OpenRaiser/Intern-Atlas huggingface dataset:
Distributional Counterfactual Explanations With Optimal Transport
Venue: arXiv cs.AI 2025
Year: 2025

Counterfactual explanations (CE) are the de facto method for providing insights into black-box decision-making models by identifying alternative inputs that lead to different outcomes. However, existing CE approaches, including group and global methods, focus predominantly on specific input modifications, lacking the ability to capture nuanced distributional characteristics that influence model outcomes across the entire input-output spectrum. This paper proposes distributional counterfactual explanation (DCE), shifting focus to the distributional properties of observed and counterfactual data, thus providing broader insights. DCE is particularly beneficial for stakeholders making strategic decisions based on statistical data analysis, as it makes the statistical distribution of the counterfactual resembles the one of the factual when aligning model outputs with a target distribution\textemdash something that the existing CE methods cannot fully achieve. We leverage optimal transport (OT) to formulate a chance-constrained optimization problem, deriving a counterfactual distribution aligned with its factual counterpart, supported by statistical confidence. The efficacy of this approach is demonstrated through experiments, highlighting its potential to provide deeper insights into decision-making models.
DittoGym: Learning to Control Soft Shape-Shifting Robots
Venue: arXiv cs.RO 2025
Year: 2025

Robot co-design, where the morphology of a robot is optimized jointly with a learned policy to solve a specific task, is an emerging area of research. It holds particular promise for soft robots, which are amenable to novel manufacturing techniques that can realize learned morphologies and actuators. Inspired by nature and recent novel robot designs, we propose to go a step further and explore the novel reconfigurable robots, defined as robots that can change their morphology within their lifetime. We formalize control of reconfigurable soft robots as a high-dimensional reinforcement learning (RL) problem. We unify morphology change, locomotion, and environment interaction in the same action space, and introduce an appropriate, coarse-to-fine curriculum that enables us to discover policies that accomplish fine-grained control of the resulting robots. We also introduce DittoGym, a comprehensive RL benchmark for reconfigurable soft robots that require fine-grained morphology changes to accomplish the tasks. Finally, we evaluate our proposed coarse-to-fine algorithm on DittoGym and demonstrate robots that learn to change their morphology several times within a sequence, uniquely enabled by our RL algorithm. More results are available at https://suninghuang19.github.io/dittogym_page/.
Explainable Bayesian Optimization
Venue: arXiv cs.LG 2025
Year: 2025

Manual parameter tuning of cyber-physical systems is a common practice, but it is labor-intensive. Bayesian Optimization (BO) offers an automated alternative, yet its black-box nature reduces trust and limits human-BO collaborative system tuning. Experts struggle to interpret BO recommendations due to the lack of explanations. This paper addresses the post-hoc BO explainability problem for cyber-physical systems. We introduce TNTRules (Tune-No-Tune Rules), a novel algorithm that provides both global and local explanations for BO recommendations. TNTRules generates actionable rules and visual graphs, identifying optimal solution bounds and ranges, as well as potential alternative solutions. Unlike existing explainable AI (XAI) methods, TNTRules is tailored specifically for BO, by encoding uncertainty via a variance pruning technique and hierarchical agglomerative clustering. A multi-objective optimization approach allows maximizing explanation quality. We evaluate TNTRules using established XAI metrics (Correctness, Completeness, and Compactness) and compare it against adapted baseline methods. The results demonstrate that TNTRules generates high-fidelity, compact, and complete explanations, significantly outperforming three baselines on 5 multi-objective testing functions and 2 hyperparameter tuning problems.
Toward A Causal Framework for Modeling Perception
Venue: arXiv cs.AI 2025
Year: 2025

Perception occurs when individuals interpret the same information differently. It is a known cognitive phenomenon with implications for bias in human decision-making. Perception, however, remains understudied in machine learning (ML). This is problematic as modern decision flows, whether partially or fully automated by ML applications, always involve human experts. For instance, how might we account for cases in which two experts interpret differently the same deferred instance or explanation from a ML model? Addressing this and similar questions requires first a formulation of perception, particularly, in a manner that integrates with ML-enabled decision flows. In this work, we present a first approach to modeling perception causally. We define perception under causal reasoning using structural causal models (SCMs). Our approach formalizes individual experience as additional causal knowledge that comes with and is used by the expert decision-maker in the form of a SCM. We define two kinds of probabilistic causal perception: structural and parametrical. We showcase our framework through a series of examples of modern decision flows. We also emphasize the importance of addressing perception in fair ML, discussing relevant fairness implications and possible applications.
Guiding Soft Robots with Motor-Imagery Brain Signals and Impedance Control
Venue: arXiv cs.RO 2025
Year: 2025

Integrating Brain-Machine Interfaces into non-clinical applications like robot motion control remains difficult - despite remarkable advancements in clinical settings. Specifically, EEG-based motor imagery systems are still error-prone, posing safety risks when rigid robots operate near humans. This work presents an alternative pathway towards safe and effective operation by combining wearable EEG with physically embodied safety in soft robots. We introduce and test a pipeline that allows a user to move a soft robot's end effector in real time via brain waves that are measured by as few as three EEG channels. A robust motor imagery algorithm interprets the user's intentions to move the position of a virtual attractor to which the end effector is attracted, thanks to a new Cartesian impedance controller. We specifically focus here on planar soft robot-based architected metamaterials, which require the development of a novel control architecture to deal with the peculiar nonlinearities - e.g., non-affinity in control. We preliminarily but quantitatively evaluate the approach on the task of setpoint regulation. We observe that the user reaches the proximity of the setpoint in 66% of steps and that for successful steps, the average response time is 21.5s. We also demonstrate the execution of simple real-world tasks involving interaction with the environment, which would be extremely hard to perform if it were not for the robot's softness.
Faster Convergence with Less Communication: Broadcast-Based Subgraph Sampling for Decentralized Learning over Wireless Networks
Venue: arXiv cs.IT 2025
Year: 2025

Consensus-based decentralized stochastic gradient descent (D-SGD) is a widely adopted algorithm for decentralized training of machine learning models across networked agents. A crucial part of D-SGD is the consensus-based model averaging, which heavily relies on information exchange and fusion among the nodes. Specifically, for consensus averaging over wireless networks, communication coordination is necessary to determine when and how a node can access the channel and transmit (or receive) information to (or from) its neighbors. In this work, we propose $\texttt{BASS}$, a broadcast-based subgraph sampling method designed to accelerate the convergence of D-SGD while considering the actual communication cost per iteration. $\texttt{BASS}$ creates a set of mixing matrix candidates that represent sparser subgraphs of the base topology. In each consensus iteration, one mixing matrix is sampled, leading to a specific scheduling decision that activates multiple collision-free subsets of nodes. The sampling occurs in a probabilistic manner, and the elements of the mixing matrices, along with their sampling probabilities, are jointly optimized. Simulation results demonstrate that $\texttt{BASS}$ enables faster convergence with fewer transmission slots compared to existing link-based scheduling methods. In conclusion, the inherent broadcasting nature of wireless channels offers intrinsic advantages in accelerating the convergence of decentralized optimization and learning.
PADTHAI-MM: Principles-based Approach for Designing Trustworthy, Human-centered AI using MAST Methodology
Venue: arXiv cs.CY 2025
Year: 2025

Despite an extensive body of literature on trust in technology, designing trustworthy AI systems for high-stakes decision domains remains a significant challenge, further compounded by the lack of actionable design and evaluation tools. The Multisource AI Scorecard Table (MAST) was designed to bridge this gap by offering a systematic, tradecraft-centered approach to evaluating AI-enabled decision support systems. Expanding on MAST, we introduce an iterative design framework called \textit{Principles-based Approach for Designing Trustworthy, Human-centered AI using MAST Methodology} (PADTHAI-MM). We demonstrate this framework in our development of the Reporting Assistant for Defense and Intelligence Tasks (READIT), a research platform that leverages data visualizations and natural language processing-based text analysis, emulating an AI-enabled system supporting intelligence reporting work. To empirically assess the efficacy of MAST on trust in AI, we developed two distinct iterations of READIT for comparison: a High-MAST version, which incorporates AI contextual information and explanations, and a Low-MAST version, akin to a ``black box'' system. This iterative design process, guided by stakeholder feedback and contemporary AI architectures, culminated in a prototype that was evaluated through its use in an intelligence reporting task. We further discuss the potential benefits of employing the MAST-inspired design framework to address context-specific needs. We also explore the relationship between stakeholder evaluators' MAST ratings and three categories of information known to impact trust: \textit{process}, \textit{purpose}, and \textit{performance}. Overall, our study supports the practical benefits and theoretical validity for PADTHAI-MM as a viable method for designing trustable, context-specific AI systems.
Driving Towards Inclusion: A Systematic Review of AI-powered Accessibility Enhancements for People with Disability in Autonomous Vehicles
Venue: arXiv cs.HC 2025
Year: 2025

This paper provides a comprehensive and, to our knowledge, the first review of inclusive human-computer interaction (HCI) within autonomous vehicles (AVs) and human-driven cars with partial autonomy, emphasizing accessibility and user-centered design principles. We explore the current technologies and HCI systems designed to enhance passenger experience, particularly for individuals with accessibility needs. Key technologies discussed include brain-computer interfaces, anthropomorphic interaction, virtual reality, augmented reality, mode adaptation, voice-activated interfaces, haptic feedback, etc. Each technology is evaluated for its role in creating an inclusive in-vehicle environment. Furthermore, we highlight recent interface designs by leading companies and review emerging concepts and prototypes under development or testing, which show significant potential to address diverse accessibility requirements. Safety considerations, ethical concerns, and adoption of AVs are other major issues that require thorough investigation. Building on these findings, we propose an end-to-end design framework that addresses accessibility requirements across diverse user demographics, including older adults and individuals with physical or cognitive impairments. This work provides actionable insights for designers, researchers, and policymakers aiming to create safer and more comfortable environments in autonomous and regular vehicles accessible to all users.
Ricci flow regularization in latent spaces for the forward learning of partial differential equations
Venue: arXiv cs.LG 2025
Year: 2025

We present a manifold-based machine learning encoder-decoder method for learning dynamics in time, notably partial differential equations (PDEs), in which the manifold latent space evolves according to Ricci flow. This can be accomplished by parameterizing the latent manifold stage and subsequently simulating Ricci flow in a physics-informed setting, matching manifold quantities so that Ricci flow is empirically achieved. We emphasize dynamics that admit low-dimensional representations. With our method, the manifold, induced by the metric, is discerned through the training procedure, while the latent evolution due to Ricci flow provides an accommodating representation. By use of this flow, we sustain a canonical manifold latent representation for all values in the ambient PDE time interval continuum. We showcase that the Ricci flow facilitates qualities such as learning for out-of-distribution data and adversarial robustness on select PDE data. Moreover, we provide a thorough expansion of our methods in regard to special cases which allow higher-dimensional representations, such as Ricci flow on the hypersphere and neural discovery of non-parametric geometric flows with entropic strategies from Ricci flow theory.
A Systematic Literature Review on Explainability for Machine/Deep Learning-based Software Engineering Research
Venue: arXiv cs.SE 2025
Year: 2025

The remarkable achievements of Artificial Intelligence (AI) algorithms, particularly in Machine Learning (ML) and Deep Learning (DL), have fueled their extensive deployment across multiple sectors, including Software Engineering (SE). However, due to their black-box nature, these promising AI-driven SE models are still far from being deployed in practice. This lack of explainability poses unwanted risks for their applications in critical tasks, such as vulnerability detection, where decision-making transparency is of paramount importance. This paper endeavors to elucidate this interdisciplinary domain by presenting a systematic literature review of approaches that aim to improve the explainability of AI models within the context of SE. The review canvasses work appearing in the most prominent SE & AI conferences and journals, and spans 108 papers across 23 unique SE tasks. Based on three key Research Questions (RQs), we aim to (1) summarize the SE tasks where XAI techniques have shown success to date; (2) classify and analyze different XAI techniques; and (3) investigate existing evaluation approaches. Based on our findings, we identified a set of challenges remaining to be addressed in existing studies, together with a set of guidelines highlighting potential opportunities we deemed appropriate and important for future work.
Fair and Efficient Ridesharing: A Dynamic Programming-based Relocation Approach
Venue: arXiv cs.DS 2025
Year: 2025

Recommending routes by their probability of having a rider has long been the goal of conventional route recommendation systems. While this maximizes the platform-specific criteria of efficiency, it results in sub-optimal outcomes with the disparity among the income of drivers who work for similar time frames. Pioneer studies on fairness in ridesharing platforms have focused on algorithms that match drivers and riders. However, these studies do not consider the time schedules of different riders sharing a ride in the ridesharing mode. To overcome this shortcoming, we present the first route recommendation system for ridesharing networks that explicitly considers fairness as an evaluation criterion. In particular, we design a routing mechanism that reduces the inequality among drivers and provides them with routes that have a similar probability of finding riders over a period of time. However, while optimizing fairness the efficiency of the platform should not be affected as both of these goals are important for the long-term sustainability of the system. In order to jointly optimize fairness and efficiency we consider repositioning drivers with low income to the areas that have a higher probability of finding riders in future. While applying driver repositioning, we design a future-aware policy and allocate the areas to the drivers considering the destination of requests in the corresponding area. Extensive simulations on real-world datasets of Washington DC and New York demonstrate superior performance by our proposed system in comparison to the existing baselines.
Improving Expressive Power of Spectral Graph Neural Networks with Eigenvalue Correction
Venue: arXiv cs.LG 2025
Year: 2025

In recent years, spectral graph neural networks, characterized by polynomial filters, have garnered increasing attention and have achieved remarkable performance in tasks such as node classification. These models typically assume that eigenvalues for the normalized Laplacian matrix are distinct from each other, thus expecting a polynomial filter to have a high fitting ability. However, this paper empirically observes that normalized Laplacian matrices frequently possess repeated eigenvalues. Moreover, we theoretically establish that the number of distinguishable eigenvalues plays a pivotal role in determining the expressive power of spectral graph neural networks. In light of this observation, we propose an eigenvalue correction strategy that can free polynomial filters from the constraints of repeated eigenvalue inputs. Concretely, the proposed eigenvalue correction strategy enhances the uniform distribution of eigenvalues, thus mitigating repeated eigenvalues, and improving the fitting capacity and expressive power of polynomial filters. Extensive experimental results on both synthetic and real-world datasets demonstrate the superiority of our method. The code is available at: https://github.com/Lukangkang123/EC-GNN
A Combinatorial Perspective on Random Access Efficiency for DNA Storage
Venue: arXiv cs.IT 2025
Year: 2025

We investigate the fundamental limits of the recently proposed random access coverage depth problem for DNA data storage. Under this paradigm, it is assumed that the user information consists of $k$ information strands, which are encoded into $n$ strands via a generator matrix $G$. During the sequencing process, the strands are read uniformly at random, as each strand is available in a large number of copies. In this context, the random access coverage depth problem refers to the expected number of reads (i.e., sequenced strands) required to decode a specific information strand requested by the user. This problem heavily depends on the generator matrix $G$, and besides computing the expectation for different choices of $G$, the goal is to construct matrices that minimize the maximum expectation over all possible requested information strands, denoted by $T_{\max}(G)$. In this paper, we introduce new techniques to investigate the random access coverage depth problem, capturing its combinatorial nature and identifying the structural properties of generator matrices that are advantageous. We establish two general formulas to determine $T_{\max}(G)$ for arbitrary generator matrices. The first formula depends on the linear dependencies between columns of $G$, whereas the second formula takes into account recovery sets and their intersection structure. We also introduce the concept of recovery balanced codes and provide three sufficient conditions for a code to be recovery balanced. These conditions can be used to compute $T_{\max}(G)$ for various families of codes, such as MDS, simplex, Hamming, and binary Reed-Muller codes. Additionally, we study the performance of modified systematic MDS and simplex matrices, showing that the best results for $T_{\max}(G)$ are achieved with a specific combination of encoded strands and replication of the information strands.
Achieving DNA Labeling Capacity with Minimum Labels through Extremal de Bruijn Subgraphs
Venue: arXiv cs.IT 2025
Year: 2025

DNA labeling is a tool in molecular biology and biotechnology to visualize, detect, and study DNA at the molecular level. In this process, a DNA molecule is labeled by a set of specific patterns, referred to as labels, and is then imaged. The resulting image is modeled as an $(\ell+1)$-ary sequence, where $\ell$ is the number of labels, in which any non-zero symbol indicates the appearance of the corresponding label in the DNA molecule. The labeling capacity refers to the maximum information rate that can be achieved by the labeling process for any given set of labels. The main goal of this paper is to study the minimum number of labels of the same length required to achieve the maximum labeling capacity of 2 for DNA sequences or $\log_2q$ for an arbitrary alphabet of size $q$. The solution to this problem requires the study of path unique subgraphs of the de Bruijn graph with the largest number of edges. We provide upper and lower bounds on this value. We draw new connections to existing literature that let us prove an asymptotic result as the label length tends to infinity.
Markov Insertion/Deletion Channels: Information Stability and Capacity Bounds
Venue: arXiv cs.IT 2025
Year: 2025

We consider channels with synchronization errors modeled as insertions and deletions. A classical result for such channels is their information stability, hence the existence of the Shannon capacity, when the synchronization errors are memoryless. In this paper, we extend this result to the case where the insertions and deletions have memory. Specifically, we assume that the synchronization errors are governed by a stationary and ergodic finite state Markov chain, and prove that such channel is information-stable, which implies the existence of a coding scheme which achieves the limit of mutual information. This result implies the existence of the Shannon capacity for a wide range of channels with synchronization errors, with different applications including DNA storage. The methods developed may also be useful to prove other coding theorems for non-trivial channel sequences.
SECOMP: Formally Secure Compilation of Compartmentalized C Programs
Venue: arXiv cs.PL 2025
Year: 2025

Undefined behavior in C often causes devastating security vulnerabilities. One practical mitigation is compartmentalization, which allows developers to structure large programs into mutually distrustful compartments with clearly specified privileges and interactions. In this paper we introduce SECOMP, a compiler for compartmentalized C code that comes with machine-checked proofs guaranteeing that the scope of undefined behavior is restricted to the compartments that encounter it and become dynamically compromised. These guarantees are formalized as the preservation of safety properties against adversarial contexts, a secure compilation criterion similar to full abstraction, and this is the first time such a strong criterion is proven for a mainstream programming language. To achieve this we extend the languages of the CompCert verified C compiler with isolated compartments that can only interact via procedure calls and returns, as specified by cross-compartment interfaces. We adapt the passes and optimizations of CompCert as well as their correctness proofs to this compartment-aware setting. We then use compiler correctness as an ingredient in a larger secure compilation proof that involves several proof engineering novelties, needed to scale formally secure compilation up to a C compiler.