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Social Aspects · Trustworthy Machine Learning

Weixin Chen, Han Zhao

Neural Probabilistic Circuits (NPCs), a new class of concept bottleneck models, comprise an attribute recognition model and a probabilistic circuit for reasoning. By integrating the outputs from these two modules, NPCs produce compositional and interpretable predictions. While offering enhanced interpretability and high performance on downstream tasks, the neural-network-based attribute recognition model remains a black box. This vulnerability allows adversarial attacks to manipulate attribute predictions by introducing carefully crafted subtle perturbations to input images, potentially compromising the final predictions. In this paper, we theoretically analyze the adversarial robustness of NPC and demonstrate that it only depends on the robustness of the attribute recognition model and is independent of the robustness of the probabilistic circuit. Moreover, we propose RNPC, the first robust neural probabilistic circuit against adversarial attacks on the recognition module. RNPC introduces a novel class-wise integration for inference, ensuring a robust combination of outputs from the two modules. Our theoretical analysis demonstrates that RNPC exhibits provably improved adversarial robustness compared to NPC. Empirical results on image classification tasks show that RNPC achieves superior adversarial robustness compared to existing concept bottleneck models while maintaining high accuracy on benign inputs. The code is available at https://github.com/uiuctml/RNPC.

Probabilistic Methods

Timo Löhr, Paul Hofman, Felix Mohr, Eyke Hüllermeier

Predictions in the form of sets of probability distributions, so-called credal sets, provide a suitable means to represent a learner's epistemic uncertainty. In this paper, we propose a theoretically grounded approach to credal prediction based on the statistical notion of relative likelihood: The target of prediction is the set of all (conditional) probability distributions produced by the collection of plausible models, namely those models whose relative likelihood exceeds a specified threshold. This threshold has an intuitive interpretation and allows for controlling the trade-off between correctness and precision of credal predictions. We tackle the problem of approximating credal sets defined in this way by means of suitably modified ensemble learning techniques. To validate our approach, we illustrate its effectiveness by experiments on benchmark datasets demonstrating superior uncertainty representation without compromising predictive performance. We also compare our method against several state-of-the-art baselines in credal prediction.

Probabilistic Methods

Brandon Feng, David Park, Xihaier Luo, Arantxa Urdangarin, Shinjae Yoo, Brian Reich

Fitting Gaussian Processes (GPs) provides interpretable aleatoric uncertainty quantification for estimation of spatio-temporal fields. Spatio-temporal deep learning models, while scalable, typically assume a simplistic independent covariance matrix for the response, failing to capture the underlying correlation structure. However, spatio-temporal GPs suffer from issues of scalability and various forms of approximation bias resulting from restrictive assumptions of the covariance kernel function. We propose STACI, a novel framework consisting of a variational Bayesian neural network approximation of non-stationary spatio-temporal GP along with a novel spatio-temporal conformal inference algorithm. STACI is highly scalable, taking advantage of GPU training capabilities for neural network models, and provides statistically valid prediction intervals for uncertainty quantification. STACI outperforms competing GPs and deep methods in accurately approximating spatio-temporal processes and we show it easily scales to datasets with millions of observations.

Probabilistic Methods · Bayesian Models and Methods

Samuel Matthiesen, Hrittik Roy, Nicholas Krämer, Yevgen Zainchkovskyy, Stas Syrota, Alejandro Valverde Mahou, Carl Henrik Ek, Søren Hauberg

Variational mean field approximations tend to struggle with contemporary overparametrized deep neural networks. Where a Bayesian treatment is usually associated with high-quality predictions and uncertainties, the practical reality has been the opposite, with unstable training, poor predictive power, and subpar calibration. Building upon recent work on reparametrizations of neural networks, we propose a simple variational family that considers two independent linear subspaces of the parameter space. These represent functional changes inside and outside the support of training data. This allows us to build a fully-correlated approximate posterior reflecting the overparametrization that tunes easy-to-interpret hyperparameters. We develop scalable numerical routines that maximize the associated evidence lower bound (ELBO) and sample from the approximate posterior. Empirically, we observe state-of-the-art performance across tasks, models, and datasets compared to a wide array of baseline methods. Our results show that approximate Bayesian inference applied to deep neural networks is far from a lost cause when constructing inference mechanisms that reflect the geometry of reparametrizations.

Social Aspects · Accountability, Transparency and Interpretability

Kentaro Kanamori, Ken Kobayashi, Takuya Takagi

This paper proposes a new algorithm for learning gradient boosted decision trees while ensuring the existence of recourse actions. Algorithmic recourse aims to provide a recourse action for altering the undesired prediction result given by a model. While existing studies often focus on extracting valid and executable actions from a given learned model, such reasonable actions do not always exist for models optimized solely for predictive accuracy. To address this issue, recent studies proposed a framework for learning a model while guaranteeing the existence of reasonable actions with high probability. However, these methods can not be applied to gradient boosted decision trees, which are renowned as one of the most popular models for tabular datasets. We propose an efficient gradient boosting algorithm that takes recourse guarantee into account, while maintaining the same time complexity as the standard ones. We also propose a post-processing method for refining a learned model under the constraint of a recourse guarantee and provide a PAC-style analysis of the refined model. Experimental results demonstrated that our method successfully provided reasonable actions to more instances than the baselines without significantly degrading accuracy and computational efficiency.

Deep Learning · Generative Models and Autoencoders

Xinyu Yang, Yuwei An, Hongyi Liu, Tianqi Chen, Beidi Chen

Autoregressive Large Language Models (AR-LLMs) frequently exhibit implicit parallelism in sequential generation. Inspired by this, we introduce Multiverse, a new generative model enabling natively parallel generation. Multiverse internalizes a MapReduce paradigm, generating automatically through three stages: (i) a Map stage for adaptive task decomposition, (ii) a Process stage for parallel subtask execution, and (iii) a Reduce stage for lossless result synthesis. Next, we build a real-world Multiverse reasoning model with co-design of data, algorithm, and system, enabling rapid and seamless transfer from frontier AR-LLMs. For data creation, we develop Multiverse Curator, an automated LLM-assisted pipeline that transforms sequential reasoning chains into structured training data, avoiding costly human annotations. Algorithmically, we design Multiverse Attention to separate parallel reasoning steps while keeping compatibility with causal attention for efficient training. Systematically, we implement Multiverse Engine to support parallel inference. It features a dedicated interpreter that dynamically switches between sequential and parallel generation, triggered directly by the model. After a 3-hour fine-tuning with 1K examples, our Multiverse-32B stands as the only open-sourced non-AR model achieving performance on par with leading AR-LLMs of the same scale, evidenced by AIME24 & 25 scores of 54% and 46%, respectively. Moreover, our budget control experiments show that Multiverse-32B exhibits superior scaling, outperforming AR-LLMs by 1.87% on average using the same context length. Such scaling further leads to practical efficiency gain, achieving up to 2x speedup across varying batch sizes. We have open-sourced the entire Multiverse ecosystem, including data, model weights, serving system, supporting tools, as well as data curation prompts and detailed training and evaluation recipes.

General Machine Learning · Everything Else

Jiahao Yu, Qizhen Ying, Leyang Wang, Ziyue Jiang, Song Liu

This paper introduces a novel iterative method for missing data imputation that sequentially reduces the mutual information between data and the corresponding missingness mask. Inspired by GAN-based approaches that train generators to decrease the predictability of missingness patterns, our method explicitly targets this reduction in mutual information. Specifically, our algorithm iteratively minimizes the KL divergence between the joint distribution of the imputed data and missingness mask, and the product of their marginals from the previous iteration. We show that the optimal imputation under this framework can be achieved by solving an ODE whose velocity field minimizes a rectified flow training objective. We further illustrate that some existing imputation techniques can be interpreted as approximate special cases of our mutual-information-reducing framework. Comprehensive experiments on synthetic and real-world datasets validate the efficacy of our proposed approach, demonstrating its superior imputation performance. Our implementation is available at \url{https://github.com/yujhml/MIRI-Imputation}.

Computer Vision · Vision Models & Multimodal

Kejia Zhang, Keda TAO, Jiasheng Tang, Huan Wang

Large vision-language models (LVMs) extend large language models (LLMs) with visual perception capabilities, enabling them to process and interpret visual information. A major challenge compromising their reliability is object hallucination that LVMs may generate plausible but factually inaccurate information. We propose a novel \textit{visual adversarial perturbation (VAP)} method to mitigate this hallucination issue. VAP alleviates LVM hallucination by applying strategically optimized visual noise without altering the base model. Our approach formulates hallucination suppression as an optimization problem, leveraging adversarial strategies to generate beneficial visual perturbations that enhance the model's factual grounding and reduce parametric knowledge bias. Extensive experimental results demonstrate that our method consistently reduces object hallucinations across 8 state-of-the-art LVMs, validating its efficacy across diverse evaluations.

Applications · Genetics, Cell Biology, etc

Zehui Li, Vallijah Subasri, Yifei Shen, Dongsheng Li, Wentao Gu, Guy-Bart Stan, Yiren Zhao, Caihua Shan

The interpretation of genomic sequences is crucial for understanding biological processes. To handle the growing volume of DNA sequence data, Genomic Foundation Models (GFMs) have been developed by adapting architectures and training paradigms from Large Language Models (LLMs). Despite their remarkable performance in DNA sequence classification tasks, there remains a lack of systematic understanding regarding the training and task-adaptation processes of GFMs. Moreover, existing GFMs cannot achieve state-of-the-art performance on both short and long-context tasks and lacks multimodal abilities. By revisiting pre-training architectures and post-training techniques, we propose **Omni-DNA**, a family of models spanning 20M to 1.1B parameters that supports sequence understanding, long-context genomic reasoning, and natural-language annotation. **Omni-DNA** establishes new state-of-the-art results on 18 of 26 evaluations drawn from Nucleotide Transformer and Genomic Benchmarks. When jointly fine-tuning on biologically related tasks, **Omni-DNA** consistently outperform existing models and demonstrate multi-tasking abilities. To enable processing of arbitrary sequence lengths, we introduce **SEQPACK**—an adaptive compression operator that packs historical tokens into a learned synopsis using a position-aware learnable sampling mechanism, enabling transformer-based models to process ultra-long sequences with minimal memory and computational requirements. Our approach demonstrates superior performance on enhancer-target interaction tasks, capturing distant regulatory interactions at the 450kbp range more effectively than existing models. Finally, we present a new dataset termed **seq2func**, enabling Omni-DNA to generate accurate and functionally meaningful interpretations of DNA sequences, unlocking new possibilities for genomic analysis and discovery.

Applications · Robotics

Dapeng Zhang, Fei Shen, Rui Zhao, Yinda Chen, Peng Zhi, Chenyang Li, Rui Zhou, Qingguo Zhou

Autonomous driving represents a prominent application of artificial intelligence. Recent approaches have shifted from focusing solely on common scenarios to addressing complex, long-tail situations such as subtle human behaviors, traffic accidents, and non-compliant driving patterns. Given the demonstrated capabilities of large language models (LLMs) in understanding visual and natural language inputs and following instructions, recent methods have integrated LLMs into autonomous driving systems to enhance reasoning, interpretability, and performance across diverse scenarios. However, existing methods typically rely either on real-world data, which is suitable for industrial deployment, or on simulation data tailored to rare or hard case scenarios. Few approaches effectively integrate the complementary advantages of both data sources. To address this limitation, we propose a novel VLM-guided, end-to-end adversarial transfer framework for autonomous driving that transfers long-tail handling capabilities from simulation to real-world deployment, named CoC-VLA. The framework comprises a teacher VLM model, a student VLM model, and a discriminator. Both the teacher and student VLM models utilize a shared base architecture, termed the Chain-of-Causality Visual–Language Model (CoC VLM), which integrates temporal information via an end-to-end text adapter. This architecture supports chain-of-thought reasoning to infer complex driving logic. The teacher and student VLM models are pre-trained separately on simulated and real-world datasets. The discriminator is trained adversarially to facilitate the transfer of long-tail handling capabilities from simulated to real-world environments by the student VLM model, using a novel backpropagation strategy. Experimental results show that our method effectively bridges the gap between simulation and real-world autonomous driving, indicating a promising direction for future research.

Applications · Everything Else

Ehsan Latif, Zirak Khan, Xiaoming Zhai

Scientific sketches (e.g., models) offer a powerful lens into students' conceptual understanding, yet AI-powered automated assessment of such free-form, visually diverse artifacts remains a critical challenge. Existing solutions often treat sketch evaluation as either an image classification task or monolithic vision-language models, which lack interpretability, pedagogical alignment, and adaptability across cognitive levels. To address these limitations, we present SketchMind, a cognitively grounded, multi-agent framework for evaluating and improving student-drawn scientific sketches. SketchMind introduces Sketch Reasoning Graphs (SRGs), semantic graph representations that embed domain concepts and Bloom's taxonomy-based cognitive labels. The system comprises modular agents responsible for rubric parsing, sketch perception, cognitive alignment, and iterative feedback with sketch modification, enabling personalized and transparent evaluation. We evaluate SketchMind on a curated dataset of 3,575 student-generated sketches across six science assessment items with different highest order of Bloom's level that require students to draw models to explain phenomena. Compared to baseline GPT-4o performance without SRG (average accuracy: 55.6%), the model with SRG integration achieves 77.1% average accuracy (+21.4% average absolute gain). We also demonstrate that multi-agent orchestration with SRG enhances SketchMind performance, for example, SketchMind with GPT-4.1 gains an average 8.9% increase in sketch prediction accuracy, outperforming single-agent pipelines across all items. Human evaluators rated the feedback and co-created sketches generated by SketchMind with GPT-4.1, which achieved an average of 4.1 out of 5, significantly higher than those of baseline models (e.g., 2.3 for GPT-4o). Experts noted the system’s potential to meaningfully support conceptual growth through guided revision. Our code and (pending approval) dataset will be released to support reproducibility and future research in AI-driven education.

Junchi Yu, Yujie Liu, Jindong Gu, Philip Torr, Dongzhan Zhou

Retrieval-Augmented Generation (RAG) based on knowledge graphs (KGs) enhances large language models (LLMs) by providing structured and interpretable external knowledge. However, existing KG-based RAG methods struggle to retrieve accurate and diverse information from text-rich KGs for complex real-world queries. Process Reward Models (PRMs) offer a way to align the retrieval process of KG-based RAG with query-specific knowledge requirements, but they heavily rely on process-level supervision signals that are expensive and hard to obtain on KGs. To address this challenge, we propose GraphFlow, a framework that efficiently retrieves accurate and diverse knowledge required for real-world queries from text-rich KGs. GraphFlow employs a transition-based flow matching objective to jointly optimize a retrieval policy and a flow estimator. The flow estimator factorizes the reward of the retrieval outcome into the intermediate retrieval states. Such reward factorization guides the retrieval policy to retrieve candidates from KGs in proportion to their reward. This allows GraphFlow to explore high-quality regions of KGs that yield diverse and relevant results. We evaluate GraphFlow on the STaRK benchmark, which includes real-world queries from multiple domains over text-rich KGs. GraphFlow outperforms strong KG-RAG baselines, including GPT-4o, by 10\% on average in hit rate and recall. It also shows strong generalization to unseen KGs, demonstrating its effectiveness and robustness.

Social Aspects · Accountability, Transparency and Interpretability

Jongseo Lee, Wooil Lee, Gyeong-Moon Park, Seong Tae Kim, Jinwoo Choi

Effective explanations of video action recognition models should disentangle how movements unfold over time from the surrounding spatial context. However, existing methods—based on saliency—produce entangled explanations, making it unclear whether predictions rely on motion or spatial context. Language-based approaches offer structure but often fail to explain motions due to their tacit nature—intuitively understood but difficult to verbalize. To address these challenges, we propose Disentangled Action aNd Context concept-based Explainable (DANCE) video action recognition, a framework that predicts actions through disentangled concept types: motion dynamics, objects, and scenes. We define motion dynamics concepts as human pose sequences. We employ a large language model to automatically extract object and scene concepts. Built on an ante-hoc concept bottleneck design, DANCE enforces prediction through these concepts. Experiments on four datasets—KTH, Penn Action, HAA500, and UCF101—demonstrate that DANCE significantly improves explanation clarity with competitive performance. Through a user study, we validate the superior interpretability of DANCE. Experimental results also show that DANCE is beneficial for model debugging, editing, and failure analysis.

Social Aspects · Trustworthy Machine Learning

Mizuki Niihori, Shuichi Nishino, Teruyuki Katsuoka, Tomohiro Shiraishi, Kouichi Taji, Ichiro Takeuchi

In real-world applications, anomaly detection (AD) often operates without access to anomalous data, necessitating semi-supervised methods that rely solely on normal data. Among these methods, deep $k$-nearest neighbor (deep $k$NN) AD stands out for its interpretability and flexibility, leveraging distance-based scoring in deep latent spaces. Despite its strong performance, deep $k$NN lacks a mechanism to quantify uncertainty—an essential feature for critical applications such as industrial inspection. To address this limitation, we propose a statistical framework that quantifies the significance of detected anomalies in the form of $p$-values, thereby enabling control over false positive rates at a user-specified significance level (e.g.,0.05). A central challenge lies in managing selection bias, which we tackle using Selective Inference—a principled method for conducting inference conditioned on data-driven selections. We evaluate our method on diverse datasets and demonstrate that it provides reliable AD well-suited for industrial use cases.

General Machine Learning · Causality

Quinn Lanners, Cynthia Rudin, Alexander Volfovsky, Harsh Parikh

Data fusion techniques integrate information from heterogeneous data sources to improve learning, generalization, and decision-making across data sciences. In causal inference, these methods leverage rich observational data to improve causal effect estimation, while maintaining the trustworthiness of randomized controlled trials. Existing approaches often relax the strong "no unobserved confounding" assumption by instead assuming exchangeability of counterfactual outcomes across data sources. However, when both assumptions simultaneously fail—a common scenario in practice—current methods cannot identify or estimate causal effects. We address this limitation by proposing a novel partial identification framework that enables researchers to answer key questions such as: *Is the causal effect positive/negative?* and *How severe must assumption violations be to overturn this conclusion?* Our approach introduces interpretable sensitivity parameters that quantify assumption violations and derives corresponding causal effect bounds. We develop doubly robust estimators for these bounds and operationalize breakdown frontier analysis to understand how causal conclusions change as assumption violations increase. We apply our framework to the Project STAR study, which investigates the effect of classroom size on students’ third-grade standardized test performance. Our analysis reveals that the Project STAR results are robust to simultaneous violations of key assumptions, both on average and across various subgroups of interest. This strengthens confidence in the study's conclusions despite potential unmeasured biases in the data.

Social Aspects · Accountability, Transparency and Interpretability

Xiaoqing Sun, Alessandro Stolfo, Joshua Engels, Ben Wu, Senthooran Rajamanoharan, Mrinmaya Sachan, Max Tegmark

Sparse autoencoders (SAEs) are designed to extract interpretable features from language models by enforcing a sparsity constraint. Ideally, training an SAE would yield latents that are both sparse and semantically meaningful. However, many SAE latents activate frequently (i.e., are *dense*), raising concerns that they may be undesirable artifacts of the training procedure. In this work, we systematically investigate the geometry, function, and origin of dense latents and show that they are not only persistent but often reflect meaningful model representations. We first demonstrate that dense latents tend to form antipodal pairs that reconstruct specific directions in the residual stream, and that ablating their subspace suppresses the emergence of new dense features in retrained SAEs---suggesting that high density features are an intrinsic property of the residual space. We then introduce a taxonomy of dense latents, identifying classes tied to position tracking, context binding, entropy regulation, letter-specific output signals, part-of-speech, and principal component reconstruction. Finally, we analyze how these features evolve across layers, revealing a shift from structural features in early layers, to semantic features in mid layers, and final to output-oriented signals in the last layers of the model. Our findings indicate that dense latents serve functional roles in language model computation and should not be dismissed as training noise.

Social Aspects · Accountability, Transparency and Interpretability

Hubert Baniecki, Maximilian Muschalik, Fabian Fumagalli, Barbara Hammer, Eyke Hüllermeier, Przemyslaw Biecek

Language-image pre-training (LIP) enables the development of vision-language models capable of zero-shot classification, localization, multimodal retrieval, and semantic understanding. Various explanation methods have been proposed to visualize the importance of input image-text pairs on the model's similarity outputs. However, popular saliency maps are limited by capturing only first-order attributions, overlooking the complex cross-modal interactions intrinsic to such encoders. We introduce faithful interaction explanations of LIP models (FIxLIP) as a unified approach to decomposing the similarity in vision-language encoders. FIxLIP is rooted in game theory, where we analyze how using the weighted Banzhaf interaction index offers greater flexibility and improves computational efficiency over the Shapley interaction quantification framework. From a practical perspective, we propose how to naturally extend explanation evaluation metrics, such as the pointing game and area between the insertion/deletion curves, to second-order interaction explanations. Experiments on the MS COCO and ImageNet-1k benchmarks validate that second-order methods, such as FIxLIP, outperform first-order attribution methods. Beyond delivering high-quality explanations, we demonstrate the utility of FIxLIP in comparing different models, e.g. CLIP vs. SigLIP-2.

Applications · Neuroscience, Cognitive Science

Zhining Zhang, Chuanyang Jin, Mung Yao Jia, Shunchi Zhang, Tianmin Shu

Theory of Mind (ToM), the ability to understand people's minds based on their behavior, is key to developing socially intelligent agents. Current approaches to ToM reasoning either rely on prompting Large Language Models (LLMs), which are prone to systematic errors, or use handcrafted, rigid agent models for model-based inference, which are more robust but fail to generalize across domains. In this work, we introduce *AutoToM*, an automated agent modeling method for scalable, robust, and interpretable mental inference. Given a ToM problem, *AutoToM* first proposes an initial agent model and then performs automated Bayesian inverse planning based on this model, leveraging an LLM backend. Guided by inference uncertainty, it iteratively refines the model by introducing additional mental variables and/or incorporating more timesteps in the context. Across five diverse benchmarks, *AutoToM* outperforms existing ToM methods and even large reasoning models. Additionally, we show that *AutoToM* can produce human‐like confidence estimates and enable online mental inference for embodied decision-making.

Probabilistic Methods · Bayesian Models and Methods

Jean Feng, Avni Kothari, Lucas Zier, Chandan Singh, Yan Shuo Tan

Concept Bottleneck Models (CBMs) have been proposed as a compromise between white-box and black-box models, aiming to achieve interpretability without sacrificing accuracy. The standard training procedure for CBMs is to predefine a candidate set of human-interpretable concepts, extract their values from the training data, and identify a sparse subset as inputs to a transparent prediction model. However, such approaches are often hampered by the tradeoff between exploring a sufficiently large set of concepts versus controlling the cost of obtaining concept extractions, resulting in a large interpretability-accuracy tradeoff. This work investigates a novel approach that sidesteps these challenges: BC-LLM iteratively searches over a potentially infinite set of concepts within a Bayesian framework, in which Large Language Models (LLMs) serve as both a concept extraction mechanism and prior. Even though LLMs can be miscalibrated and hallucinate, we prove that BC-LLM can provide rigorous statistical inference and uncertainty quantification. Across image, text, and tabular datasets, BC-LLM outperforms interpretable baselines and even black-box models in certain settings, converges more rapidly towards relevant concepts, and is more robust to out-of-distribution samples.

Computer Vision · Vision Models & Multimodal

Duo Zheng, shijia Huang, Yanyang Li, Liwei Wang

Previous research has investigated the application of Multimodal Large Language Models (MLLMs) in understanding 3D scenes by interpreting them as videos. These approaches generally depend on comprehensive 3D data inputs, such as point clouds or reconstructed Bird's-Eye View (BEV) maps. In our research, we advance this field by enhancing the capability of MLLMs to understand and reason in 3D spaces directly from video data, without the need for additional 3D input. We propose a novel and efficient method called the Video-3D Geometry Large Language Model (VG LLM). Our approach utilizes a 3D visual geometry encoder to extract 3D prior information from video sequences. This information is then integrated with visual tokens and input into the MLLM. Extensive experiments have shown that our method has achieved substantial improvements in various tasks related to 3D scene understanding and spatial reasoning, all directly learned from video sources. Impressively, our 4B model, which does not rely on explicit 3D data inputs, achieves competitive results compared to existing state-of-the-art methods, and even surpasses the Gemini-1.5-Pro in the VSI-Bench evaluations.