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Shusen Liu

Publications and source records attributed to Shusen Liu.

At least 19 recordsLinked to original sources

Instance-wise Linearization of Neural Network for Model Interpretation

Neural network have achieved remarkable successes in many scientific fields. However, the interpretability of the neural network model is still a major bottlenecks to deploy such technique into our daily life. The challenge can dive into the non-linear behavior of the neural network, which rises a critical question that how a model use input feature to make a decision. The classical approach to address this challenge is feature attribution, which assigns an important score to each input feature and reveal its importance of current prediction. However, current feature attribution approaches often indicate the importance of each input feature without detail of how they are actually processed by a model internally. These attribution approaches often raise a concern that whether they highlight correct features for a model prediction. For a neural network model, the non-linear behavior is often caused by non-linear activation units of a model. However, the computation behavior of a prediction from a neural network model is locally linear, because one prediction has only one activation pattern. Base on the observation, we propose an instance-wise linearization approach to reformulates the forward computation process of a neural network prediction. This approach reformulates different layers of convolution neural networks into linear matrix multiplication. Aggregating all layers' computation, a prediction complex convolution neural network operations can be described as a linear matrix multiplication $F(x) = W \cdot x + b$. This equation can not only provides a feature attribution map that highlights the important of the input features but also tells how each input feature contributes to a prediction exactly. Furthermore, we discuss the application of this technique in both supervise classification and unsupervised neural network learning parametric t-SNE dimension reduction.

cs.LG↗

Unsupervised Latent Space Alignment with Hyperspherical Geodesic Matching

Independently trained neural networks tend to encode the same data with similar latent geometries. These latent geometries are not directly compatible, yet they can be nearly the same up to some class of transformations. While there exists many methods for alignment between different latent spaces, it is typically done using a set of shared sample correspondences, known as anchors. This leaves a fundamental question: are the geometric signatures of different latent spaces representing similar data sufficient to recover an alignment between them? To that end, we introduce HGA (Hyperspherical Gaussian Alignment), a method that directly optimizes a transformation between two latent spaces by maximizing a geometric measure of "fit" between them. Since it is driven by the geometry of the latent spaces rather than paired data, HGA can operate in both an unsupervised and weakly supervised regime. On tasks such as model stitching or multilingual word embedding correspondence recovery, HGA manages to match supervised results with minimal or no supervision.

cs.LG↗

LEDGER: Claim-to-Evidence Trace Graphs for Auditing LLM Agents

Large language model (LLM) agents can now carry out long-horizon technical workflows involving complex tool use, code execution, file edits, and generated artifacts. As agents do more work faster, the productivity bottleneck shifts from producing outputs to auditing whether those outputs are correct and trustworthy. Agent observability systems make fine-grained execution events visible, but visibility alone still leaves reviewers to reconstruct which actions, artifacts, and validation steps matter for a particular conclusion. We introduce LEDGER - Layered Evidence and Decision Graphs for Execution Review, a tracing and review system that builds layered trace graphs over observed agent sessions. LEDGER preserves Trace Records while grouping them into Evidence Nodes and Workflow Nodes, representing artifacts as evidence anchors, and adding typed semantic edges that connect claims to supporting actions, artifacts, and checks. Through data-analysis and coding examples, we show how the resulting traces expose workflow decisions, artifact lineage, repair steps, validation coverage, and claim-support paths for evidence-centered audit.

cs.HC↗

QSimAdv: A Late-Bound, Vendor-Agnostic Architecture for High-Performance Quantum-Circuit Simulation

Portability in high-performance quantum-circuit simulation need not begin at the kernel. We present QSimAdv, which makes late binding, rather than a common kernel, the basis of vendor independence. Representation, operator lowering, and data placement are bound only when their required inputs become available. Before full-state allocation, circuit, noise, and output inspection can route eligible generic sampled-count requests to a stabiliser tableau; explicitly requested representations remain fixed. For full-state execution, backend constraints shape fusion; an ordered fused operator binds to a native lowering only after its physical targets are known. A first-class logical-to-physical layout map records non-canonical order across local and rank-address bits, so the dispatcher moves nonlocal targets only on demand. GPU, CPU, and Message Passing Interface (MPI) backends share these semantics while retaining native execution paths. We realize this design on NVIDIA GH200 and AMD MI250X/EPYC systems across local and distributed execution. With matched complex 32-bit floating-point state storage, QSimAdv leads both Aer Hopper configurations at $N=32$ and Aer's HIP backend at four shared MI250X sizes from $N=24$ to 30. Strong scaling exposes platform dependence: on setonix, QSimAdv leads both GPU and CPU comparisons at every measured rank, achieving $3.4\times$ and $2.8\times$ speedups, respectively, from one to eight ranks; neither the GH200 path nor the CPU path speeds up at eight ranks. Weak scaling reaches 256 ranks with 2 TiB GPU and 1 TiB CPU states. Together, these results support that portability can reside above the kernel boundary while execution remains native and extends across distributed memory.

quant-ph↗

SciVisAgentBench: A Benchmark for Evaluating Scientific Data Analysis and Visualization Agents

Recent advances in large language models (LLMs) have enabled agentic systems to translate natural-language intent into executable scientific visualization (SciVis) tasks. Despite rapid progress, the community lacks a principled and reproducible benchmark for evaluating these emerging SciVis agents in realistic, multi-step analysis settings. We present SciVisAgentBench, a comprehensive and extensible benchmark for evaluating scientific data analysis and visualization agents. Our benchmark is grounded in a structured taxonomy spanning four dimensions: application domain, data type, complexity level, and visualization operation. It currently comprises 108 expert-crafted cases covering diverse SciVis scenarios. To enable reliable assessment, we introduce a multimodal outcome-centric evaluation pipeline that combines LLM-based judging with deterministic evaluators, including image-based metrics, code checkers, rule-based verifiers, and case-specific evaluators. We also conduct a validity study with 12 SciVis experts to examine the agreement between human and LLM judges. Using this framework, we evaluate representative SciVis agents and general-purpose coding agents to establish initial baselines and reveal capability gaps. SciVisAgentBench is designed as a living benchmark to support systematic comparison, diagnose failure modes, and drive progress in agentic SciVis. The benchmark is available at https://scivisagentbench.github.io/.

cs.AI↗

Exploring LLM Agent Designs and Interaction Modalities for Scientific Visualization

This paper examines how large language model (LLM) agents perform on scientific visualization (SciVis) tasks that require generating visualization workflows from natural-language instructions. We compare three representative agent designs: domain-specific agents with structured tool use, computer-use agents, and general-purpose coding agents, across 15 benchmark tasks, evaluating visualization quality, efficiency, robustness, computational cost, and the impact of persistent memory. We further study interaction modalities, including code scripts, model context protocol (MCP) or API calls, command-line interfaces (CLI), and graphical user interfaces (GUI). Our goal is to characterize the tradeoffs among representative SciVis agent configurations used in practice. The results reveal clear tradeoffs across agent designs and interaction modalities. General-purpose coding agents achieve the highest task success rates but incur greater computational cost, whereas domain-specific agents are more efficient and stable but less flexible. Computer-use agents perform well on individual operations but struggle with multi-step workflows. Across both CLI- and GUI-based settings, persistent memory improves performance over repeated trials, but its effectiveness depends on the interaction mode and the quality of feedback. These findings suggest that future SciVis systems should combine structured tool use, interactive capabilities, and adaptive memory mechanisms to balance performance, robustness, and flexibility.

cs.AI↗

SciVisAgentSkills: Design and Evaluation of Agent Skills for Scientific Data Analysis and Visualization

Recent advances in agentic visualization have enabled the translation of natural language into executable scientific visualization (SciVis) workflows. While general-purpose coding agents show strong capabilities, they often lack the tool-specific expertise required for SciVis tasks. In this work, we present SciVisAgentSkills, a collection of reusable agent skills that augment coding agents for scientific data analysis and visualization by encoding environment assumptions, tool usage patterns, and domain heuristics across scientific tools such as ParaView, napari, VMD, and TTK. We evaluate these skills on Codex and Claude Code using SciVisAgentBench, a benchmark of 108 expert-designed multi-step tasks. Results show that agent skills improve mean task scores across the evaluated suites, with token-efficiency benefits that depend on the agent harness and tool setting. These findings highlight the importance of structured procedural knowledge for enabling reliable, long-horizon SciVis workflows, while also showing that skills should be studied alongside the execution harness that loads and applies them. The skills are available at https://github.com/KuangshiAi/SciVisAgentSkills.

cs.AI↗

Nuclear Reaction Data for Fission Products Off Stability

Neutron cross sections on fission products are relevant to a wide range of applications, including nuclear nonproliferation and forensics, spent-fuel assay, reactor burnup and design, as well as astrophysics. Evaluated nuclear data libraries generally fulfill application needs for isotopes on or near stability, however, for unstable fission products, theoretical descriptions of neutron-induced reactions often constitute the only available source of information. These models often make use of simplified assumptions, leading to unquantified impacts on predicted cross sections. In this work, we discuss possible approaches to addressing these issues, particularly by leveraging machine-learning methods, improved predictive reaction modeling, and experimental data to better constrain model parameters. Our goal is to eventually produce evaluated files for the most-produced nuclei off stability in the fission process of $^{235}$U and submit them to the ENDF/B for consideration in the future ENDF/B-IX.0 release. Here we present the methodology and discuss preliminary results comparing usual simplified approaches with a more realistic one accounting for nuclear deformation.

nucl-th↗

Toward AI VIS Co-Scientists: A General and End-to-End Agent Harness for Solving Complex Data Visualization Tasks

The ability to inspect, interpret, and communicate complex data is crucial for virtually any scientific endeavor, but often requires significant expertise outside the core domain ranging from data management and analysis to visualization design and implementation. We present an end-to-end agentic harness that, based on only the data and a high level description of the tasks, independently designs custom visual analysis applications (VIS apps). This represents an important step towards a general AI co-scientist envisioned by many as an autonomous system that can autonomously execute long horizon tasks based on high-level directions. Our proposed VIS co-scientist is an essential component of this broader AI co-scientist vision: a harness that can autonomously analyze data and design visualization solutions using a collection of agents and specialized skills that coordinate exploratory analysis, plan, configure the environment, implement, validate the interface, and most importantly evaluate the overall task completion. Each stage produces document and instruction artifacts that guide downstream work and enable iterative refinement. We validate this approach on IEEE SciVis Contests spanning multiple science and engineering fields. These contests serve as ideal proving grounds because they encode real-world complexity: ambiguous requirements, diverse data modalities, design trade-offs, and task-driven validation. Given only the data and target tasks, our system autonomously produces functional single-page VIS Apps with verified linked-view behavior, highly customized to domain experts' specified tasks and needs.

cs.AI↗

HPC-vQPU: A Service-Export Architecture for Virtual QPUs on Batch-Scheduled HPC Systems

Device-aware quantum simulation increasingly requires HPC-scale accelerators, yet secure supercomputers expose batch-scheduled execution environments rather than the interactive, backend-oriented interfaces expected by quantum software. The key obstacle is not only remote job submission: an HPC-hosted virtual QPU must preserve topology, native-gate, and calibration semantics across queue delay, scheduler allocation, compute-node isolation, and partial execution-side failures, without opening inbound paths into the cluster. We present HPC-vQPU, a service-export architecture for virtual QPUs on batch-scheduled HPC systems. HPC-vQPU separates a cloud-facing control plane, which owns device identity, task lifecycle, snapshot binding, and event projection, from an HPC-resident execution plane, which claims work and realises it through scheduler-backed GPU jobs. Coordination is exclusively outbound and agent initiated. The central abstraction is a topology- and calibration-aware device snapshot bound atomically at claim time and carried into execution as an immutable contract, making each scheduled job hermetic while preserving fresh device semantics. We implement HPC-vQPU at the Pawsey Supercomputing Research Centre using Setonix GPUs, Qiskit-Aer/cuQuantum, and IBM Fez calibration data. Production experiments show that service overhead is bounded and additive, while workload scaling remains confined to the simulator; calibration-bearing snapshots produce measurable output shifts; claim-time binding prevents stale execution after pre-claim device mutation; concurrent agents complete 50/50 tasks exactly once; and explicit recovery restores stale running tasks after agent failure. These results show that secure, scheduler-mediated HPC infrastructure can export device-faithful quantum simulation as an interactive virtual-QPU service.

cs.DC↗

LatentDiff: Scaling Semantic Dataset Comparison to Millions of Images

We present LatentDiff, a scalable framework for semantic dataset comparison that operates directly in the latent space of pretrained vision encoders. By combining sparse autoencoder-based divergence testing with density ratio estimation, LatentDiff identifies interpretable semantic differences between datasets at a fraction of the computational cost of caption-based alternatives. We also introduce Noisy-Diff, a benchmark capturing realistic sparse distribution shifts that cause existing methods to struggle. Experiments demonstrate that LatentDiff achieves superior accuracy while remaining robust to settings where an extremely small fraction of images (from 5% to <1% ) differ semantically.

cs.CV↗

DynQ: A Dynamic Topology-Agnostic Quantum Virtual Machine via Quality-Weighted Community Detection

Quantum cloud platforms have scaled hardware capacity but not the abstraction exposed to users: small programs still monopolise entire processors, and existing Quantum Virtual Machine (QVM) designs often rely on fixed, topology-specific partitions that are brittle under calibration drift, spatial heterogeneity, and transient defects. We present DynQ, a dynamic topology-agnostic QVM that derives execution regions directly from live calibration data. DynQ models a processor as a quality-weighted coupling graph and formulates region discovery as community detection, turning high internal cohesion and low external coupling into a hardware-aware objective for quantum virtualisation. This produces regions that are compilation-friendly, quality-aware, and resilient to degraded couplers and unavailable qubits. DynQ separates offline region discovery from online allocation, enabling low-latency scheduling over pre-validated regions while allowing recomputation under changing hardware conditions. Across five IBM backends, real-device experiments on IBM Kingston and Torino, and cross-architecture evaluation on Rigetti Ankaa-3 via AWS Braket, DynQ improves execution quality, recovers workloads lost under transient defects, and maintains stable output under concurrent batching. It reduces L1 error by up to 45.1% and improves output similarity by up to 19.1% on heterogeneous hardware, while eliminating observed baseline failures on real devices. These results position quantum virtualisation as a graph-driven systems problem and show that adaptive, quality-aware QVMs enable reliable multi-tenant quantum cloud services.

quant-ph↗

Learning noisy phase transition dynamics from stochastic partial differential equations

The non-equilibrium dynamics of mesoscale phase transitions are fundamentally shaped by thermal fluctuations, which not only seed instabilities but actively control kinetic pathways, including rare barrier-crossing events such as nucleation that are entirely inaccessible to deterministic models. Machine-learning surrogates for such systems must therefore represent stochasticity explicitly, enforce conservation laws by construction, and expose physically interpretable structure. We develop physics-aware surrogate models for the stochastic Cahn-Hilliard equation in 3D that satisfy all three requirements simultaneously. The key innovation is to parameterize the surrogate at the level of inter-cell fluxes, decomposing each flux into a deterministic mobility-weighted chemical-potential gradient and a learnable noise amplitude. This design guarantees exact mass conservation at every step and adds physical fluctuations to inter-cell mass transport. A learnable free energy functional provides thermodynamic interpretability, validated by independent recovery of the bulk double-well landscape, interfacial excess energy, and curvature-independent interfacial tension. Tests demonstrate accurate reproduction of ensemble statistics and noise-accelerated coarsening, with generalization to spatial domains 64 times larger in volume and temporal horizons 160x longer than those seen during training. Critically, the stochastic surrogate captures thermally activated nucleation in the metastable regime, a qualitative capability that no deterministic surrogate can provide regardless of training, thus establishing flux-level stochasticity as an architectural necessity rather than an optional enhancement.

physics.comp-ph↗

Interpretable and Steerable Concept Bottleneck Sparse Autoencoders

Sparse autoencoders (SAEs) promise a unified approach for mechanistic interpretability, concept discovery, and model steering in LLMs and LVLMs. However, realizing this potential requires learned features to be both interpretable and steerable. To that end, we introduce two new computationally inexpensive interpretability and steerability metrics for a systematic analysis of LVLM SAEs. This uncovers two observations; (i) a majority of SAE neurons exhibit either low interpretability or low steerability or both, rendering them ineffective for downstream use; and (ii) user-desired concepts are often absent in the SAE, thus limiting their practical utility. To address these limitations, we propose Concept Bottleneck Sparse Autoencoders (CB-SAE) - a novel post-hoc framework that prunes low-utility neurons and augments the latent space with a lightweight concept bottleneck aligned to a user-defined concept set. The resulting CB-SAE improves interpretability by +32.1% and steerability by +14.5% across LVLMs and image generation tasks.

cs.LG↗

Sparse Autoencoders as a Steering Basis for Phase Synchronization in Graph-Based CFD Surrogates

Graph-based surrogate models provide fast alternatives to high-fidelity CFD solvers, but their opaque latent spaces and limited controllability restrict use in safety-critical settings. A key failure mode in oscillatory flows is phase drift, where predictions remain qualitatively correct but gradually lose temporal alignment with observations, limiting use in digital twins and closed-loop control. Correcting this through retraining is expensive and impractical during deployment. We ask whether phase drift can instead be corrected post hoc by manipulating the latent space of a frozen surrogate. We propose a phase-steering framework for pretrained graph-based CFD models that combines the right representation with the right intervention mechanism. To obtain disentangled representation for effective steering, we use sparse autoencoders (SAEs) on frozen MeshGraphNet embeddings. To steer dynamics, we move beyond static per-feature interventions such as scaling or clamping, and introduce a temporally coherent, phase-aware method. Specifically, we identify oscillatory feature pairs with Hilbert analysis, project spatial fields into low-rank temporal coefficients via SVD, and apply smooth time-varying rotations to advance or delay periodic modes while preserving amplitude-phase structure. Using a representation-agnostic setup, we compare SAE-based steering with PCA and raw embedding spaces under the same intervention pipeline. Results show that sparse, disentangled representations outperform dense or entangled ones, while static interventions fail in this dynamical setting. Overall, this work shows that latent-space steering can be extended from semantic domains to time-dependent physical systems when interventions respect the underlying dynamics, and that the same sparse features used for interpretability can also serve as physically meaningful control axes.

cs.CE↗

TopoPilot: Reliable Conversational Workflow Automation for Topological Data Analysis and Visualization

Recent agentic systems demonstrate that large language models can generate scientific visualizations from natural language. However, reliability remains a major limitation: systems may execute invalid operations, introduce subtle but consequential errors, or fail to request missing information when inputs are underspecified. These issues are amplified in real-world workflows, which often exceed the complexity of standard benchmarks. Ensuring reliability in autonomous visualization pipelines therefore remains an open challenge. We present TopoPilot, a reliable and extensible agentic framework for automating complex scientific visualization workflows. TopoPilot incorporates systematic guardrails and verification mechanisms to ensure reliable operation. While we focus on topological data analysis and visualization as a primary use case, the framework is designed to generalize across visualization domains. TopoPilot adopts a reliability-centered two-agent architecture. An orchestrator agent translates user prompts into workflows composed of atomic backend actions, while a verifier agent evaluates these workflows prior to execution, enforcing structural validity and semantic consistency. This separation of interpretation and verification reduces code-generation errors and enforces correctness guarantees. A modular architecture further improves robustness by isolating components and enabling seamless integration of new descriptors and domain-specific workflows without modifying the core system. To systematically address reliability, we introduce a taxonomy of failure modes and implement targeted safeguards for each class. In evaluations simulating 1,000 multi-turn conversations across 100 prompts, including adversarial and infeasible requests, TopoPilot achieves a success rate exceeding 99%, compared to under 50% for baselines without comprehensive guardrails and checks.

cs.HC↗

TRAM: A Transverse Relaxation Time-Aware Qubit Mapping Algorithm for NISQ Devices

Noisy intermediate-scale quantum (NISQ) devices impose dual challenges on quantum circuit execution: limited qubit connectivity requires extensive SWAP-gate routing, while time-dependent decoherence progressively degrades quantum information. Existing qubit mapping algorithms optimize for hardware topology and static calibration metrics but systematically neglect transverse relaxation dynamics (T2), creating a fundamental gap between compiler decisions and evolving noise characteristics. We present TRAM (Transverse Relaxation Time-Aware Qubit Mapping), a coherence-guided compilation framework that elevates decoherence mitigation to a primary optimization objective. TRAM integrates calibration-informed community detection to construct noise-resilient qubit partitions, generates time-weighted initial mappings that anticipate coherence decay, and dynamically schedules SWAP operations to minimize cumulative error accumulation. Evaluated on Qiskit-based simulators with realistic noise models, TRAM outperforms SABRE by 3.59% in fidelity, reduces gate count by 11.49%, and shortens circuit depth by 12.28%, establishing coherence-aware optimization as essential for practical quantum compilation in the NISQ era.

quant-ph↗

VERIRAG: A Post-Retrieval Auditing of Scientific Study Summaries

Can democratized information gatekeepers and community note writers effectively decide what scientific information to amplify? Lacking domain expertise, such gatekeepers rely on automated reasoning agents that use RAG to ground evidence to cited sources. But such standard RAG systems validate summaries via semantic grounding and suffer from "methodological blindness," treating all cited evidence as equally valid regardless of rigor. To address this, we introduce VERIRAG, a post-retrieval auditing framework that shifts the task from classification to methodological vulnerability detection. Using private Small Language Models (SLMs), VERIRAG audits source papers against the Veritable taxonomy of statistical rigor. We contribute: (1) a benchmark of 1,730 summaries with realistic, non-obvious perturbations modeled after retracted papers; (2) the auditable Veritable taxonomy; and (3) an operational system that improves Macro F1 by at least 19 points over baselines using GPT-based SLMs, a result that replicates across MISTRAL and Gemma architectures. Given the complexity of detecting non-obvious flaws, we view VERIRAG as a "vulnerability-detection copilot," providing structured audit trails for human editors. In our experiments, individual human testers found over 80% of the generated audit trails useful for decision-making. We plan to release the dataset and code to support responsible science advocacy.

cs.IR↗