arXiv subjects

Tianyu Ren

Publications and source records attributed to Tianyu Ren.

At least 19 recordsLinked to original sources

arXiv2026

Topological Mixing and Braiding Universality in Polar Active Matter

Connecting the autonomous kinematics of active matter to its emergent macroscopic transport is constrained by the requirement for high-resolution Eulerian velocity fields. Here, we use confined bacterial suspensions as a model active fluid, mapping the sparse Lagrangian trajectories of fluorescent spy cells into (2+1)-dimensional geometric braids that directly encode the spatiotemporal entanglement of the flow. We use the finite-time braiding exponent (FTBE) as a proxy to quantify the topological entropy and chaotic mixing of confined bacterial suspensions. In moderately confined wet systems, we find that hydrodynamic coupling drives a structural transition from a dilute active gas to coherent vortices, and ultimately to active turbulence, revealing three distinct density-dependent regimes of topological mixing. Conversely, truncating the hydrodynamic screening length via extreme confinement drives the system toward a dry active matter limit. In this limit, dense in-plane steric collisions suppress irreducible entanglement and substantially reduce the FTBE at high particle densities. By evaluating the topological complexity generated per encounter, we reveal a transition from a discrete geometric encounter regime to an areal escape mechanism. Finally, we establish a square-root scaling between the FTBE and the effective diffusivity, placing the self-sustained mixing of active fluids into the pathline braiding universality class.

cond-mat.soft↗

arXiv2026

TBSG-Net: Temporal Bipartite Scene Graph Network for Fine-Grained Video Moment Retrieval

Recent advances in proposal-free Video Moment Retrieval (VMR) have highlighted the effectiveness of Static Scene Graphs (SSGs). By modeling objects and their relations at the frame level, SSGs enrich retrieval-oriented video representations. However, integrating SSGs into VMR remains constrained by two inherent limitations: (1) Lack of Temporal Dynamics. SSGs fail to model how objects and their relationships evolve over time, leading to the loss of essential temporal dependencies in video representation; and (2) Lack of Explicit Temporal Span Encoding. SSGs do not explicitly encode the duration of relationships, making precise localization challenging. To address these limitations, we propose Temporal Bipartite Scene Graph Network (TBSG-Net)---to the best of our knowledge, the first Dynamic Scene Graph (DSG) based proposal-free VMR model. Specifically, TBSG-Net leverages DSGs to extract event-centric graph representations of the input video, enabling the modeling of object interactions over time and thus addressing limitation (1). These DSGs are then processed by a novel Dynamic Scene Graph Embedding (DSG-E) module to capture both Temporal Span and spatio-temporal information. First, DSG-E utilizes a TBSG Constructor to transform DSGs into TBSGs, explicitly encoding objects, relationships, and time spans to tackle limitation (2). Second, the resultant TBSGs are passed into a hybrid TBSG Encoder that integrates a Transformer variant for global event modeling and a Graph Convolutional Network for detailed relational reasoning, ultimately producing a more comprehensive spatio-temporal representation. Our experiments demonstrate substantial improvements of TBSG-Net over all baselines.

cs.CV↗

arXiv2026

Autonomous mechanistic discovery of colorectal cancer vulnerabilities via multi-scale AI swarms

The acceleration of automated scientific discovery has been fundamentally bottlenecked by the epistemic gap between the semantic reasoning of large language models (LLMs) and the deterministic physics of mammalian biology. While recent multi-agent frameworks have achieved autonomous hypothesis generation and in vitro experimental analysis, they lack the mathematically grounded, causal constraints required for multi-scale clinical translation. Furthermore, while algorithmic clinical digital twins successfully forecast biological states, they rely on black-box latent spaces, sacrificing mechanistic interpretability for predictive accuracy. Here, we introduce the Multi-Scale Autonomous Discovery Engine (Octopus), a neuro-symbolic architecture that unites zero-leakage, local LLM swarms with strict algorithmic physics engines. Rather than stopping at isolated cellular assays, the system autonomously generated therapeutic hypotheses against in vitro CRISPR dependency data (CCLE), traced dynamic causal cascades using mechanistic interpretability (XGBoost SHAP vectors), and orthogonally translated the emergent vulnerabilities in silico to predict in vivo mammalian tumor trajectory (PDX) and human overall survival (Marisa). In a fully unsupervised sweep of colorectal cancer transcriptomes, the pipeline autonomously identified Insulin-like Growth Factor 2 (IGF2) as a strictly bounded vulnerability to 5-Fluorouracil resistance. The discovery maintained significance after rigorous Benjamini-Hochberg false discovery rate correction (q=0.0292, Log-Rank p=0.0007 ) and successfully predicted significant in vivo tumor volume shrinkage in an independent mouse cohort (Mann-Whitney p=0.0373). By bridging the chasm between multi-agent reasoning and mathematically bounded clinical survival, this framework establishes a verifiable, zero-leakage paradigm for automated, end-to-end biomedical discovery.

cs.LG↗

arXiv2026

Latent World Recovery for Multimodal Learning with Missing Modalities

We study multimodal learning under missing modalities, with particular motivation from bioscience applications in which heterogeneous modalities are often only partially available when decisions need to be made. We propose Latent World Recovery (LWR), a framework built on two key ideas: (i) modality-specific embeddings from different modalities are aligned in a shared latent space, and (ii) a unified representation is constructed by fusing only the embeddings of the modalities that are actually available at both training and inference time. Rather than imputing missing modalities or requiring a fixed modality set, LWR treats each modality as a partial perception of an underlying latent state and performs availability-aware representation learning directly from the observed modalities. This combination of neighbor-based latent alignment and availability-aware modality fusion enables robust multimodal prediction under partial observation, while avoiding error propagation from explicit reconstruction of missing modalities. We evaluate the proposed framework on real-world incomplete multi-omics benchmarks and demonstrate that it provides an effective approach to downstream tasks such as cancer phenotype classification and survival prediction.

cs.LG↗

arXiv2026

Edge slip stabilizes confined active vortices by suppressing localized instabilities

Confined active systems can sustain persistent vortical flows whose stability is strongly influenced by boundary conditions. At the individual level, active units generate internal stresses that drive spontaneous flows, which in turn advect and reorient the particles. This nonlinear coupling between active flow and orientational order is significantly mediated by the system's boundaries, where the specific slip condition governs how these internal stresses generate active flow then rearrange the local orientations. However, a quantitative understanding of how boundary slip dictates their dynamical stability remains lacking. Here, we study how the slip boundary condition controls the stability of a steady vortex state in a circularly confined active nematic system. Using a continuum model in a flow-dominated regime, we perform a linear stability analysis and derive an explicit criterion incorporating the slip velocity and flow-alignment coupling. We find that increasing slip velocity suppresses localized linear instabilities, thereby promoting the persistence of the steady vortex state. This reveals a relaxing the boundary friction actually stabilizes the macroscopic coherent structure by depressing flow induced reorientation that typically destroys single-vortex states. Our findings establish boundary slip as a nontrivial hydrodynamic control parameter for engineering stable active flows.

cond-mat.soft↗

arXiv2026

Dissociating spatial frequency reliance from adversarial robustness advantages in neurally guided deep convolutional neural networks

Deep convolutional neural networks (DCNNs) have rivaled humans on many visual tasks, yet they remain vulnerable to near-imperceptible perturbations generated by adversarial attacks. Recent work shows that aligning DCNN representations with human visual cortex activity improves adversarial robustness, but the mechanisms driving this advantage are unclear. One hypothesis suggests that neural alignment confers robustness by biasing models away from brittle high-frequency details and towards the low spatial frequencies (LSF). However, recent work shows that human object recognition critically depends on a narrow, mid-frequency "human channel". Interestingly, this band was partially preserved in prior LSF-focused studies. Here, we investigate whether a spectral bias towards the LSF or the human channel is the primary driver of the adversarial robustness observed in neurally aligned DCNNs. We first show that DCNNs aligned to higher-order regions of the human ventral visual stream systematically increase reliance on both LSF and the human channel. However, directly steering DCNNs towards these bands revealed a clear dissociation. Biasing models towards the human channel, either alone or together with LSF, does not improve robustness and even impairs it. LSF bias produced some robustness gains, but such improvements are modest despite inducing much larger shifts in spatial-frequency reliance than neurally aligned models. Spatial-frequency-biased models overall show little, if any, increase in similarity to human neural representational geometry. Together, our results suggest that altered spatial-frequency reliance is likely an emergent property of learning more human-like representations rather than the primary mechanism by which neural alignment confers adversarial robustness, and motivate the need for future research examining representational properties beyond spatial-frequency profiles.

q-bio.NC↗

arXiv2026

Contextual Invertible World Models: A Neuro-Symbolic Agentic Framework for Colorectal Cancer Drug Response

Precision oncology is currently limited by the small-N, large-P paradox, where high-dimensional genomic data is abundant but pharmacological response samples are sparse. While deep learning achieves predictive accuracy, it frequently fails to provide the mechanistic clarity required for clinical adoption. We present the Contextual Invertible World Model (CIWM), a Neuro-Symbolic Agentic Framework that bridges this gap by integrating a quantitative machine learning emulator with a Large Language Model reasoning layer. Utilising a stringently curated, high-fidelity data engineering pipeline on the Sanger GDSC dataset ($ N=83 $), we isolate true biological signals from in vitro artifacts to establish a rigorous baseline predictive correlation for complex transcriptomics ($ r=0.268 $). Through Inverse Reasoning, we perform in silico CRISPR perturbations across the colorectal landscape. The framework autonomously overturns classical mechanistic assumptions, identifying a hierarchical dominance of mutant KRAS over the APC/Wnt-axis in driving 5-fluorouracil resistance ($ \Delta=-0.0469 $) via a "KRAS Shield" mapped to MAPK/PI3K networks. Furthermore, the agentic layer identified a "PIK3CA Paradox", revealing that repairing PIK3CA inadvertently increases chemoresistance ($ \Delta=+0.0085 $) by triggering a compensatory feedback loop that hyperactivates the dominant MAPK survival pathway.

q-bio.QM↗

arXiv2025

Contact-Safe Reinforcement Learning with ProMP Reparameterization and Energy Awareness

Reinforcement learning (RL) approaches based on Markov Decision Processes (MDPs) are predominantly applied in the robot joint space, often relying on limited task-specific information and partial awareness of the 3D environment. In contrast, episodic RL has demonstrated advantages over traditional MDP-based methods in terms of trajectory consistency, task awareness, and overall performance in complex robotic tasks. Moreover, traditional step-wise and episodic RL methods often neglect the contact-rich information inherent in task-space manipulation, especially considering the contact-safety and robustness. In this work, contact-rich manipulation tasks are tackled using a task-space, energy-safe framework, where reliable and safe task-space trajectories are generated through the combination of Proximal Policy Optimization (PPO) and movement primitives. Furthermore, an energy-aware Cartesian Impedance Controller objective is incorporated within the proposed framework to ensure safe interactions between the robot and the environment. Our experimental results demonstrate that the proposed framework outperforms existing methods in handling tasks on various types of surfaces in 3D environments, achieving high success rates as well as smooth trajectories and energy-safe interactions.

cs.RO↗

arXiv2025

Learning a Shape-adaptive Assist-as-needed Rehabilitation Policy from Therapist-informed Input

Therapist-in-the-loop robotic rehabilitation has shown great promise in enhancing rehabilitation outcomes by integrating the strengths of therapists and robotic systems. However, its broader adoption remains limited due to insufficient safe interaction and limited adaptation capability. This article proposes a novel telerobotics-mediated framework that enables therapists to intuitively and safely deliver assist-as-needed~(AAN) therapy based on two primary contributions. First, our framework encodes the therapist-informed corrective force into via-points in a latent space, allowing the therapist to provide only minimal assistance while encouraging patient maintaining own motion preferences. Second, a shape-adaptive ANN rehabilitation policy is learned to partially and progressively deform the reference trajectory for movement therapy based on encoded patient motion preferences and therapist-informed via-points. The effectiveness of the proposed shape-adaptive AAN strategy was validated on a telerobotic rehabilitation system using two representative tasks. The results demonstrate its practicality for remote AAN therapy and its superiority over two state-of-the-art methods in reducing corrective force and improving movement smoothness.

eess.SY↗

arXiv2025

Device-Level Optimization Techniques for Solid-State Drives: A Survey

Solid-state drives (SSDs) have revolutionized data storage with their high performance, energy efficiency, and reliability. However, as storage demands grow, SSDs face critical challenges in scalability, endurance, latency, and security. This survey provides a comprehensive analysis of SSD architecture, key challenges, and device-level optimization techniques. We first examine the fundamental components of SSDs, including NAND flash memory structures, SSD controller functionalities (e.g., address mapping, garbage collection, wear leveling), and host interface protocols. Next, we discuss major challenges such as reliability degradation, endurance limitations, latency variations, and security threats. We then explore advanced optimization techniques, including error correction mechanisms, flash translation layer (FTL) enhancements, and emerging architectures like zoned namespace (ZNS) SSDs and flexible data placement (FDP). Finally, we highlight open research challenges, such as QLC/PLC NAND scalability, performance-reliability trade-offs, and SSD optimizations for AI/LLM workloads. This survey aims to guide future research in the development of next-generation SSDs that balance performance, endurance, and security in evolving storage ecosystems.

cs.AR↗

arXiv2025

Safe-Construct: Redefining Construction Safety Violation Recognition as 3D Multi-View Engagement Task

Recognizing safety violations in construction environments is critical yet remains underexplored in computer vision. Existing models predominantly rely on 2D object detection, which fails to capture the complexities of real-world violations due to: (i) an oversimplified task formulation treating violation recognition merely as object detection, (ii) inadequate validation under realistic conditions, (iii) absence of standardized baselines, and (iv) limited scalability from the unavailability of synthetic dataset generators for diverse construction scenarios. To address these challenges, we introduce Safe-Construct, the first framework that reformulates violation recognition as a 3D multi-view engagement task, leveraging scene-level worker-object context and 3D spatial understanding. We also propose the Synthetic Indoor Construction Site Generator (SICSG) to create diverse, scalable training data, overcoming data limitations. Safe-Construct achieves a 7.6% improvement over state-of-the-art methods across four violation types. We rigorously evaluate our approach in near-realistic settings, incorporating four violations, four workers, 14 objects, and challenging conditions like occlusions (worker-object, worker-worker) and variable illumination (back-lighting, overexposure, sunlight). By integrating 3D multi-view spatial understanding and synthetic data generation, Safe-Construct sets a new benchmark for scalable and robust safety monitoring in high-risk industries. Project Website: https://Safe-Construct.github.io/Safe-Construct

cs.CV↗

arXiv2025

KunPeng: A Global Ocean Environmental Model

Inspired by the similarity of the atmosphere-ocean physical coupling mechanism, this study innovatively migrates meteorological large-model techniques to the ocean domain, constructing the KunPeng global ocean environmental prediction model. Aimed at the discontinuous characteristics of marine space, we propose a terrain-adaptive mask constraint mechanism to mitigate effectively training divergence caused by abrupt gradients at land-sea boundaries. To fully integrate far-, medium-, and close-range marine features, a longitude-cyclic deformable convolution network (LC-DCN) is employed to enhance the dynamic receptive field, achieving refined modeling of multi-scale oceanic characteristics. A Deformable Convolution-enhanced Multi-Step Prediction module (DC-MTP) is employed to strengthen temporal dependency feature extraction capabilities. Experimental results demonstrate that this model achieves an average ACC of 0.80 in 15-day global predictions at 0.25$^\circ$ resolution, outperforming comparative models by 0.01-0.08. The average mean squared error (MSE) is 0.41 (representing a 5%-31% reduction) and the average mean absolute error (MAE) is 0.44 (0.6%-21% reduction) compared to other models. Significant improvements are particularly observed in sea surface parameter prediction, deep-sea region characterization, and current velocity field forecasting. Through a horizontal comparison of the applicability of operators at different scales in the marine domain, this study reveals that local operators significantly outperform global operators under slow-varying oceanic processes, demonstrating the effectiveness of dynamic feature pyramid representations in predicting marine physical parameters.

cs.LG↗

arXiv2025

Bottom-Up Reputation Promotes Cooperation with Multi-Agent Reinforcement Learning

Reputation serves as a powerful mechanism for promoting cooperation in multi-agent systems, as agents are more inclined to cooperate with those of good social standing. While existing multi-agent reinforcement learning methods typically rely on predefined social norms to assign reputations, the question of how a population reaches a consensus on judgement when agents hold private, independent views remains unresolved. In this paper, we propose a novel bottom-up reputation learning method, Learning with Reputation Reward (LR2), designed to promote cooperative behaviour through rewards shaping based on assigned reputation. Our agent architecture includes a dilemma policy that determines cooperation by considering the impact on neighbours, and an evaluation policy that assigns reputations to affect the actions of neighbours while optimizing self-objectives. It operates using local observations and interaction-based rewards, without relying on centralized modules or predefined norms. Our findings demonstrate the effectiveness and adaptability of LR2 across various spatial social dilemma scenarios. Interestingly, we find that LR2 stabilizes and enhances cooperation not only with reward reshaping from bottom-up reputation but also by fostering strategy clustering in structured populations, thereby creating environments conducive to sustained cooperation.

cs.MA↗

arXiv2024

Temporal Interaction and its Role in the Evolution of Cooperation

This research investigates the impact of dynamic, time-varying interactions on cooperative behaviour in social dilemmas. Traditional research has focused on deterministic rules governing pairwise interactions, yet the impact of interaction frequency and synchronization in groups on cooperation remains underexplored. Addressing this gap, our work introduces two temporal interaction mechanisms to model the stochastic or periodic participation of individuals in public goods games, acknowledging real-life variances due to exogenous temporal factors and geographical time differences. We consider that the interaction state significantly influences both game payoff calculations and the strategy updating process, offering new insights into the emergence and sustainability of cooperation. Our results indicate that maximum game participation frequency is suboptimal under a stochastic interaction mechanism. Instead, an intermediate activation probability maximizes cooperation, suggesting a vital balance between interaction frequency and inactivity security. Furthermore, local synchronization of interactions within specific areas is shown to be beneficial, as time differences hinder the spread of cross-structures but promote the formation of dense cooperative clusters with smoother boundaries. We also note that stronger clustering in networks, larger group sizes and lower noise increase cooperation. This research contributes to understanding the role of node-based temporality and probabilistic interactions in social dilemmas, offering insights into fostering cooperation.

physics.soc-ph↗

arXiv2024

Enhancing Cooperation through Selective Interaction and Long-term Experiences in Multi-Agent Reinforcement Learning

The significance of network structures in promoting group cooperation within social dilemmas has been widely recognized. Prior studies attribute this facilitation to the assortment of strategies driven by spatial interactions. Although reinforcement learning has been employed to investigate the impact of dynamic interaction on the evolution of cooperation, there remains a lack of understanding about how agents develop neighbour selection behaviours and the formation of strategic assortment within an explicit interaction structure. To address this, our study introduces a computational framework based on multi-agent reinforcement learning in the spatial Prisoner's Dilemma game. This framework allows agents to select dilemma strategies and interacting neighbours based on their long-term experiences, differing from existing research that relies on preset social norms or external incentives. By modelling each agent using two distinct Q-networks, we disentangle the coevolutionary dynamics between cooperation and interaction. The results indicate that long-term experience enables agents to develop the ability to identify non-cooperative neighbours and exhibit a preference for interaction with cooperative ones. This emergent self-organizing behaviour leads to the clustering of agents with similar strategies, thereby increasing network reciprocity and enhancing group cooperation.

cs.MA↗

arXiv2022

Accelerating Integrated Task and Motion Planning with Neural Feasibility Checking

As robots play an increasingly important role in the industrial, the expectations about their applications for everyday living tasks are getting higher. Robots need to perform long-horizon tasks that consist of several sub-tasks that need to be accomplished. Task and Motion Planning (TAMP) provides a hierarchical framework to handle the sequential nature of manipulation tasks by interleaving a symbolic task planner that generates a possible action sequence, with a motion planner that checks the kinematic feasibility in the geometric world, generating robot trajectories if several constraints are satisfied, e.g., a collision-free trajectory from one state to another. Hence, the reasoning about the task plan's geometric grounding is taken over by the motion planner. However, motion planning is computationally intense and is usability as feasibility checker casts TAMP methods inapplicable to real-world scenarios. In this paper, we introduce neural feasibility classifier (NFC), a simple yet effective visual heuristic for classifying the feasibility of proposed actions in TAMP. Namely, NFC will identify infeasible actions of the task planner without the need for costly motion planning, hence reducing planning time in multi-step manipulation tasks. NFC encodes the image of the robot's workspace into a feature map thanks to convolutional neural network (CNN). We train NFC using simulated data from TAMP problems and label the instances based on IK feasibility checking. Our empirical results in different simulated manipulation tasks show that our NFC generalizes to the entire robot workspace and has high prediction accuracy even in scenes with multiple obstructions. When combined with state-of-the-art integrated TAMP, our NFC enhances its performance while reducing its planning time.

cs.RO↗

arXiv2022

Learning Geometric Constraints in Task and Motion Planning

Searching for bindings of geometric parameters in task and motion planning (TAMP) is a finite-horizon stochastic planning problem with high-dimensional decision spaces. A robot manipulator can only move in a subspace of its whole range that is subjected to many geometric constraints. A TAMP solver usually takes many explorations before finding a feasible binding set for each task. It is favorable to learn those constraints once and then transfer them over different tasks within the same workspace. We address this problem by representing constraint knowledge with transferable primitives and using Bayesian optimization (BO) based on these primitives to guide binding search in further tasks. Via semantic and geometric backtracking in TAMP, we construct constraint primitives to encode the geometric constraints respectively in a reusable form. Then we devise a BO approach to efficiently utilize the accumulated constraints for guiding node expansion of an MCTS-based binding planner. We further compose a transfer mechanism to enable free knowledge flow between TAMP tasks. Results indicate that our approach reduces the expensive exploration calls in binding search by 43.60to 71.69 when compared to the baseline unguided planner.

cs.RO↗

arXiv2021

Extended Tree Search for Robot Task and Motion Planning

Integrated task and motion planning (TAMP) is desirable for generalized autonomy robots but it is challenging at the same time. TAMP requires the planner to not only search in both the large symbolic task space and the high-dimension motion space but also deal with the infeasible task actions due to its intrinsic hierarchical process. We propose a novel decision-making framework for TAMP by constructing an extended decision tree for both symbolic task planning and high-dimension motion variable binding. We integrate top-k planning for generating explicitly a skeleton space where a variety of candidate skeleton plans are at disposal. Moreover, we effectively combine this skeleton space with the resultant motion variable spaces into a single extended decision space. Accordingly, we use Monte-Carlo Tree Search (MCTS) to ensure an exploration-exploitation balance at each decision node and optimize globally to produce optimal solutions. The proposed seamless combination of symbolic top-k planning with streams, with the proved optimality of MCTS, leads to a powerful planning algorithm that can handle the combinatorial complexity of long-horizon manipulation tasks. We empirically evaluate our proposed algorithm in challenging robot tasks with different domains that require multi-stage decisions and show how our method can overcome the large task space and motion space through its effective tree search compared to its most competitive baseline method.

cs.RO↗