arXiv subjects

Jiahan Li

Publications and source records attributed to Jiahan Li.

At least 19 recordsLinked to original sources

arXiv2026

Multimodal Filesystem Memory For Long-Horizon Embodied Agents

Agents operating over long horizons need an effective memory that allows them to reuse their experience throughout long interactions. If the entire history of an interaction is retained, it becomes difficult to find the relevant experience, while compressing it into summaries may result in the loss of visual and spatial details that are required later on. We present \textbf{MFM}, a multimodal filesystem memory architecture that keeps complementary types of agent memory. \textbf{Episodic memory} stores the observations, actions, and outcomes, and \textbf{spatial memory} associates experiences with locations. \textbf{Semantic and procedural memory} build up general knowledge and reusable methods of acting, and \textbf{working memory} holds the current plans. MFM makes use of searchable textual records to connect these different representations to the underlying multimodal episodes. The agents are able to find previous experiences by means of contextual cues and to examine the original observations in order to recover details that are missing from their textual descriptions. Through consolidation, the agents convert experience into higher-level knowledge and procedures while still keeping references to the original episodes. In the case of long-horizon Minecraft and computer-use tasks, MFM leads to improved performance with three base models. With GPT-6-Astra, MFM completes \emph{Mine Diamond from Scratch} and reaches 16 out of 24 milestones on the \emph{Ender Dragon} task, as against 12.7 for the best baseline. On CUABench-KiCad it attains a mean reward of 0.440, as compared to 0.400 for the best baseline and 0.267 in the case of no persistent memory.

cs.CL↗

arXiv2026

LabWorld: Learning Interactive 4D Worlds for Scientific Experimentation

Autonomous scientific agents must not only reason about experiments but also interact with the physical environments in which they are executed. Existing laboratory simulators typically rely on manually constructed assets and predefined procedures, while laboratory videos capture real equipment, layouts, and interactions but leave this information implicit in pixels. We introduce LabWorld, an agent-driven Real2Sim framework for reconstructing interactive 4D laboratory worlds from monocular RGB video. LabWorld recovers reusable 3D assets, a metric scene, time-varying object states, and procedure events. Multi-frame observations provide complementary evidence for asset and scene reconstruction, while motion reconstruction combines visual and geometric observations with event constraints encoding the spatial and temporal requirements of laboratory interactions. We evaluate LabWorld on real pipetting and vortexing videos collected in our laboratory against general-purpose agentic and dedicated reconstruction baselines. For pipetting, LabWorld achieves a mean Mask IoU of 0.501, exceeding the strongest baseline by 0.033. For vortexing, it achieves a mean Tube-Length-Normalized PCK-AUC of 0.638, exceeding the strongest baseline by 0.035. On five pipetting videos, event-conditioned reconstruction increases the fraction of modeled physical constraints satisfied from 14.3% (5/35) to 100% (35/35). The resulting worlds expose geometry, motion, articulation, and events as explicit, editable state for replay, inspection, and future embodied scientific systems.

cs.CV↗

arXiv2026

VEOcc++: Learning Persistent Voxel Feature Maps for Embodied Online Semantic Occupancy Mapping and Offline Refinement

Semantic occupancy mapping supports embodied perception during exploration and detailed scene understanding afterward, giving rise to two complementary requirements: online incremental mapping for maintaining an up-to-date global map under causal constraints, and offline global map refinement for improving the completed scene representation with additional computation. We present VEOcc++, a unified voxel-centric framework that connects both stages through a persistent sparse voxel feature map. During exploration, the map expands with newly observed regions and integrates aligned local features through reliability-guided updates, while context-aware decoding produces the current semantic occupancy map. After exploration, cached local features are consolidated as complementary evidence and combined with the completed online representation for multi-scale spatial refinement. On EmbodiedOcc-ScanNet, VEOcc++ achieves 67.12\% IoU and 58.40\% mIoU, establishing new state-of-the-art performance for online incremental mapping. With the local predictor fixed, our online mapping pipeline outperforms VEOcc fusion by 3.70 IoU and 3.74 mIoU points, demonstrating substantial gains from the proposed global mapping design. Offline global map refinement further improves the completed map to 67.79% IoU and 59.37% mIoU using only the observations acquired during exploration. Zero-shot deployment on a mobile robot further demonstrates transferability to unseen environments, onboard feasibility, and scalability to large-scale indoor mapping. Project page: https://wryzju.github.io/VEOccpp/.

cs.CV↗

arXiv2026

JUICE: Unified Multimodal Modeling in Pretrained Representation Spaces

Most unified multimodal models treat images and text asymmetrically: a pretrained language model generates text, an attached diffusion head generates images, and outputs that contain both are produced in a fixed order, so the first output cannot adapt to the second. We ask whether both modalities can instead be generated by one process that is trained on them jointly from scratch. Pretrained encoder spaces hold both modalities in one continuous form and carry knowledge learned at scale, and recent work finds them effective as generative targets for vision and language. We therefore model the joint distribution directly in these spaces. We introduce JUICE (Joint Unified multimodal modeling In Continuous Encoder spaces), a single flow matching Transformer over frozen image and text representations, in which each modality has its own noise level. Which modalities are clean and which are generated then decides the task: image generation, captioning, visual question answering, or joint generation. Controlled pretraining runs test each design choice. At equal guidance, generating text as continuous states leaves image generation intact (48.41 GenEval, against 47.86 for a model trained only for text-to-image generation), while captions lose some exact wording. Training on joint and conditional denoising together beats either alone, and semantic encoder spaces beat VAE latents and raw pixels as targets. At 2.1B parameters, with no language model initialization and at 224x224, JUICE reaches up to 0.88 on GenEval and 73.1 on VQAv2. By sampling both modalities from the joint distribution (coupled sampling), it can also draw a route on a map while writing out the matching moves. On mazes with several valid solutions, joint success rises from 54.6% with independent sampling to 93.7%, and no modality has to go first. On visual spatial planning, JUICE solves 99.8% of maps at its training sizes.

cs.CV↗

arXiv2026

IACM-RL: Intent-Aware Context Management and Reinforcement Learning for Complex Tool Invocation under Dynamic Intent Fluctuations

Executing long-horizon tool invocations in real-world environments is severely challenged by dynamic user intent noise. Existing methods attempt robustness via implicit history scanning or text compression, yet predominantly assume perfect instructions in simplistic scenarios. Inevitably, under fluctuating contexts, obsolete constraints dilute model attention, triggering intent deviation and repetitive API loops. To resolve this, we propose IACM-RL, a comprehensive framework for robust tool invocation. First, we introduce the DynamicIntent pipeline, synthesizing trajectories across several fine-grained fluctuation scenarios, paired with a five-dimensional diagnostic metric suite. Second, IACM-RL deploys a BeliefState-based Self-Generated Context Manager that proactively tracks shifting goals and isolates overwritten parameters using structural stale flags. To autonomously internalize this state-tracking capability, we optimize the policy using a hierarchical intent-driven reward alongside two auxiliary losses (CM extraction and state distillation). Experiments on DynamicIntent, BFCL-V3, and $\mathrmτ^2$-Bench demonstrate that IACM-RL outperforms baselines, reducing infinite loops and stale context errors while enhancing out-of-domain generalization.

cs.CL↗

arXiv2026

VEOcc: Voxel-Centric Online Semantic Occupancy Prediction For Embodied Scene Understanding

Crucial for autonomous exploration, online 3D occupancy prediction and mapping incrementally construct dense spatial representations on the fly. Embodied online occupancy prediction remains predominantly Gaussian-centric, despite the wide use of voxel representations for frame-wise scene completion. We present VEOcc, to the best of our knowledge, the first voxel-centric framework for online embodied semantic occupancy prediction. It incrementally maintains a sparse global semantic voxel map from monocular observations and enables open-ended expansion without predefined scene bounds. To robustly integrate noisy multi-view predictions, we further introduce a Spatio-Temporal-Aware Online Update Strategy comprising Cross-Temporal Logit Aggregation (TLA) for short-term temporal consistency, Reliability-Aware Confidence Modulation (RCM) for spatial uncertainty calibration, and Confidence-Driven Incremental State Update (CSU) for robust global state assimilation. Extensive experiments on Occ-ScanNet and EmbodiedOcc-ScanNet demonstrate state-of-the-art performance among models of comparable scale in both local and embodied settings. Moreover, onboard deployment on a mobile robot validates practical online operation and long-horizon scalability, while results on self-collected handheld sequences demonstrate zero-shot generalization to unseen real-world environments. Code and supplementary visualizations are available on our project page: https://wryzju.github.io/VEOcc/.

cs.CV↗

arXiv2026

Smoothing Dark Areas in Molecular Latent Diffusion

Latent diffusion is a promising framework for scalable 3D molecular generation, but it requires a latent space that remains smooth, valid, and navigable beyond posterior samples. Existing molecular VAEs, however, are typically learned through reconstruction-based objectives, which do not guarantee such a latent space. We show that this leads to dark areas: regions of latent space that are reachable during diffusion sampling but decode to disconnected or chemically invalid molecules. Unlike in image generation, molecular decoding requires strict structural and chemical precision, so even small latent perturbations can produce catastrophic failures. We therefore propose TopVAE, a topology-optimized VAE that reduces dark areas by making the decoder internalize structural and chemical constraints during training, eliminating the need for test-time chemical correction. TopVAE greatly improves off-posterior robustness, and when paired with a standard DiT, achieves $77\%$ lower FCD-3D on QM9, the highest V&C, $52\%$ lower FCD-3D on GEOM-Drugs, and $1.29{\times}$ more stable and connected molecules on zero-shot scaffold inpainting.

cs.LG↗

arXiv2026

DFPO: Scaling Value Modeling via Distributional Flow towards Robust and Generalizable LLM Post-Training

Training reinforcement learning (RL) systems in real-world environments remains challenging due to noisy supervision and poor out-of-domain (OOD) generalization, especially in LLM post-training. Recent distributional RL methods improve robustness by modeling values with multiple quantile points, but they still learn each quantile independently as a scalar. This results in rough-grained value representations that lack fine-grained conditioning on state information, struggling under complex and OOD conditions. We propose DFPO (Distributional Value Flow Policy Optimization with Conditional Risk and Consistency Control), a robust distributional RL framework that models values as continuous flows across time steps. By scaling value modeling through learning of a value flow field instead of isolated quantile predictions, DFPO captures richer state information for more accurate advantage estimation. To stabilize training under noisy feedback, DFPO further integrates conditional risk control and consistency constraints along value flow trajectories. Experiments on dialogue, math reasoning, and scientific tasks show that DFPO outperforms PPO, FlowRL, and other robust baselines under noisy supervision, achieving improved training stability and generalization.

cs.LG↗

arXiv2025

Categorical Flow Matching on Statistical Manifolds

We introduce Statistical Flow Matching (SFM), a novel and mathematically rigorous flow-matching framework on the manifold of parameterized probability measures inspired by the results from information geometry. We demonstrate the effectiveness of our method on the discrete generation problem by instantiating SFM on the manifold of categorical distributions whose geometric properties remain unexplored in previous discrete generative models. Utilizing the Fisher information metric, we equip the manifold with a Riemannian structure whose intrinsic geometries are effectively leveraged by following the shortest paths of geodesics. We develop an efficient training and sampling algorithm that overcomes numerical stability issues with a diffeomorphism between manifolds. Our distinctive geometric perspective of statistical manifolds allows us to apply optimal transport during training and interpret SFM as following the steepest direction of the natural gradient. Unlike previous models that rely on variational bounds for likelihood estimation, SFM enjoys the exact likelihood calculation for arbitrary probability measures. We manifest that SFM can learn more complex patterns on the statistical manifold where existing models often fail due to strong prior assumptions. Comprehensive experiments on real-world generative tasks ranging from image, text to biological domains further demonstrate that SFM achieves higher sampling quality and likelihood than other discrete diffusion or flow-based models.

cs.LG↗

arXiv2025

AHDMIL: Asymmetric Hierarchical Distillation Multi-Instance Learning for Fast and Accurate Whole-Slide Image Classification

Although multi-instance learning (MIL) has succeeded in pathological image classification, it faces the challenge of high inference costs due to the need to process thousands of patches from each gigapixel whole slide image (WSI). To address this, we propose AHDMIL, an Asymmetric Hierarchical Distillation Multi-Instance Learning framework that enables fast and accurate classification by eliminating irrelevant patches through a two-step training process. AHDMIL comprises two key components: the Dynamic Multi-Instance Network (DMIN), which operates on high-resolution WSIs, and the Dual-Branch Lightweight Instance Pre-screening Network (DB-LIPN), which analyzes corresponding low-resolution counterparts. In the first step, self-distillation (SD), DMIN is trained for WSI classification while generating per-instance attention scores to identify irrelevant patches. These scores guide the second step, asymmetric distillation (AD), where DB-LIPN learns to predict the relevance of each low-resolution patch. The relevant patches predicted by DB-LIPN have spatial correspondence with patches in high-resolution WSIs, which are used for fine-tuning and efficient inference of DMIN. In addition, we design the first Chebyshev-polynomial-based Kolmogorov-Arnold (CKA) classifier in computational pathology, which improves classification performance through learnable activation layers. Extensive experiments on four public datasets demonstrate that AHDMIL consistently outperforms previous state-of-the-art methods in both classification performance and inference speed. For example, on the Camelyon16 dataset, it achieves a relative improvement of 5.3% in accuracy and accelerates inference by 1.2.times. Across all datasets, area under the curve (AUC), accuracy, f1 score, and brier score show consistent gains, with average inference speedups ranging from 1.2 to 2.1 times. The code is available.

cs.CV↗

arXiv2025

Designing Cyclic Peptides via Harmonic SDE with Atom-Bond Modeling

Cyclic peptides offer inherent advantages in pharmaceuticals. For example, cyclic peptides are more resistant to enzymatic hydrolysis compared to linear peptides and usually exhibit excellent stability and affinity. Although deep generative models have achieved great success in linear peptide design, several challenges prevent the development of computational methods for designing diverse types of cyclic peptides. These challenges include the scarcity of 3D structural data on target proteins and associated cyclic peptide ligands, the geometric constraints that cyclization imposes, and the involvement of non-canonical amino acids in cyclization. To address the above challenges, we introduce CpSDE, which consists of two key components: AtomSDE, a generative structure prediction model based on harmonic SDE, and ResRouter, a residue type predictor. Utilizing a routed sampling algorithm that alternates between these two models to iteratively update sequences and structures, CpSDE facilitates the generation of cyclic peptides. By employing explicit all-atom and bond modeling, CpSDE overcomes existing data limitations and is proficient in designing a wide variety of cyclic peptides. Our experimental results demonstrate that the cyclic peptides designed by our method exhibit reliable stability and affinity.

cs.LG↗

arXiv2025

Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension

Peptides, short chains of amino acids, interact with target proteins, making them a unique class of protein-based therapeutics for treating human diseases. Recently, deep generative models have shown great promise in peptide generation. However, several challenges remain in designing effective peptide binders. First, not all residues contribute equally to peptide-target interactions. Second, the generated peptides must adopt valid geometries due to the constraints of peptide bonds. Third, realistic tasks for peptide drug development are still lacking. To address these challenges, we introduce PepHAR, a hot-spot-driven autoregressive generative model for designing peptides targeting specific proteins. Building on the observation that certain hot spot residues have higher interaction potentials, we first use an energy-based density model to fit and sample these key residues. Next, to ensure proper peptide geometry, we autoregressively extend peptide fragments by estimating dihedral angles between residue frames. Finally, we apply an optimization process to iteratively refine fragment assembly, ensuring correct peptide structures. By combining hot spot sampling with fragment-based extension, our approach enables de novo peptide design tailored to a target protein and allows the incorporation of key hot spot residues into peptide scaffolds. Extensive experiments, including peptide design and peptide scaffold generation, demonstrate the strong potential of PepHAR in computational peptide binder design. Source code will be available at https://github.com/Ced3-han/PepHAR.

q-bio.BM↗

arXiv2025

Magnetization Dependent In-plane Anomalous Hall Effect in a Low-dimensional System

Anomalous Hall Effect (AHE) response in magnetic systems is typically proportional to an out-of-plane magnetization component because of the restriction imposed by system symmetries, which demands that the magnetization, applied electric field, and induced Hall current are mutually orthogonal to each other. Here, we report experimental realization of an unconventional form of AHE in a low-dimensional heterostructure, wherein the Hall response is not only proportional to the out-of-plane magnetization component but also to the in-plane magnetization component. By interfacing a low-symmetry topological semimetal (TaIrTe4) with the ferromagnetic insulator (Cr2Ge2Te6), we create a low-dimensional magnetic system, where only one mirror symmetry is preserved. We show that as long as the magnetization has a finite component in the mirror plane, this last mirror symmetry is broken, allowing the emergence of an AHE signal proportional to in-plane magnetization. Our experiments, conducted on multiple devices, reveal a gate-voltage-dependent AHE response, suggesting that the underlying mechanisms responsible for the Hall effect in our system can be tuned via electrostatic gating. A minimal microscopic model constrained by the symmetry of the heterostructure shows that both interfacial spin-orbit coupling and time-reversal symmetry breaking via the exchange interaction from magnetization are responsible for the emergence of the in-plane AHE. Our work highlights the importance of system symmetries and exchange interaction in low-dimensional heterostructures for designing novel and tunable Hall effects in layered quantum systems.

cond-mat.mes-hall↗

arXiv2025

$α$-Flow: A Unified Framework for Continuous-State Discrete Flow Matching Models

Recent efforts have extended the flow-matching framework to discrete generative modeling. One strand of models directly works with the continuous probabilities instead of discrete tokens, which we colloquially refer to as Continuous-State Discrete Flow Matching (CS-DFM). Existing CS-DFM models differ significantly in their representations and geometric assumptions. This work presents a unified framework for CS-DFM models, under which the existing variants can be understood as operating on different $α$-representations of probabilities. Building upon the theory of information geometry, we introduce $α$-Flow, a family of CS-DFM models that adheres to the canonical $α$-geometry of the statistical manifold, and demonstrate its optimality in minimizing the generalized kinetic energy. Theoretically, we show that the flow matching loss for $α$-flow establishes a unified variational bound for the discrete negative log-likelihood. We comprehensively evaluate different instantiations of $α$-flow on various discrete generation domains to demonstrate their effectiveness in discrete generative modeling, including intermediate values whose geometries have never been explored before. $α$-flow significantly outperforms its discrete-state counterpart in image and protein sequence generation and better captures the entropy in language modeling.

cs.LG↗

arXiv2025

Fast and Accurate Gigapixel Pathological Image Classification with Hierarchical Distillation Multi-Instance Learning

Although multi-instance learning (MIL) has succeeded in pathological image classification, it faces the challenge of high inference costs due to processing numerous patches from gigapixel whole slide images (WSIs). To address this, we propose HDMIL, a hierarchical distillation multi-instance learning framework that achieves fast and accurate classification by eliminating irrelevant patches. HDMIL consists of two key components: the dynamic multi-instance network (DMIN) and the lightweight instance pre-screening network (LIPN). DMIN operates on high-resolution WSIs, while LIPN operates on the corresponding low-resolution counterparts. During training, DMIN are trained for WSI classification while generating attention-score-based masks that indicate irrelevant patches. These masks then guide the training of LIPN to predict the relevance of each low-resolution patch. During testing, LIPN first determines the useful regions within low-resolution WSIs, which indirectly enables us to eliminate irrelevant regions in high-resolution WSIs, thereby reducing inference time without causing performance degradation. In addition, we further design the first Chebyshev-polynomials-based Kolmogorov-Arnold classifier in computational pathology, which enhances the performance of HDMIL through learnable activation layers. Extensive experiments on three public datasets demonstrate that HDMIL outperforms previous state-of-the-art methods, e.g., achieving improvements of 3.13% in AUC while reducing inference time by 28.6% on the Camelyon16 dataset.

cs.CV↗

arXiv2025

Orientation-Aware Graph Neural Networks for Protein Structure Representation Learning

By folding into particular 3D structures, proteins play a key role in living beings. To learn meaningful representation from a protein structure for downstream tasks, not only the global backbone topology but the local fine-grained orientational relations between amino acids should also be considered. In this work, we propose the Orientation-Aware Graph Neural Networks (OAGNNs) to better sense the geometric characteristics in protein structure (e.g. inner-residue torsion angles, inter-residue orientations). Extending a single weight from a scalar to a 3D vector, we construct a rich set of geometric-meaningful operations to process both the classical and SO(3) representations of a given structure. To plug our designed perceptron unit into existing Graph Neural Networks, we further introduce an equivariant message passing paradigm, showing superior versatility in maintaining SO(3)-equivariance at the global scale. Experiments have shown that our OAGNNs have a remarkable ability to sense geometric orientational features compared to classical networks. OAGNNs have also achieved state-of-the-art performance on various computational biology applications related to protein 3D structures. The code is available at https://github.com/Ced3-han/OAGNN/tree/main.

q-bio.BM↗

arXiv2025

Group Ligands Docking to Protein Pockets

Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation. Inspired by the biochemical observation that ligands binding to the same target protein tend to adopt similar poses, we propose \textsc{GroupBind}, a novel molecular docking framework that simultaneously considers multiple ligands docking to a protein. This is achieved by introducing an interaction layer for the group of ligands and a triangle attention module for embedding protein-ligand and group-ligand pairs. By integrating our approach with diffusion-based docking model, we set a new S performance on the PDBBind blind docking benchmark, demonstrating the effectiveness of our proposed molecular docking paradigm.

q-bio.BM↗

arXiv2024

Driving with InternVL: Oustanding Champion in the Track on Driving with Language of the Autonomous Grand Challenge at CVPR 2024

This technical report describes the methods we employed for the Driving with Language track of the CVPR 2024 Autonomous Grand Challenge. We utilized a powerful open-source multimodal model, InternVL-1.5, and conducted a full-parameter fine-tuning on the competition dataset, DriveLM-nuScenes. To effectively handle the multi-view images of nuScenes and seamlessly inherit InternVL's outstanding multimodal understanding capabilities, we formatted and concatenated the multi-view images in a specific manner. This ensured that the final model could meet the specific requirements of the competition task while leveraging InternVL's powerful image understanding capabilities. Meanwhile, we designed a simple automatic annotation strategy that converts the center points of objects in DriveLM-nuScenes into corresponding bounding boxes. As a result, our single model achieved a score of 0.6002 on the final leadboard.

cs.CV↗