Understanding the reasoning behind deep learning model predictions is crucial in cheminformatics and drug discovery, where molecular design determines their properties. However, current evaluation frameworks for Explainable AI (XAI) in this domain often rely on artificial datasets or simplified tasks, employing data-derived metrics that fail to capture the complexity of real-world scenarios and lack a direct link to explanation faithfulness. To address this, we introduce B-XAIC, a novel benchmark constructed from real-world molecular data and diverse tasks with known ground-truth rationales for assigned labels. Through a comprehensive evaluation using B-XAIC, we reveal limitations of existing XAI methods for Graph Neural Networks (GNNs) in the molecular domain. This benchmark provides a valuable resource for gaining deeper insights into the faithfulness of XAI, facilitating the development of more reliable and interpretable models.
Recent advances on 6D object pose estimation have achieved high performance on representative benchmarks such as LM-O, YCB-V, and T-Less. These datasets capture natural-occurring variations in illumination and camera setup but do not systematically explore the effects of controllable sensor configurations, such as exposure, gain, and depth-sensor modes. To bridge this gap, we introduce SenseShift6D, the first RGB-D object-pose benchmark that physically sweeps 13 RGB exposures, 9 RGB gains, auto-exposure, 4 depth-capture modes, and 5 illumination levels. For six common household objects, we acquire 198.8k RGB and 20.0k depth images (i.e., 795.4k RGB-D scenes), providing 1,380 unique sensor-lighting permutations per object pose. Experiments with state-of-the-art pretrained, generalizable pose estimators reveal substantial performance variation across lighting and sensor settings, despite their large-scale pretraining. Strikingly, even instance-level estimators-trained and tested on identical objects and backgrounds-exhibit pronounced sensitivity to environmental and sensor shifts. These findings establish sensor- and environment-aware robustness as an underexplored yet essential dimension of 6D pose estimation. To illustrate the opportunity enabled by this benchmark, we evaluate test-time sensor selection without retraining. An idealized controller yields remarkable gains of up to +16.2 pp for generalizable models, whereas a practical consistency-based proxy provides only limited improvements, highlighting substantial headroom and the need for future research on reliable sensor-aware adaptation. SenseShift6D is available at huggingface.co/datasets/Yegyu/SenseShift6D.
The landscape of video recognition has evolved significantly, shifting from traditional Convolutional Neural Networks (CNNs) to Transformer-based architectures for improved accuracy. While 3D CNNs have been effective at capturing spatiotemporal dynamics, recent Transformer models leverage self-attention to model long-range spatial and temporal dependencies. Despite achieving state-of-the-art performance on major benchmarks, Transformers remain computationally expensive, particularly with dense video data. To address this, we propose a lightweight Video Focal Modulation Network, DVFL-Net, which distills spatiotemporal knowledge from a large pre-trained teacher into a compact nano student model, enabling efficient on-device deployment. DVFL-Net utilizes knowledge distillation and spatial-temporal feature modulation to significantly reduce computation while preserving high recognition performance. We employ forward Kullback-Leibler (KL) divergence alongside spatio-temporal focal modulation to effectively transfer both local and global context from the Video-FocalNet Base (teacher) to the proposed VFL-Net (student). We evaluate DVFL-Net on UCF50, UCF101, HMDB51, SSV2, and Kinetics-400, benchmarking it against recent state-of-the-art methods in Human Action Recognition (HAR). Additionally, we conduct a detailed ablation study analyzing the impact of forward KL divergence. The results confirm the superiority of DVFL-Net in achieving an optimal balance between performance and efficiency, demonstrating lower memory usage, reduced GFLOPs, and strong accuracy, making it a practical solution for real-time HAR applications.
Pretraining on large-scale, in-domain datasets grants histopathology foundation models (FM) the ability to learn task-agnostic data representations, enhancing transfer learning on downstream tasks. In computational pathology, automated whole slide image analysis requires multiple instance learning (MIL) frameworks due to the gigapixel scale of the slides. The diversity among histopathology FMs has highlighted the need to design real-world challenges for evaluating their effectiveness. To bridge this gap, our work presents a novel benchmark for evaluating histopathology FMs as patch-level feature extractors within a MIL classification framework. For that purpose, we leverage the AI4SkIN dataset, a multi-center cohort encompassing slides with challenging cutaneous spindle cell neoplasm subtypes. We also define the Foundation Model - Silhouette Index (FM-SI), a novel metric to measure model consistency against distribution shifts. Our experimentation shows that extracting less biased features enhances classification performance, especially in similarity-based MIL classifiers.
Large Language Model (LLM) agents have shown great potential for solving real-world problems and promise to be a solution for tasks automation in industry. However, more benchmarks are needed to systematically evaluate automation agents from an industrial perspective, for example, in Civil Engineering. Therefore, we propose DrafterBench for the comprehensive evaluation of LLM agents in the context of technical drawing revision, a representation task in civil engineering. DrafterBench contains twelve types of tasks summarized from real-world drawing files, with 46 customized functions/tools and 1920 tasks in total. DrafterBench is an open-source benchmark to rigorously test AI agents' proficiency in interpreting intricate and long-context instructions, leveraging prior knowledge, and adapting to dynamic instruction quality via implicit policy awareness. The toolkit comprehensively assesses distinct capabilities in structured data comprehension, function execution, instruction following, and critical reasoning. DrafterBench offers detailed analysis of task accuracy and error statistics, aiming to provide deeper insight into agent capabilities and identify improvement targets for integrating LLMs in engineering applications. Our benchmark is available at https://github.com/Eason-Li-AIS/DrafterBench, with the test set hosted at https://huggingface.co/datasets/Eason666/DrafterBench.
Modern Artificial Intelligence (AI) increasingly relies on multi-agent architectures that blend visual and language understanding. Yet, a pressing challenge remains: How can we trust these agents especially in zero-shot settings with no fine-tuning? We introduce a novel modular Agentic AI visual classification framework that integrates generalist multimodal agents with a non-visual reasoning orchestrator and a Retrieval-Augmented Generation (RAG) module. Applied to apple leaf disease diagnosis, we benchmark three configurations: (I) zero-shot with confidence-based orchestration, (II) fine-tuned agents with improved performance, and (III) trust-calibrated orchestration enhanced by CLIP-based image retrieval and re-evaluation loops. Using confidence calibration metrics (ECE, OCR, CCC), the orchestrator modulates trust across agents. Our results demonstrate a 77.94\% accuracy improvement in the zero-shot setting using trust-aware orchestration and RAG, achieving 85.63\% overall. GPT-4o showed better calibration, while Qwen-2.5-VL displayed overconfidence. Furthermore, image-RAG grounded predictions with visually similar cases, enabling correction of agent overconfidence via iterative re-evaluation. The proposed system separates perception (vision agents) from meta-reasoning (orchestrator), enabling scalable and interpretable multi-agent AI. This blueprint is extensible to diagnostics, biology, and other trust-critical domains. All models, prompts, results, and system components including the complete software source code are openly released to support reproducibility, transparency, and community benchmarking at Github: https://github.com/Applied-AI-Research-Lab/Orchestrator-Agent-Trust
Federated Learning (FL) has undergone significant development since its inception in 2016, advancing from basic algorithms to complex methodologies tailored to address diverse challenges and use cases. However, research and benchmarking of novel FL techniques against a plethora of established state-of-the-art solutions remain challenging. To streamline this process, we introduce FLsim, a comprehensive FL simulation framework designed to meet the diverse requirements of FL workflows in the literature. FLsim is characterized by its modularity, scalability, resource efficiency, and controlled reproducibility of experimental outcomes. Its easy to use interface allows users to specify customized FL requirements through job configuration, which supports: (a) customized data distributions, ranging from non-independent and identically distributed (non-iid) data to independent and identically distributed (iid) data, (b) selection of local learning algorithms according to user preferences, with complete agnosticism to ML libraries, (c) choice of network topology illustrating communication patterns among nodes, (d) definition of model aggregation and consensus algorithms, and (e) pluggable blockchain support for enhanced robustness. Through a series of experimental evaluations, we demonstrate the effectiveness and versatility of FLsim in simulating a diverse range of state-of-the-art FL experiments. We envisage that FLsim would mark a significant advancement in FL simulation frameworks, offering unprecedented flexibility and functionality for researchers and practitioners alike.
The rapid advancement of large language models (LLMs) has heightened concerns about benchmark data contamination (BDC), where models inadvertently memorize evaluation data, inflating performance metrics and undermining genuine generalization assessment. This paper introduces the Data Contamination Risk (DCR) framework, a lightweight, interpretable pipeline designed to detect and quantify BDC across four granular levels: semantic, informational, data, and label. By synthesizing contamination scores via a fuzzy inference system, DCR produces a unified DCR Factor that adjusts raw accuracy to reflect contamination-aware performance. Validated on 9 LLMs (0.5B-72B) across sentiment analysis, fake news detection, and arithmetic reasoning tasks, the DCR framework reliably diagnoses contamination severity and with accuracy adjusted using the DCR Factor to within 4% average error across the three benchmarks compared to the uncontaminated baseline. Emphasizing computational efficiency and transparency, DCR provides a practical tool for integrating contamination assessment into routine evaluations, fostering fairer comparisons and enhancing the credibility of LLM benchmarking practices.
What is the globally smallest load perturbation that renders DC-OPF infeasible? Reliably identifying such "adversarial attack" perturbations has useful applications in a variety of emerging grid-related contexts, including machine learning performance verification, cybersecurity, and operational robustness of power systems dominated by stochastic renewable energy resources. In this paper, we formulate the inherently nonconvex adversarial attack problem by applying a parameterized version of Farkas' lemma to a perturbed set of DC-OPF equations. Since the resulting formulation is very hard to globally optimize, we also propose a parameterized generation control policy which, when applied to the primal DC-OPF problem, provides solvability guarantees. Together, these nonconvex problems provide guaranteed upper and lower bounds on adversarial attack size; by combining them into a single optimization problem, we can efficiently "squeeze" these bounds towards a common global solution. We apply these methods on a range of small- to medium-sized test cases from PGLib, benchmarking our results against the best adversarial attack lower bounds provided by Gurobi 12.0's spatial Branch and Bound solver.
Long-context language models (LCLMs) have exhibited impressive capabilities in long-context understanding tasks. Among these, long-context referencing -- a crucial task that requires LCLMs to attribute items of interest to specific parts of long-context data -- remains underexplored. To bridge this gap, this paper proposes Referencing Evaluation for Long-context Language Models (Ref-Long), a novel benchmark designed to assess the long-context referencing capability of LCLMs. Specifically, Ref-Long requires LCLMs to identify the indexes of documents that reference a specific key, emphasizing contextual relationships between the key and the documents over simple retrieval. Based on the task design, we construct three subsets ranging from synthetic to realistic scenarios to form the Ref-Long benchmark. Experimental results of 13 LCLMs reveal significant shortcomings in long-context referencing, even among advanced models like GPT-4o. To further investigate these challenges, we conduct comprehensive analyses, including human evaluations, task format adjustments, fine-tuning experiments, and error analyses, leading to several key insights. Our data and code can be found in https://github. com/wujunjie1998/Ref-Long.
The discovery of new ionizable lipids for efficient lipid nanoparticle (LNP)-mediated RNA delivery remains a critical bottleneck for RNA-based therapeutics development. Recent advances have highlighted the potential of machine learning (ML) to predict transfection efficiency from molecular structure, enabling high-throughput virtual screening and accelerating lead identification. However, existing approaches are hindered by inadequate data quality, ineffective feature representations, low predictive accuracy, and poor generalizability. Here, we present LANTERN (Lipid nANoparticle Transfection Efficiency pRedictioN), a robust ML framework for predicting transfection efficiency based on ionizable lipid representation. We benchmarked a diverse set of ML models against AGILE, a previously published model developed for transfection prediction. Our results show that combining simpler models with chemically informative features, particularly count-based Morgan fingerprints, outperforms more complex models that rely on internally learned embeddings, such as AGILE. We also show that a multi-layer perceptron trained on a combination of Morgan fingerprints and Expert descriptors achieved the highest performance ($\text{R}^2$ = 0.8161, r = 0.9053), significantly exceeding AGILE ($\text{R}^2$ = 0.2655, r = 0.5488). We show that the models in LANTERN consistently have strong performance across multiple evaluation metrics. Thus, LANTERN offers a robust benchmarking framework for LNP transfection prediction and serves as a valuable tool for accelerating lipid-based RNA delivery systems design.
Large Language Models (LLMs) have achieved remarkable performance on complex mathematical benchmarks, yet often struggle with simple arithmetic tasks and exhibit a tendency toward over-explaining or "overthinking" answers. To systematically assess this phenomenon, we introduce LLMThinkBench, a modular benchmarking framework that enables researchers to evaluate basic math reasoning and overthinking in LLMs. The framework provides 14 configurable math tasks with randomized test data generation and robust parsing strategies. Researchers can quantify overthinking using our Overthinking Score metric, which captures accuracy-verbosity tradeoffs through harmonic mean formulation. The tool offers flexible evaluation with a scalable vLLM/Transformers backend, multi-GPU support, and full configurability. Users can extend the tool with custom tasks, reproduce experiments with seeding, and generate detailed efficiency reports. Distributed as a pip-installable package with CLI and API access, LLMThinkBench provides researchers and practitioners an accessible, cost-effective alternative to expensive LLM-as-a-judge methods for diagnosing basic reasoning capabilities and efficiency analysis. Package can be installed as: pip install llmthinkbench
Despite the rapid advance of 3D-aware image synthesis, existing studies usually adopt a mixture of techniques and tricks, leaving it unclear how each part contributes to the final performance in terms of generality. Following the most popular and effective paradigm in this field, which incorporates a neural radiance field (NeRF) into the generator of a generative adversarial network (GAN), we build a well-structured codebase, dubbed Carver, through modularizing the generation process. Such a design allows researchers to develop and replace each module independently, and hence offers an opportunity to fairly compare various approaches and recognize their contributions from the module perspective. The reproduction of a range of cutting-edge algorithms demonstrates the availability of our modularized codebase. We also perform a variety of in-depth analyses, such as the comparison across different types of point feature, the necessity of the tailing upsampler in the generator, the reliance on the camera pose prior, etc., which deepen our understanding of existing methods and point out some further directions of the research work. We release code and models at https://github.com/qiuyu96/Carver to facilitate the development and evaluation of this field.
The ability to extract structured information from unstructured sources-such as free-text documents and scientific literature-is critical for accelerating scientific discovery and knowledge synthesis. Large Language Models (LLMs) have demonstrated remarkable capabilities in various natural language processing tasks, including structured information extraction. However, their effectiveness often diminishes in specialized, domain-specific contexts that require nuanced understanding and expert-level domain knowledge. In addition, existing LLM-based approaches frequently exhibit poor transferability across tasks and domains, limiting their scalability and adaptability. To address these challenges, we introduce StructSense, a modular, task-agnostic, open-source framework for structured information extraction built on LLMs. StructSense is guided by domain-specific symbolic knowledge encoded in ontologies, enabling it to navigate complex domain content more effectively. It further incorporates agentic capabilities through self-evaluative judges that form a feedback loop for iterative refinement, and includes human-in-the-loop mechanisms to ensure quality and validation. We demonstrate that StructSense can overcome both the limitations of domain sensitivity and the lack of cross-task generalizability, as shown through its application to diverse neuroscience information extraction tasks.
Accurate characterization of the equilibrium distributions of complex molecular systems and their dependence on environmental factors such as temperature is essential for understanding thermodynamic properties and transition mechanisms. Projecting these distributions onto meaningful low-dimensional representations enables interpretability and downstream analysis. Recent advances in generative AI, particularly flow models such as Normalizing Flows (NFs), have shown promise in modeling such distributions, but their scope is limited without tailored representation learning. In this work, we introduce Latent Thermodynamic Flows (LaTF), an end-to-end framework that tightly integrates representation learning and generative modeling. LaTF unifies the State Predictive Information Bottleneck (SPIB) with NFs to simultaneously learn low-dimensional latent representations, referred to as Collective Variables (CVs), classify metastable states, and generate equilibrium distributions across temperatures beyond the training data. The two components of representation learning and generative modeling are optimized jointly, ensuring that the learned latent features capture the system's slow, important degrees of freedom while the generative model accurately reproduces the system's equilibrium behavior. We demonstrate LaTF's effectiveness across diverse systems, including a model potential, the Chignolin protein, and cluster of Lennard Jones particles, with thorough evaluations and benchmarking using multiple metrics and extensive simulations. Finally, we apply LaTF to a RNA tetraloop system, where despite using simulation data from only two temperatures, LaTF reconstructs the temperature-dependent structural ensemble and melting behavior, consistent with experimental and prior extensive computational results.
Multivariate time series anomaly detection (MTS-AD) is critical in domains like healthcare, cybersecurity, and industrial monitoring, yet remains challenging due to complex inter-variable dependencies, temporal dynamics, and sparse anomaly labels. We introduce mTSBench, the largest benchmark to date for MTS-AD and unsupervised model selection, spanning 344 labeled time series across 19 datasets and 12 diverse application domains. mTSBench evaluates 24 anomaly detection methods, including large language model (LLM)-based detectors for multivariate time series, and systematically benchmarks unsupervised model selection techniques under standardized conditions. Consistent with prior findings, our results confirm that no single detector excels across datasets, underscoring the importance of model selection. However, even state-of-the-art selection methods remain far from optimal, revealing critical gaps. mTSBench provides a unified evaluation suite to enable rigorous, reproducible comparisons and catalyze future advances in adaptive anomaly detection and robust model selection.
Text-driven image editing has achieved remarkable success in following single instructions. However, real-world scenarios often involve complex, multi-step instructions, particularly ``chain'' instructions where operations are interdependent. Current models struggle with these intricate directives, and existing benchmarks inadequately evaluate such capabilities. Specifically, they often overlook multi-instruction and chain-instruction complexities, and common consistency metrics are flawed. To address this, we introduce ComplexBench-Edit, a novel benchmark designed to systematically assess model performance on complex, multi-instruction, and chain-dependent image editing tasks. ComplexBench-Edit also features a new vision consistency evaluation method that accurately assesses non-modified regions by excluding edited areas. Furthermore, we propose a simple yet powerful Chain-of-Thought (CoT)-based approach that significantly enhances the ability of existing models to follow complex instructions. Our extensive experiments demonstrate ComplexBench-Edit's efficacy in differentiating model capabilities and highlight the superior performance of our CoT-based method in handling complex edits. The data and code are released at https://github.com/llllly26/ComplexBench-Edit.
Editing images with instructions to reflect non-rigid motions, camera viewpoint shifts, object deformations, human articulations, and complex interactions, poses a challenging yet underexplored problem in computer vision. Existing approaches and datasets predominantly focus on static scenes or rigid transformations, limiting their capacity to handle expressive edits involving dynamic motion. To address this gap, we introduce ByteMorph, a comprehensive framework for instruction-based image editing with an emphasis on non-rigid motions. ByteMorph comprises a large-scale dataset, ByteMorph-6M, and a strong baseline model built upon the Diffusion Transformer (DiT), named ByteMorpher. ByteMorph-6M includes over 6 million high-resolution image editing pairs for training, along with a carefully curated evaluation benchmark ByteMorph-Bench. Both capture a wide variety of non-rigid motion types across diverse environments, human figures, and object categories. The dataset is constructed using motion-guided data generation, layered compositing techniques, and automated captioning to ensure diversity, realism, and semantic coherence. We further conduct a comprehensive evaluation of recent instruction-based image editing methods from both academic and commercial domains.
Ensuring that Large Language Models (LLMs) align with mainstream human values and ethical norms is crucial for the safe and sustainable development of AI. Current value evaluation and alignment are constrained by Western cultural bias and incomplete domestic frameworks reliant on non-native rules; furthermore, the lack of scalable, rule-driven scenario generation methods makes evaluations costly and inadequate across diverse cultural contexts. To address these challenges, we propose a hierarchical value framework grounded in core Chinese values, encompassing three main dimensions, 12 core values, and 50 derived values. Based on this framework, we construct a large-scale Chinese Values Corpus (CVC) containing over 250,000 value rules enhanced and expanded through human annotation. Experimental results show that CVC-guided scenarios outperform direct generation ones in value boundaries and content diversity. In the evaluation across six sensitive themes (e.g., surrogacy, suicide), seven mainstream LLMs preferred CVC-generated options in over 70.5% of cases, while five Chinese human annotators showed an 87.5% alignment with CVC, confirming its universality, cultural relevance, and strong alignment with Chinese values. Additionally, we construct 400,000 rule-based moral dilemma scenarios that objectively capture nuanced distinctions in conflicting value prioritization across 17 LLMs. Our work establishes a culturally-adaptive benchmarking framework for comprehensive value evaluation and alignment, representing Chinese characteristics. All data are available at https://huggingface.co/datasets/Beijing-AISI/CVC, and the code is available at https://github.com/Beijing-AISI/CVC.
Atypical mitoses mark a deviation in the cell division process that can be an independent prognostically relevant marker for tumor malignancy. However, their identification remains challenging due to low prevalence, at times subtle morphological differences from normal mitoses, low inter-rater agreement among pathologists, and class imbalance in datasets. Building on the Atypical Mitosis dataset for Breast Cancer (AMi-Br), this study presents a comprehensive benchmark comparing deep learning approaches for automated atypical mitotic figure (AMF) classification, including baseline models, foundation models with linear probing, and foundation models fine-tuned with low-rank adaptation (LoRA). For rigorous evaluation, we further introduce two new hold-out AMF datasets - AtNorM-Br, a dataset of mitoses from the The TCGA breast cancer cohort, and AtNorM-MD, a multi-domain dataset of mitoses from the MIDOG++ training set. We found average balanced accuracy values of up to 0.8135, 0.7696, and 0.7705 on the in-domain AMi-Br and the out-of-domain AtNorm-Br and AtNorM-MD datasets, respectively, with the results being particularly good for LoRA-based adaptation of the Virchow-line of foundation models. Our work shows that atypical mitosis classification, while being a challenging problem, can be effectively addressed through the use of recent advances in transfer learning and model fine-tuning techniques. We make available all code and data used in this paper in this github repository: https://github.com/DeepMicroscopy/AMi-Br_Benchmark.