arXiv subjects

Jiahan Li

Publications and source records attributed to Jiahan Li.

At least 19 recordsLinked to original sources

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 catastrophic intent deviation and infinite 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 13 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 three auxiliary losses (action calibration, CM extraction, and state distillation). Experiments on DynamicIntent, BFCL-V3, and $\mathrm{\tau}^2$-Bench demonstrate that IACM-RL significantly outperforms baselines, reducing infinite loops and stale context errors while enhancing out-of-domain generalization.

cs.CL↗

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↗

arXiv2024

Geometric Point Attention Transformer for 3D Shape Reassembly

Shape assembly, which aims to reassemble separate parts into a complete object, has gained significant interest in recent years. Existing methods primarily rely on networks to predict the poses of individual parts, but often fail to effectively capture the geometric interactions between the parts and their poses. In this paper, we present the Geometric Point Attention Transformer (GPAT), a network specifically designed to address the challenges of reasoning about geometric relationships. In the geometric point attention module, we integrate both global shape information and local pairwise geometric features, along with poses represented as rotation and translation vectors for each part. To enable iterative updates and dynamic reasoning, we introduce a geometric recycling scheme, where each prediction is fed into the next iteration for refinement. We evaluate our model on both the semantic and geometric assembly tasks, showing that it outperforms previous methods in absolute pose estimation, achieving accurate pose predictions and high alignment accuracy.

cs.CV↗

arXiv2024

FAFE: Immune Complex Modeling with Geodesic Distance Loss on Noisy Group Frames

Despite the striking success of general protein folding models such as AlphaFold2(AF2, Jumper et al. (2021)), the accurate computational modeling of antibody-antigen complexes remains a challenging task. In this paper, we first analyze AF2's primary loss function, known as the Frame Aligned Point Error (FAPE), and raise a previously overlooked issue that FAPE tends to face gradient vanishing problem on high-rotational-error targets. To address this fundamental limitation, we propose a novel geodesic loss called Frame Aligned Frame Error (FAFE, denoted as F2E to distinguish from FAPE), which enables the model to better optimize both the rotational and translational errors between two frames. We then prove that F2E can be reformulated as a group-aware geodesic loss, which translates the optimization of the residue-to-residue error to optimizing group-to-group geodesic frame distance. By fine-tuning AF2 with our proposed new loss function, we attain a correct rate of 52.3\% (DockQ $>$ 0.23) on an evaluation set and 43.8\% correct rate on a subset with low homology, with substantial improvement over AF2 by 182\% and 100\% respectively.

q-bio.QM↗

arXiv2024

Is Ego Status All You Need for Open-Loop End-to-End Autonomous Driving?

End-to-end autonomous driving recently emerged as a promising research direction to target autonomy from a full-stack perspective. Along this line, many of the latest works follow an open-loop evaluation setting on nuScenes to study the planning behavior. In this paper, we delve deeper into the problem by conducting thorough analyses and demystifying more devils in the details. We initially observed that the nuScenes dataset, characterized by relatively simple driving scenarios, leads to an under-utilization of perception information in end-to-end models incorporating ego status, such as the ego vehicle's velocity. These models tend to rely predominantly on the ego vehicle's status for future path planning. Beyond the limitations of the dataset, we also note that current metrics do not comprehensively assess the planning quality, leading to potentially biased conclusions drawn from existing benchmarks. To address this issue, we introduce a new metric to evaluate whether the predicted trajectories adhere to the road. We further propose a simple baseline able to achieve competitive results without relying on perception annotations. Given the current limitations on the benchmark and metrics, we suggest the community reassess relevant prevailing research and be cautious whether the continued pursuit of state-of-the-art would yield convincing and universal conclusions. Code and models are available at \url{https://github.com/NVlabs/BEV-Planner}

cs.CV↗

arXiv2024

Full-Atom Peptide Design based on Multi-modal Flow Matching

Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present PepFlow, the first multi-modal deep generative model grounded in the flow-matching framework for the design of full-atom peptides that target specific protein receptors. Drawing inspiration from the crucial roles of residue backbone orientations and side-chain dynamics in protein-peptide interactions, we characterize the peptide structure using rigid backbone frames within the $\mathrm{SE}(3)$ manifold and side-chain angles on high-dimensional tori. Furthermore, we represent discrete residue types in the peptide sequence as categorical distributions on the probability simplex. By learning the joint distributions of each modality using derived flows and vector fields on corresponding manifolds, our method excels in the fine-grained design of full-atom peptides. Harnessing the multi-modal paradigm, our approach adeptly tackles various tasks such as fix-backbone sequence design and side-chain packing through partial sampling. Through meticulously crafted experiments, we demonstrate that PepFlow exhibits superior performance in comprehensive benchmarks, highlighting its significant potential in computational peptide design and analysis.

q-bio.BM↗

arXiv2024

Unconventional Unidirectional Magnetoresistance in vdW Heterostructures

Electrical readout of magnetic states is a key to realize novel spintronics devices for efficient computing and data storage. Unidirectional magnetoresistance (UMR) in bilayer systems, consisting of a spin source material and a magnetic layer, refers to a change in the longitudinal resistance upon the reversal of magnetization, which typically originates from the interaction of spin-current and magnetization at the interface. Because of UMR s linear dependence on applied charge current and magnetization, it can be used to electrically read the magnetization state. However, in conventional spin source materials, the spin polarization of an electric field induced spin current is restricted to be in the film plane and hence the ensuing UMR can only respond to the in plane component of the magnetization. On the other hand, magnets with perpendicular magnetic anisotropy (PMA) are highly desired for magnetic memory and spin-logic devices, while the electrical read out of PMA magnets through UMR is critically missing. Here, we report the discovery of an unconventional UMR in bilayer heterostructures of a topological semimetal (WTe2) and a PMA ferromagnetic insulator (Cr2Ge2Te6, CGT), which allows to electrically read the up and down magnetic states of the CGT layer by measuring the longitudinal resistance. Our theoretical calculations based on a tight binding model show that the unconventional UMR originates from the interplay of crystal symmetry breaking in WTe2 and magnetic exchange interaction across the WTe2 and CGT interface. Combining with the ability of WTe2 to obtain magnetic field free switching of the PMA magnets, our discoveries open an exciting pathway to achieve two terminal magnetic memory devices that operate solely on the spin orbit torque and UMR, which is critical for developing next-generation non volatile and low power consumption data storage technologies.

cond-mat.mes-hall↗