Deep Learning
VCWorld: A Biological World Model for Virtual Cell Simulation
Wei, Zhijian, Ma, Runze, Wang, Zichen, Li, Zhongmin, Song, Shuotong, Zheng, Shuangjia
Virtual cell modeling aims to predict cellular responses to perturbations. Existing virtual cell models rely heavily on large-scale single-cell datasets, learning explicit mappings between gene expression and perturbations. Although recent models attempt to incorporate multi-source biological information, their generalization remains constrained by data quality, coverage, and batch effects. More critically, these models often function as black boxes, offering predictions without interpretability or consistency with biological principles, which undermines their credibility in scientific research. To address these challenges, we present VCWorld, a cell-level white-box simulator that integrates structured biological knowledge with the iterative reasoning capabilities of large language models to instantiate a biological world model. VCWorld operates in a data-efficient manner to reproduce perturbation-induced signaling cascades and generates interpretable, stepwise predictions alongside explicit mechanistic hypotheses. In drug perturbation benchmarks, VCWorld achieves state-of-the-art predictive performance, and the inferred mechanistic pathways are consistent with publicly available biological evidence.
ChartPoint: Guiding MLLMs with Grounding Reflection for Chart Reasoning
Xu, Zhengzhuo, Du, SiNan, Qi, Yiyan, SiwenLu, null, Xu, Chengjin, Yuan, Chun, Guo, Jian
Multimodal Large Language Models (MLLMs) have emerged as powerful tools for chart comprehension. However, they heavily rely on extracted content via OCR, which leads to numerical hallucinations when chart textual annotations are sparse. While existing methods focus on scaling instructions, they fail to address the fundamental challenge, i.e., reasoning with visual perception. In this paper, we identify a critical observation: MLLMs exhibit weak grounding in chart elements and proportional relationships, as evidenced by their inability to localize key positions to match their reasoning. To bridge this gap, we propose PointCoT, which integrates reflective interaction into chain-of-thought reasoning in charts. By prompting MLLMs to generate bounding boxes and re-render charts based on location annotations, we establish connections between textual reasoning steps and visual grounding regions. We further introduce an automated pipeline to construct ChartPoint-SFT-62k, a dataset featuring 19.2K high-quality chart samples with step-by-step CoT, bounding box, and re-rendered visualizations. Leveraging this data, we develop two instruction-tuned models, ChartPointQ2 and ChartPointQ2.5, which outperform state-of-the-art across several chart benchmarks, e.g., +5.04\% on ChartBench.
Challenges of Heterogeneity in Big Data: A Comparative Study of Classification in Large-Scale Structured and Unstructured Domains
Eduardo, Gonzรกlez Trigueros Jesรบs, Alejandro, Alonso Sรกnchez, Emilio, Muรฑoz Rivera, Jaqueline, Peรฑarรกn Prieto Mariana, Natalia, Mendoza Gonzรกlez Camila
This study analyzes the impact of heterogeneity ("Variety") in Big Data by comparing classification strategies across structured (Epsilon) and unstructured (Rest-Mex, IMDB) domains. A dual methodology was implemented: evolutionary and Bayesian hyperparameter optimization (Genetic Algorithms, Optuna) in Python for numerical data, and distributed processing in Apache Spark for massive textual corpora. The results reveal a "complexity paradox": in high-dimensional spaces, optimized linear models (SVM, Logistic Regression) outperformed deep architectures and Gradient Boosting. Conversely, in text-based domains, the constraints of distributed fine-tuning led to overfitting in complex models, whereas robust feature engineering -- specifically Transformer-based embeddings (ROBERTa) and Bayesian Target Encoding -- enabled simpler models to generalize effectively. This work provides a unified framework for algorithm selection based on data nature and infrastructure constraints.
FiCoTS: Fine-to-Coarse LLM-Enhanced Hierarchical Cross-Modality Interaction for Time Series Forecasting
Lyu, Yafei, Zhou, Hao, Zhang, Lu, Yang, Xu, Liu, Zhiyong
Time series forecasting is central to data analysis and web technologies. The recent success of Large Language Models (LLMs) offers significant potential for this field, especially from the cross-modality aspect. Most methods adopt an LLM-as-Predictor paradigm, using LLM as the forecasting backbone and designing modality alignment mechanisms to enable LLM to understand time series data. However, the semantic information in the two modalities of time series and text differs significantly, making it challenging for LLM to fully understand time series data. To mitigate this challenge, our work follows an LLM-as-Enhancer paradigm to fully utilize the advantage of LLM in text understanding, where LLM is only used to encode text modality to complement time series modality. Based on this paradigm, we propose FiCoTS, an LLM-enhanced fine-to-coarse framework for multimodal time series forecasting. Specifically, the framework facilitates progressive cross-modality interaction by three levels in a fine-to-coarse scheme: First, in the token-level modality alignment module, a dynamic heterogeneous graph is constructed to filter noise and align time series patches with text tokens; Second, in the feature-level modality interaction module, a global cross-attention mechanism is introduced to enable each time series variable to connect with relevant textual contexts; Third, in the decision-level modality fusion module, we design a gated network to adaptively fuse the results of the two modalities for robust predictions. These three modules work synergistically to let the two modalities interact comprehensively across three semantic levels, enabling textual information to effectively support temporal prediction. Extensive experiments on seven real-world benchmarks demonstrate that our model achieves state-of-the-art performance. The codes will be released publicly.
EduEval: A Hierarchical Cognitive Benchmark for Evaluating Large Language Models in Chinese Education
Ma, Guoqing, Zhu, Jia, Guo, Hanghui, Shi, Weijie, Cui, Yue, Shen, Jiawei, Li, Zilong, Liang, Yidan
Large language models (LLMs) demonstrate significant potential for educational applications. However, their unscrutinized deployment poses risks to educational standards, underscoring the need for rigorous evaluation. We introduce EduEval, a comprehensive hierarchical benchmark for evaluating LLMs in Chinese K-12 education. This benchmark makes three key contributions: (1) Cognitive Framework: We propose the EduAbility Taxonomy, which unifies Bloom's Taxonomy and Webb's Depth of Knowledge to organize tasks across six cognitive dimensions including Memorization, Understanding, Application, Reasoning, Creativity, and Ethics. (2) Authenticity: Our benchmark integrates real exam questions, classroom conversation, student essays, and expert-designed prompts to reflect genuine educational challenges; (3) Scale: EduEval comprises 24 distinct task types with over 11,000 questions spanning primary to high school levels. We evaluate 14 leading LLMs under both zero-shot and few-shot settings, revealing that while models perform well on factual tasks, they struggle with classroom dialogue classification and exhibit inconsistent results in creative content generation. Interestingly, several open source models outperform proprietary systems on complex educational reasoning. Few-shot prompting shows varying effectiveness across cognitive dimensions, suggesting that different educational objectives require tailored approaches. These findings provide targeted benchmarking metrics for developing LLMs specifically optimized for diverse Chinese educational tasks.
Data-Driven Modeling and Correction of Vehicle Dynamics
Ly, Nguyen, Tatsuoka, Caroline, Nagaraj, Jai, Levy, Jacob, Palafox, Fernando, Fridovich-Keil, David, Lu, Hannah
We develop a data-driven framework for learning and correcting non-autonomous vehicle dynamics. Physics-based vehicle models are often simplified for tractability and therefore exhibit inherent model-form uncertainty, motivating the need for data-driven correction. Moreover, non-autonomous dynamics are governed by time-dependent control inputs, which pose challenges in learning predictive models directly from temporal snapshot data. To address these, we reformulate the vehicle dynamics via a local parameterization of the time-dependent inputs, yielding a modified system composed of a sequence of local parametric dynamical systems. We approximate these parametric systems using two complementary approaches. First, we employ the DRIPS (dimension reduction and interpolation in parameter space) methodology to construct efficient linear surrogate models, equipped with lifted observable spaces and manifold-based operator interpolation. This enables data-efficient learning of vehicle models whose dynamics admit accurate linear representations in the lifted spaces. Second, for more strongly nonlinear systems, we employ FML (Flow Map Learning), a deep neural network approach that approximates the parametric evolution map without requiring special treatment of nonlinearities. We further extend FML with a transfer-learning-based model correction procedure, enabling the correction of misspecified prior models using only a sparse set of high-fidelity or experimental measurements, without assuming a prescribed form for the correction term. Through a suite of numerical experiments on unicycle, simplified bicycle, and slip-based bicycle models, we demonstrate that DRIPS offers robust and highly data-efficient learning of non-autonomous vehicle dynamics, while FML provides expressive nonlinear modeling and effective correction of model-form errors under severe data scarcity.
RealAppliance: Let High-fidelity Appliance Assets Controllable and Workable as Aligned Real Manuals
Gao, Yuzheng, Long, Yuxing, Kang, Lei, Guo, Yuchong, Yu, Ziyan, Mao, Shangqing, Zhang, Jiyao, Wu, Ruihai, Li, Dongjiang, Shen, Hui, Dong, Hao
Existing appliance assets suffer from poor rendering, incomplete mechanisms, and misalignment with manuals, leading to simulation-reality gaps that hinder appliance manipulation development. In this work, we introduce the RealAppliance dataset, comprising 100 high-fidelity appliances with complete physical, electronic mechanisms, and program logic aligned with their manuals. Based on these assets, we propose the RealAppliance-Bench benchmark, which evaluates multimodal large language models and embodied manipulation planning models across key tasks in appliance manipulation planning: manual page retrieval, appliance part grounding, open-loop manipulation planning, and closed-loop planning adjustment. Our analysis of model performances on RealAppliance-Bench provides insights for advancing appliance manipulation research.
HIMOSA: Efficient Remote Sensing Image Super-Resolution with Hierarchical Mixture of Sparse Attention
Liu, Yi, Wan, Yi, Liu, Xinyi, Wu, Qiong, Xia, Panwang, Huang, Xuejun, Zhang, Yongjun
In remote sensing applications, such as disaster detection and response, real-time efficiency and model lightweighting are of critical importance. Consequently, existing remote sensing image super-resolution methods often face a trade-off between model performance and computational efficiency. In this paper, we propose a lightweight super-resolution framework for remote sensing imagery, named HIMOSA. Specifically, HIMOSA leverages the inherent redundancy in remote sensing imagery and introduces a content-aware sparse attention mechanism, enabling the model to achieve fast inference while maintaining strong reconstruction performance. Furthermore, to effectively leverage the multi-scale repetitive patterns found in remote sensing imagery, we introduce a hierarchical window expansion and reduce the computational complexity by adjusting the sparsity of the attention. Extensive experiments on multiple remote sensing datasets demonstrate that our method achieves state-of-the-art performance while maintaining computational efficiency.
Lost without translation -- Can transformer (language models) understand mood states?
Shivaprakash, Prakrithi, Mukherjee, Diptadhi, Shukla, Lekhansh, Mukherjee, Animesh, Chand, Prabhat, Murthy, Pratima
Background: Large Language Models show promise in psychiatry but are English-centric. Their ability to understand mood states in other languages is unclear, as different languages have their own idioms of distress. Aim: To quantify the ability of language models to faithfully represent phrases (idioms of distress) of four distinct mood states (depression, euthymia, euphoric mania, dysphoric mania) expressed in Indian languages. Methods: We collected 247 unique phrases for the four mood states across 11 Indic languages. We tested seven experimental conditions, comparing k-means clustering performance on: (a) direct embeddings of native and Romanised scripts (using multilingual and Indic-specific models) and (b) embeddings of phrases translated to English and Chinese. Performance was measured using a composite score based on Adjusted Rand Index, Normalised Mutual Information, Homogeneity and Completeness. Results: Direct embedding of Indic languages failed to cluster mood states (Composite Score = 0.002). All translation-based approaches showed significant improvement. High performance was achieved using Gemini-translated English (Composite=0.60) and human-translated English (Composite=0.61) embedded with gemini-001. Surprisingly, human-translated English, further translated into Chinese and embedded with a Chinese model, performed best (Composite = 0.67). Specialised Indic models (IndicBERT and Sarvam-M) performed poorly. Conclusion: Current models cannot meaningfully represent mood states directly from Indic languages, posing a fundamental barrier to their psychiatric application for diagnostic or therapeutic purposes in India. While high-quality translation bridges this gap, reliance on proprietary models or complex translation pipelines is unsustainable. Models must first be built to understand diverse local languages to be effective in global mental health.
Teleportation-Based Defenses for Privacy in Approximate Machine Unlearning
Maheri, Mohammad M, Cadet, Xavier, Chin, Peter, Haddadi, Hamed
Approximate machine unlearning aims to efficiently remove the influence of specific data points from a trained model, offering a practical alternative to full retraining. However, it introduces privacy risks: an adversary with access to pre- and post-unlearning models can exploit their differences for membership inference or data reconstruction. We show these vulnerabilities arise from two factors: large gradient norms of forget-set samples and the close proximity of unlearned parameters to the original model. To demonstrate their severity, we propose unlearning-specific membership inference and reconstruction attacks, showing that several state-of-the-art methods (e.g., NGP, SCRUB) remain vulnerable. To mitigate this leakage, we introduce WARP, a plug-and-play teleportation defense that leverages neural network symmetries to reduce forget-set gradient energy and increase parameter dispersion while preserving predictions. This reparameterization obfuscates the signal of forgotten data, making it harder for attackers to distinguish forgotten samples from non-members or recover them via reconstruction. Across six unlearning algorithms, our approach achieves consistent privacy gains, reducing adversarial advantage (AUC) by up to 64% in black-box and 92% in white-box settings, while maintaining accuracy on retained data. These results highlight teleportation as a general tool for reducing attack success in approximate unlearning.