its performance is sensitive to demonstration configurations and computationally expensive. Mathematically, the influence of these demonstrations can be decomposed into a dynamic mixture of the standard attention output and the context values. Current approximation methods simplify this process by learning a "shift vector". Inspired by the exact decomposition, we introduce High-Fidelity In-Context Learning (HIFICL) to more faithfully model the ICL mechanism. HIFICL consists of three key components: 1) a set of "virtual key-value pairs" to act as a learnable context, 2) a low-rank factorization for stable and regularized training, and 3) a simple end-to-end training objective. From another perspective, this mechanism constitutes a form of context-aware Parameter-Efficient Fine-Tuning (PEFT). Extensive experiments show that HiFICL consistently outperforms existing approximation methods on several multimodal benchmarks. The code is available at https://github.com/bbbandari/HiFICL.

Graph-GRPO: Stabilizing Multi-Agent Topology Learning via Group Relative Policy Optimization

Optimizing communication topology is fundamental to the efficiency and effectiveness of Large Language Model (LLM)-based Multi-Agent Systems (MAS). While recent approaches utilize reinforcement learning to dynamically construct task-specific graphs, they typically rely on single-sample policy gradients with absolute rewards (e.g., binary correctness). This paradigm suffers from severe gradient variance and the credit assignment problem: simple queries yield non-informative positive rewards for suboptimal structures, while difficult queries often result in failures that provide no learning signal. To address these challenges, we propose Graph-GRPO, a novel topology optimization framework that integrates Group Relative Policy Optimization. Instead of evaluating a single topology in isolation, Graph-GRPO samples a group of diverse communication graphs for each query and computes the advantage of specific edges based on their relative performance within the group. By normalizing rewards across the sampled group, our method effectively mitigates the noise derived from task difficulty variance and enables fine-grained credit assignment. Extensive experiments on reasoning and code generation benchmarks demonstrate that Graph-GRPO significantly outperforms state-of-the-art baselines, achieving superior training stability and identifying critical communication pathways previously obscured by reward noise.

Intelligent Pathological Diagnosis of Gestational Trophoblastic Diseases via Visual-Language Deep Learning Model

The pathological diagnosis of gestational trophoblastic disease(GTD) takes a long time, relies heavily on the experience of pathologists, and the consistency of initial diagnosis is low, which seriously threatens maternal health and reproductive outcomes. We developed an expert model for GTD pathological diagnosis, named GTDoctor. GTDoctor can perform pixel-based lesion segmentation on pathological slides, and output diagnostic conclusions and personalized pathological analysis results. We developed a software system, GTDiagnosis, based on this technology and conducted clinical trials. The retrospective results demonstrated that GTDiagnosis achieved a mean precision of over 0.91 for lesion detection in pathological slides (n=679 slides). In prospective studies, pathologists using GTDiagnosis attained a Positive Predictive Value of 95.59% (n=68 patients). The tool reduced average diagnostic time from 56 to 16 seconds per case (n=285 patients). GTDoctor and GTDiagnosis offer a novel solution for GTD pathological diagnosis, enhancing diagnostic performance and efficiency while maintaining clinical interpretability.

RAIN-Merging: A Gradient-Free Method to Enhance Instruction Following in Large Reasoning Models with Preserved Thinking Format

Large reasoning models (LRMs) excel at a long chain of reasoning but often fail to faithfully follow instructions regarding output format, constraints, or specific requirements. We investigate whether this gap can be closed by integrating an instruction-tuned model (ITM) into an LRM. Analyzing their differences in parameter space, namely task vectors, we find that their principal subspaces are nearly orthogonal across key modules, suggesting a lightweight merging with minimal interference. However, we also demonstrate that naive merges are fragile because they overlook the output format mismatch between LRMs (with explicit thinking and response segments) and ITMs (answers-only). We introduce RAIN-Merging (Reasoning-Aware Instruction-attention guided Null-space projection Merging), a gradient-free method that integrates instruction following while preserving thinking format and reasoning performance. First, with a small reasoning calibration set, we project the ITM task vector onto the null space of forward features at thinking special tokens, which preserves the LRM's structured reasoning mechanisms. Second, using a small instruction calibration set, we estimate instruction attention to derive module-specific scaling that amplifies instruction-relevant components and suppresses leakage. Across four instruction-following benchmarks and nine reasoning & general capability benchmarks, RAIN-Merging substantially improves instruction adherence while maintaining reasoning quality. The gains are consistent across model scales and architectures, translating to improved performance in agent settings.