arXiv subjects

Hikaru Shindo

Publications and source records attributed to Hikaru Shindo.

At least 19 recordsLinked to original sources

arXiv2026

MolBioKG: Grounding Out-of-Graph Molecules in Biomedical Knowledge Graphs via Multi-Resolution Structural Anchoring

Biomedical knowledge graphs (KGs) accelerate drug discovery, but standard pipelines assume query molecules already exist as graph entities, leaving unregistered molecules disconnected. We address this cold-start challenge, termed the out-of-graph molecule problem, by introducing MolBioKG. This two-layer system grounds unseen molecules in biomedical evidence via multi-resolution structural anchoring. It connects an index of 2.74 million molecules (represented by scaffolds, fragments, functional groups, and fingerprints) to a 9.6-million-edge KG. Given only a SMILES string, MolBioKG retrieves structurally related graph entities and traverses their biomedical neighborhoods without task-specific training. It features two inference mechanisms: static multi-anchor retrieval using Reciprocal Rank Fusion, and Adapt-KG, a tool-using LLM policy for adaptive traversal. Evaluated across in-graph link recovery, complex multi-hop reasoning, and out-of-graph generalization, MolBioKG outperforms strong baselines. Notably, it raises Hits@10 from 0.585 to 0.876 in multi-hop reasoning and out-of-graph target recall from 0.145 to 0.269, all while ensuring predictions retain traceable structural anchors and source-attributed KG evidence.

cs.AI↗

arXiv2026

Pepti-drift: Toxicity-Repulsive Drifting for Antigen-Conditioned Discrete Peptide Generation

Peptides are a promising therapeutic modality that combine the chemical tunability of small molecules with the target specificity of macromolecular therapeutics. However, designing antigen-specific binding peptides while avoiding toxicity remains a major challenge for therapeutic peptide discovery. Here, we present Pepti-drift, a toxicity-aware latent refinement framework that generates peptide candidates through a single antigen-conditioned drift step. In a peptide embedding space, Pepti-drift learns to attract generated peptide latents toward antigen-matched binding peptides while repelling them from toxicity-associated regions. This is challenging because binding-promoting physicochemical features often overlap with toxicity-associated features in peptide representation space. To address this, we introduce a warm-up strategy to stabilize this competing objective by first learning binding-oriented attraction and then increasing toxicity repulsion. Pepti-drift achieves highly efficient generation, running 16.2-fold faster than PepMLM and 1,092.0-fold faster than PepTune. Generated peptides show 100% validity, 98.1% uniqueness, the highest sequence diversity, and near-zero cross-antigen reuse. Further evaluation indicates consistently reduced toxicity and hemolysis risk across most peptide-length ranges while retaining target-related predictive binding signal. Pepti-drift thus provides a fast, scalable, and controllable framework for antigen-specific peptide design that directly encodes safe-and-active properties.

cs.LG↗

arXiv2026

Learning Explicit Behavioral Models with Adaptive Questions and World-Model Probes

Interactive agents trained only against task return can achieve high scores while failing to represent the mechanisms that make their actions succeed. This makes brittle behavior difficult to diagnose and limits adaptation when environment dynamics change. Existing LLM reflection and policy-code repair can revise behavior from failed trajectories, but questions and world-understanding tests are usually used only after training. We introduce an Explicit Symbolic Behavioral Model (ESBM), a trainable behavioral model that couples task performance with evidence-grounded question answering and executable mechanism prediction. An ESBM represents behavior through typed predicates, weighted rules, bounded options and mechanism memory; the mechanism layer predicts symbolic events, object changes, rewards and terminal consequences under action interventions. After each rollout, adaptive questions and active world-model probes convert score failures, QA errors and transition-prediction errors into constraints for local ESBM edits. Candidate models are selected by a multi-criterion rule that jointly evaluates task score, answerability and active world-model consistency. Under the tested Atari-style protocols, ESBM learns high-scoring policies while producing explicit answers and executable mechanism predictions, indicating that adaptive questions can serve as both training pressure and reusable benchmarks for mechanistic policy learning in this setting.

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arXiv2026

SLR: Automated Synthesis for Scalable Logical Reasoning

We introduce SLR, an end-to-end framework for systematic evaluation and training of Large Language Models (LLMs) via Scalable Logical Reasoning. Given a user's task specification, SLR automatically synthesizes (i) an instruction prompt for an inductive reasoning task, (ii) a validation program, executable on model outputs to provide verifiable rewards, and (iii) the latent ground-truth rule. This process is fully automated, scalable, requires no human annotations, and offers precise control over task difficulty. Using SLR, we create SLR-Bench, a benchmark comprising 19k prompts organized into 20 curriculum levels that progressively increase in relational, arithmetic, and recursive complexity. Large-scale evaluation reveals that contemporary LLMs readily produce syntactically valid rules, yet often fail at correct logical inference. Recent reasoning LLMs demonstrate improved performance but incur very high test-time computation, with costs exceeding $300 for just 1,000 prompts. Finally, curriculum learning via SLR doubles Llama-3-8B accuracy on SLR-Bench, achieving parity with Gemini-Flash-Thinking at a fraction of computational cost. Moreover, these reasoning capabilities generalize to a wide range of established benchmarks, underscoring the effectiveness of SLR for downstream reasoning.

cs.AI↗

arXiv2026

ActivationReasoning: Logical Reasoning in Latent Activation Spaces

Large language models (LLMs) excel at generating fluent text, but their internal reasoning remains opaque and difficult to control. Sparse autoencoders (SAEs) make hidden activations more interpretable by exposing latent features that often align with human concepts. Yet, these features are fragile and passive, offering no mechanism for systematic reasoning or model control. To address this, we introduce ActivationReasoning (AR), a framework that embeds explicit logical reasoning into the latent space of LLMs. It proceeds in three stages: (1) Finding latent representations, first latent concept representations are identified (e.g., via SAEs) and organized into a dictionary; (2) Activating propositions, at inference time AR detects activating concepts and maps them to logical propositions; and (3)Logical reasoning, applying logical rules over these propositions to infer higher-order structures, compose new concepts, and steer model behavior. We evaluate AR on multi-hop reasoning (PrOntoQA), abstraction and robustness to indirect concept cues (Rail2Country), reasoning over natural and diverse language (ProverQA), and context-sensitive safety (BeaverTails). Across all tasks, AR scales robustly with reasoning complexity, generalizes to abstract and context-sensitive tasks, and transfers across model backbones. These results demonstrate that grounding logical structure in latent activations not only improves transparency but also enables structured reasoning, reliable control, and alignment with desired behaviors, providing a path toward more reliable and auditable AI.

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arXiv2026

Kintsugi: Learning Policies by Repairing Executable Knowledge Bases

Modern embodied agents achieve impressive performance, but their task knowledge is often stored in neural weights, latent state, or prompt-bound memory, making individual policy knowledge difficult to inspect, validate, recombine, and reuse. We introduce \textbf{Kintsugi}, a white-box policy-learning framework that treats embodied policy improvement as verifier-gated construction of a typed executable Knowledge Base (KB). Kintsugi represents task-level policy knowledge as composable typed entries -- predicates, operators, policy schemas, monitors, recovery rules, experience records, and goals -- and improves this artifact through localized typed edits induced from rollout evidence, rather than relying on test-time language-model reasoning. Between rollouts, a tool-constrained agentic editing loop diagnoses trajectory failures, localizes them to editable KB layers, and proposes candidate edits. A deterministic verification gate admits an edit only when the candidate type-checks, the resulting KB executes, and focused validation success or trajectory-health metrics improve without violating protected-regression checks. At inference, the accepted KB is executed by a deterministic symbolic executor with zero LLM calls. Across long-horizon text-agent benchmarks and representative object-centric manipulation settings, Kintsugi achieves strong endpoint performance while preserving inspectability, local editability, and verifier-gated deployment. These results suggest that embodied policy improvement can be organized around executable task knowledge.

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arXiv2026

GRAIL: Autonomous Concept Grounding for Neuro-Symbolic Reinforcement Learning

Neuro-symbolic Reinforcement Learning (NeSy-RL) combines symbolic reasoning with gradient-based optimization to achieve interpretable and generalizable policies. Relational concepts, such as "left of" or "close by", serve as foundational building blocks that structure how agents perceive and act. However, conventional approaches require human experts to manually define these concepts, limiting adaptability since concept semantics vary across environments. We propose GRAIL (Grounding Relational Agents through Interactive Learning), a framework that autonomously grounds relational concepts through environmental interaction. GRAIL leverages large language models (LLMs) to provide generic concept representations as weak supervision, then refines them to capture environment-specific semantics. This approach addresses both sparse reward signals and concept misalignment prevalent in underdetermined environments. Experiments on the Atari games Kangaroo, Seaquest, and Skiing demonstrate that GRAIL matches or outperforms agents with manually crafted concepts in simplified settings, and reveals informative trade-offs between reward maximization and high-level goal completion in the full environment.

cs.AI↗

arXiv2026

SocialGrid: A Benchmark for Planning and Social Reasoning in Embodied Multi-Agent Systems

As Large Language Models (LLMs) transition from text processors to autonomous agents, evaluating their social reasoning in embodied multi-agent settings becomes critical. We introduce SocialGrid, an embodied multi-agent environment inspired by Among Us that evaluates LLM agents on planning, task execution, and social reasoning. Our evaluations reveal that even the strongest open model (GPT-OSS-120B) achieves below 60% accuracy in task completion and planning, with agents getting stuck in repetitive behaviors or failing to navigate basic obstacles. Since poor navigation confounds evaluation of social intelligence, SocialGrid offers an optional Planning Oracle to isolate social reasoning from planning deficits. While planning assistance improves task completion, social reasoning remains a bottleneck: agents fail to detect deception at near-random chance regardless of scale, relying on shallow heuristics rather than accumulating behavioral evidence. SocialGrid provides automatic failure analysis and fine-grained metrics, enabling developers to diagnose and improve their agents. We also establish a competitive leaderboard using Elo ratings from adversarial league play.

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arXiv2026

LLMs Gaming Verifiers: RLVR can Lead to Reward Hacking

As reinforcement Learning with Verifiable Rewards (RLVR) has become the dominant paradigm for scaling reasoning capabilities in LLMs, a new failure mode emerges: LLMs gaming verifiers. We study this phenomenon on inductive reasoning tasks, where models must induce and output logical rules. We find that RLVR-trained models systematically abandon rule induction. Instead of learning generalizable patterns (e.g., ``trains carrying red cars go east''), they enumerate instance-level labels, producing outputs that pass verifiers without capturing the relational patterns required by the task. We show that this behavior is not a failure of understanding but a form of reward hacking: imperfect verifiers that check only extensional correctness admit false positives. To detect such shortcuts, we introduce Isomorphic Perturbation Testing (IPT), which evaluates a single model output under both extensional and isomorphic verification, where the latter enforces invariance under logically isomorphic tasks. While genuine rule induction remains invariant, shortcut strategies fail. We find that shortcut behavior is specific to RLVR-trained reasoning models (e.g., GPT-5, Olmo3) and absent in non-RLVR models (e.g., GPT-4o, GPT-4.5, Ministral). Moreover, shortcut prevalence increases with task complexity and inference-time compute. In controlled training experiments, extensional verification directly induces shortcut strategies, while isomorphic verification eliminates them. These results show that RLVR can incentivize reward hacking not only through overt manipulation but also by exploiting what the verifier fails to enforce.

cs.LG↗

arXiv2025

Synthesizing Visual Concepts as Vision-Language Programs

Vision-Language models (VLMs) achieve strong performance on multimodal tasks but often fail at systematic visual reasoning tasks, leading to inconsistent or illogical outputs. Neuro-symbolic methods promise to address this by inducing interpretable logical rules, though they exploit rigid, domain-specific perception modules. We propose Vision-Language Programs (VLP), which combine the perceptual flexibility of VLMs with systematic reasoning of program synthesis. Rather than embedding reasoning inside the VLM, VLP leverages the model to produce structured visual descriptions that are compiled into neuro-symbolic programs. The resulting programs execute directly on images, remain consistent with task constraints, and provide human-interpretable explanations that enable easy shortcut mitigation. Experiments on synthetic and real-world datasets demonstrate that VLPs outperform direct and structured prompting, particularly on tasks requiring complex logical reasoning.

cs.AI↗

arXiv2025

STORM: Segment, Track, and Object Re-Localization from a Single Image

Accurate 6D pose estimation and tracking are core capabilities for physical AI systems, yet real-world deployment remains brittle and labor-intensive. Many pipelines rely on CAD models, manual masking, or per-object adaptation, and still fail under occlusion or fast motion without a principled way to recognize failure. We propose STORM, a unified framework for reference-conditioned 6D tracking that can operate from a single reference image, with minimal manual input and improved robustness. STORM combines: (i) Hierarchical Spatial Fusion Attention (HSFA), a task-driven reference-query fusion architecture that supports both single-reference and multi-reference conditioning and can optionally use vision-language semantic conditioning to resolve instance ambiguities; and (ii) a BCE-trained tracking verifier whose continuous compatibility logit is used as an energy-like score to detect drift and trigger automatic re-initialization. Experiments on LM-O and YCB-Video show that STORM improves annotation-free pose tracking accuracy over strong baselines and recovers reliably from severe occlusions and rapid viewpoint changes with minimal overhead.

cs.CV↗

arXiv2025

Human-Allied Relational Reinforcement Learning

Reinforcement learning (RL) has experienced a second wind in the past decade. While incredibly successful in images and videos, these systems still operate within the realm of propositional tasks ignoring the inherent structure that exists in the problem. Consequently, relational extensions (RRL) have been developed for such structured problems that allow for effective generalization to arbitrary number of objects. However, they inherently make strong assumptions about the problem structure. We introduce a novel framework that combines RRL with object-centric representation to handle both structured and unstructured data. We enhance learning by allowing the system to actively query the human expert for guidance by explicitly modeling the uncertainty over the policy. Our empirical evaluation demonstrates the effectiveness and efficiency of our proposed approach.

cs.LG↗

arXiv2025

ART: Adaptive Relation Tuning for Generalized Relation Prediction

Visual relation detection (VRD) is the task of identifying the relationships between objects in a scene. VRD models trained solely on relation detection data struggle to generalize beyond the relations on which they are trained. While prompt tuning has been used to adapt vision-language models (VLMs) for VRD, it uses handcrafted prompts and struggles with novel or complex relations. We argue that instruction tuning offers a more effective solution by fine-tuning VLMs on diverse instructional data. We thus introduce ART, an Adaptive Relation Tuning framework that adapts VLMs for VRD through instruction tuning and strategic instance selection. By converting VRD datasets into an instruction tuning format and employing an adaptive sampling algorithm, ART directs the VLM to focus on informative relations while maintaining generalizability. Specifically, we focus on the relation classification, where subject-object boxes are given and the model predicts the predicate between them. We tune on a held-in set and evaluate across multiple held-out datasets of varying complexity. Our approach strongly improves over its baselines and can infer unseen relation concepts, a capability absent in mainstream VRD methods. We demonstrate ART's practical value by using the predicted relations for segmenting complex scenes.

cs.CV↗

arXiv2025

Learning Differentiable Logic Programs for Abstract Visual Reasoning

Visual reasoning is essential for building intelligent agents that understand the world and perform problem-solving beyond perception. Differentiable forward reasoning has been developed to integrate reasoning with gradient-based machine learning paradigms. However, due to the memory intensity, most existing approaches do not bring the best of the expressivity of first-order logic, excluding a crucial ability to solve abstract visual reasoning, where agents need to perform reasoning by using analogies on abstract concepts in different scenarios. To overcome this problem, we propose NEUro-symbolic Message-pAssiNg reasoNer (NEUMANN), which is a graph-based differentiable forward reasoner, passing messages in a memory-efficient manner and handling structured programs with functors. Moreover, we propose a computationally-efficient structure learning algorithm to perform explanatory program induction on complex visual scenes. To evaluate, in addition to conventional visual reasoning tasks, we propose a new task, visual reasoning behind-the-scenes, where agents need to learn abstract programs and then answer queries by imagining scenes that are not observed. We empirically demonstrate that NEUMANN solves visual reasoning tasks efficiently, outperforming neural, symbolic, and neuro-symbolic baselines.

cs.LG↗

arXiv2025

BlendRL: A Framework for Merging Symbolic and Neural Policy Learning

Humans can leverage both symbolic reasoning and intuitive reactions. In contrast, reinforcement learning policies are typically encoded in either opaque systems like neural networks or symbolic systems that rely on predefined symbols and rules. This disjointed approach severely limits the agents' capabilities, as they often lack either the flexible low-level reaction characteristic of neural agents or the interpretable reasoning of symbolic agents. To overcome this challenge, we introduce BlendRL, a neuro-symbolic RL framework that harmoniously integrates both paradigms within RL agents that use mixtures of both logic and neural policies. We empirically demonstrate that BlendRL agents outperform both neural and symbolic baselines in standard Atari environments, and showcase their robustness to environmental changes. Additionally, we analyze the interaction between neural and symbolic policies, illustrating how their hybrid use helps agents overcome each other's limitations.

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arXiv2024

DeiSAM: Segment Anything with Deictic Prompting

Large-scale, pre-trained neural networks have demonstrated strong capabilities in various tasks, including zero-shot image segmentation. To identify concrete objects in complex scenes, humans instinctively rely on deictic descriptions in natural language, i.e., referring to something depending on the context such as "The object that is on the desk and behind the cup.". However, deep learning approaches cannot reliably interpret such deictic representations due to their lack of reasoning capabilities in complex scenarios. To remedy this issue, we propose DeiSAM -- a combination of large pre-trained neural networks with differentiable logic reasoners -- for deictic promptable segmentation. Given a complex, textual segmentation description, DeiSAM leverages Large Language Models (LLMs) to generate first-order logic rules and performs differentiable forward reasoning on generated scene graphs. Subsequently, DeiSAM segments objects by matching them to the logically inferred image regions. As part of our evaluation, we propose the Deictic Visual Genome (DeiVG) dataset, containing paired visual input and complex, deictic textual prompts. Our empirical results demonstrate that DeiSAM is a substantial improvement over purely data-driven baselines for deictic promptable segmentation.

cs.LG↗

arXiv2024

V-LoL: A Diagnostic Dataset for Visual Logical Learning

Despite the successes of recent developments in visual AI, different shortcomings still exist; from missing exact logical reasoning, to abstract generalization abilities, to understanding complex and noisy scenes. Unfortunately, existing benchmarks, were not designed to capture more than a few of these aspects. Whereas deep learning datasets focus on visually complex data but simple visual reasoning tasks, inductive logic datasets involve complex logical learning tasks, however, lack the visual component. To address this, we propose the diagnostic visual logical learning dataset, V-LoL, that seamlessly combines visual and logical challenges. Notably, we introduce the first instantiation of V-LoL, V-LoL-Train, - a visual rendition of a classic benchmark in symbolic AI, the Michalski train problem. By incorporating intricate visual scenes and flexible logical reasoning tasks within a versatile framework, V-LoL-Train provides a platform for investigating a wide range of visual logical learning challenges. We evaluate a variety of AI systems including traditional symbolic AI, neural AI, as well as neuro-symbolic AI. Our evaluations demonstrate that even SOTA AI faces difficulties in dealing with visual logical learning challenges, highlighting unique advantages and limitations of each methodology. Overall, V-LoL opens up new avenues for understanding and enhancing current abilities in visual logical learning for AI systems.

cs.AI↗

arXiv2024

Learning by Self-Explaining

Much of explainable AI research treats explanations as a means for model inspection. Yet, this neglects findings from human psychology that describe the benefit of self-explanations in an agent's learning process. Motivated by this, we introduce a novel workflow in the context of image classification, termed Learning by Self-Explaining (LSX). LSX utilizes aspects of self-refining AI and human-guided explanatory machine learning. The underlying idea is that a learner model, in addition to optimizing for the original predictive task, is further optimized based on explanatory feedback from an internal critic model. Intuitively, a learner's explanations are considered "useful" if the internal critic can perform the same task given these explanations. We provide an overview of important components of LSX and, based on this, perform extensive experimental evaluations via three different example instantiations. Our results indicate improvements via Learning by Self-Explaining on several levels: in terms of model generalization, reducing the influence of confounding factors, and providing more task-relevant and faithful model explanations. Overall, our work provides evidence for the potential of self-explaining within the learning phase of an AI model.

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