arXiv subjects

Chenhao Li

Publications and source records attributed to Chenhao Li.

52 records · Page 3Linked to original sources

arXiv2024

GenoCraft: A Comprehensive, User-Friendly Web-Based Platform for High-Throughput Omics Data Analysis and Visualization

The surge in high-throughput omics data has reshaped the landscape of biological research, underlining the need for powerful, user-friendly data analysis and interpretation tools. This paper presents GenoCraft, a web-based comprehensive software solution designed to handle the entire pipeline of omics data processing. GenoCraft offers a unified platform featuring advanced bioinformatics tools, covering all aspects of omics data analysis. It encompasses a range of functionalities, such as normalization, quality control, differential analysis, network analysis, pathway analysis, and diverse visualization techniques. This software makes state-of-the-art omics data analysis more accessible to a wider range of users. With GenoCraft, researchers and data scientists have access to an array of cutting-edge bioinformatics tools under a user-friendly interface, making it a valuable resource for managing and analyzing large-scale omics data. The API with an interactive web interface is publicly available at https://genocraft.stanford. edu/. We also release all the codes in https://github.com/futianfan/GenoCraft.

q-bio.GN↗

arXiv2024

NeISF++: Neural Incident Stokes Field for Polarized Inverse Rendering of Conductors and Dielectrics

Recent inverse rendering methods have greatly improved shape, material, and illumination reconstruction by utilizing polarization cues. However, existing methods only support dielectrics, ignoring conductors that are found everywhere in life. Since conductors and dielectrics have different reflection properties, using previous conductor methods will lead to obvious errors. In addition, conductors are glossy, which may cause strong specular reflection and is hard to reconstruct. To solve the above issues, we propose NeISF++, an inverse rendering pipeline that supports conductors and dielectrics. The key ingredient for our proposal is a general pBRDF that describes both conductors and dielectrics. As for the strong specular reflection problem, we propose a novel geometry initialization method using DoLP images. This physical cue is invariant to intensities and thus robust to strong specular reflections. Experimental results on our synthetic and real datasets show that our method surpasses the existing polarized inverse rendering methods for geometry and material decomposition as well as downstream tasks like relighting.

cs.CV↗

arXiv2024

Deep Polarization Cues for Single-shot Shape and Subsurface Scattering Estimation

In this work, we propose a novel learning-based method to jointly estimate the shape and subsurface scattering (SSS) parameters of translucent objects by utilizing polarization cues. Although polarization cues have been used in various applications, such as shape from polarization (SfP), BRDF estimation, and reflection removal, their application in SSS estimation has not yet been explored. Our observations indicate that the SSS affects not only the light intensity but also the polarization signal. Hence, the polarization signal can provide additional cues for SSS estimation. We also introduce the first large-scale synthetic dataset of polarized translucent objects for training our model. Our method outperforms several baselines from the SfP and inverse rendering realms on both synthetic and real data, as demonstrated by qualitative and quantitative results.

cs.CV↗

arXiv2024

DrugCLIP: Contrastive Drug-Disease Interaction For Drug Repurposing

Bringing a novel drug from the original idea to market typically requires more than ten years and billions of dollars. To alleviate the heavy burden, a natural idea is to reuse the approved drug to treat new diseases. The process is also known as drug repurposing or drug repositioning. Machine learning methods exhibited huge potential in automating drug repurposing. However, it still encounter some challenges, such as lack of labels and multimodal feature representation. To address these issues, we design DrugCLIP, a cutting-edge contrastive learning method, to learn drug and disease's interaction without negative labels. Additionally, we have curated a drug repurposing dataset based on real-world clinical trial records. Thorough empirical studies are conducted to validate the effectiveness of the proposed DrugCLIP method.

cs.LG↗

arXiv2024

Dataset and Lessons Learned from the 2024 SaTML LLM Capture-the-Flag Competition

Large language model systems face important security risks from maliciously crafted messages that aim to overwrite the system's original instructions or leak private data. To study this problem, we organized a capture-the-flag competition at IEEE SaTML 2024, where the flag is a secret string in the LLM system prompt. The competition was organized in two phases. In the first phase, teams developed defenses to prevent the model from leaking the secret. During the second phase, teams were challenged to extract the secrets hidden for defenses proposed by the other teams. This report summarizes the main insights from the competition. Notably, we found that all defenses were bypassed at least once, highlighting the difficulty of designing a successful defense and the necessity for additional research to protect LLM systems. To foster future research in this direction, we compiled a dataset with over 137k multi-turn attack chats and open-sourced the platform.

cs.CR↗

arXiv2024

FLD: Fourier Latent Dynamics for Structured Motion Representation and Learning

Motion trajectories offer reliable references for physics-based motion learning but suffer from sparsity, particularly in regions that lack sufficient data coverage. To address this challenge, we introduce a self-supervised, structured representation and generation method that extracts spatial-temporal relationships in periodic or quasi-periodic motions. The motion dynamics in a continuously parameterized latent space enable our method to enhance the interpolation and generalization capabilities of motion learning algorithms. The motion learning controller, informed by the motion parameterization, operates online tracking of a wide range of motions, including targets unseen during training. With a fallback mechanism, the controller dynamically adapts its tracking strategy and automatically resorts to safe action execution when a potentially risky target is proposed. By leveraging the identified spatial-temporal structure, our work opens new possibilities for future advancements in general motion representation and learning algorithms.

cs.LG↗

arXiv2023

NeISF: Neural Incident Stokes Field for Geometry and Material Estimation

Multi-view inverse rendering is the problem of estimating the scene parameters such as shapes, materials, or illuminations from a sequence of images captured under different viewpoints. Many approaches, however, assume single light bounce and thus fail to recover challenging scenarios like inter-reflections. On the other hand, simply extending those methods to consider multi-bounced light requires more assumptions to alleviate the ambiguity. To address this problem, we propose Neural Incident Stokes Fields (NeISF), a multi-view inverse rendering framework that reduces ambiguities using polarization cues. The primary motivation for using polarization cues is that it is the accumulation of multi-bounced light, providing rich information about geometry and material. Based on this knowledge, the proposed incident Stokes field efficiently models the accumulated polarization effect with the aid of an original physically-based differentiable polarimetric renderer. Lastly, experimental results show that our method outperforms the existing works in synthetic and real scenarios.

cs.CV↗

arXiv2023

Learning Diverse Skills for Local Navigation under Multi-constraint Optimality

Despite many successful applications of data-driven control in robotics, extracting meaningful diverse behaviors remains a challenge. Typically, task performance needs to be compromised in order to achieve diversity. In many scenarios, task requirements are specified as a multitude of reward terms, each requiring a different trade-off. In this work, we take a constrained optimization viewpoint on the quality-diversity trade-off and show that we can obtain diverse policies while imposing constraints on their value functions which are defined through distinct rewards. In line with previous work, further control of the diversity level can be achieved through an attract-repel reward term motivated by the Van der Waals force. We demonstrate the effectiveness of our method on a local navigation task where a quadruped robot needs to reach the target within a finite horizon. Finally, our trained policies transfer well to the real 12-DoF quadruped robot, Solo12, and exhibit diverse agile behaviors with successful obstacle traversal.

cs.RO↗

arXiv2023

Inverse Rendering of Translucent Objects using Physical and Neural Renderers

In this work, we propose an inverse rendering model that estimates 3D shape, spatially-varying reflectance, homogeneous subsurface scattering parameters, and an environment illumination jointly from only a pair of captured images of a translucent object. In order to solve the ambiguity problem of inverse rendering, we use a physically-based renderer and a neural renderer for scene reconstruction and material editing. Because two renderers are differentiable, we can compute a reconstruction loss to assist parameter estimation. To enhance the supervision of the proposed neural renderer, we also propose an augmented loss. In addition, we use a flash and no-flash image pair as the input. To supervise the training, we constructed a large-scale synthetic dataset of translucent objects, which consists of 117K scenes. Qualitative and quantitative results on both synthetic and real-world datasets demonstrated the effectiveness of the proposed model.

cs.CV↗

arXiv2023

Efficient and Secure Federated Learning for Financial Applications

The conventional machine learning (ML) and deep learning approaches need to share customers' sensitive information with an external credit bureau to generate a prediction model that opens the door to privacy leakage. This leakage risk makes financial companies face an enormous challenge in their cooperation. Federated learning is a machine learning setting that can protect data privacy, but the high communication cost is often the bottleneck of the federated systems, especially for large neural networks. Limiting the number and size of communications is necessary for the practical training of large neural structures. Gradient sparsification has received increasing attention as a method to reduce communication cost, which only updates significant gradients and accumulates insignificant gradients locally. However, the secure aggregation framework cannot directly use gradient sparsification. This article proposes two sparsification methods to reduce communication cost in federated learning. One is a time-varying hierarchical sparsification method for model parameter update, which solves the problem of maintaining model accuracy after high ratio sparsity. It can significantly reduce the cost of a single communication. The other is to apply the sparsification method to the secure aggregation framework. We sparse the encryption mask matrix to reduce the cost of communication while protecting privacy. Experiments show that under different Non-IID experiment settings, our method can reduce the upload communication cost to about 2.9% to 18.9% of the conventional federated learning algorithm when the sparse rate is 0.01.

cs.LG↗

arXiv2023

Metafiber transforming arbitrarily structured light

Structured light has proven useful for numerous photonic applications. However, the current use of structured light in optical fiber science and technology is severely limited by mode mixing or by the lack of optical elements that can be integrated onto fiber end-faces for complex wavefront control, and hence generation of structured light is still handled outside the fiber via bulky optics in free space. We report a metafiber platform capable of creating arbitrarily structured light on the hybrid-order Poincaré sphere. Polymeric metasurfaces, with unleashed height degree of freedom and a greatly expanded 3D meta-atom library, were laser nanoprinted and interfaced with polarization-maintaining single-mode fibers. Multiple metasurfaces were interfaced on the fiber end-faces, transforming the fiber output into different structured-light fields, including cylindrical vector beams, circularly polarized vortex beams, and an arbitrary vector field. Our work provides a new paradigm for advancing optical fiber science and technology towards fiber-integrated light shaping, which may find important applications in fiber communications, fiber lasers and sensors, endoscopic imaging, fiber lithography, and lab-on-fiber technology.

physics.optics↗

arXiv2023

Versatile Skill Control via Self-supervised Adversarial Imitation of Unlabeled Mixed Motions

Learning diverse skills is one of the main challenges in robotics. To this end, imitation learning approaches have achieved impressive results. These methods require explicitly labeled datasets or assume consistent skill execution to enable learning and active control of individual behaviors, which limits their applicability. In this work, we propose a cooperative adversarial method for obtaining single versatile policies with controllable skill sets from unlabeled datasets containing diverse state transition patterns by maximizing their discriminability. Moreover, we show that by utilizing unsupervised skill discovery in the generative adversarial imitation learning framework, novel and useful skills emerge with successful task fulfillment. Finally, the obtained versatile policies are tested on an agile quadruped robot called Solo 8 and present faithful replications of diverse skills encoded in the demonstrations.

cs.RO↗

arXiv2022

Learning Agile Skills via Adversarial Imitation of Rough Partial Demonstrations

Learning agile skills is one of the main challenges in robotics. To this end, reinforcement learning approaches have achieved impressive results. These methods require explicit task information in terms of a reward function or an expert that can be queried in simulation to provide a target control output, which limits their applicability. In this work, we propose a generative adversarial method for inferring reward functions from partial and potentially physically incompatible demonstrations for successful skill acquirement where reference or expert demonstrations are not easily accessible. Moreover, we show that by using a Wasserstein GAN formulation and transitions from demonstrations with rough and partial information as input, we are able to extract policies that are robust and capable of imitating demonstrated behaviors. Finally, the obtained skills such as a backflip are tested on an agile quadruped robot called Solo 8 and present faithful replication of hand-held human demonstrations.

cs.RO↗

arXiv2022

Ultrafast modulation of the molten metal surface tension under femtosecond laser irradiation

We predict ultrafast modulation of the pure molten metal surface stress fields under the irradiation of the single femtosecond laser pulse through the two-temperature model molecular-dynamics simulations. High-resolution and precision calculations are used to resolve the ultrafast laser-induced anisotropic relaxations of the pressure components on the time-scale comparable to the intrinsic liquid density relaxation time. The magnitudes of the dynamic surface tensions are found being modulated sharply within picoseconds after the irradiation, due to the development of the nanometer scale non-hydrostatic regime behind the exterior atomic layer of the liquid surfaces. The reported novel regulation mechanism of the liquid surface stress field and the dynamic surface tension hints at levitating the manipulation of liquid surfaces, such as ultrafast steering the surface directional transport and patterning.

cond-mat.mtrl-sci↗

arXiv2022

An achromatic metafiber for focusing and imaging across the entire telecommunication range

Dispersion engineering is essential to the performance of most modern optical systems including fiber-optic devices. Even though the chromatic dispersion of a meter-scale single-mode fiber used for endoscopic applications is negligible, optical lenses located on the fiber end face for optical focusing and imaging suffer from strong chromatic aberration. Here we present the design and nanoprinting of a 3D achromatic diffractive metalens on the end face of a single-mode fiber, capable of performing achromatic and polarization-insensitive focusing across the entire near-infrared telecommunication wavelength band ranging from 1.25 to 1.65 um. This represents the whole single-mode domain of commercially used fibers. The unlocked height degree of freedom in a 3D nanopillar meta-atom largely increases the upper bound of the time-bandwidth product of an achromatic metalens up to 21.34, leading to a wide group delay modulation range spanning from -8 to 14 fs. Furthermore, we demonstrate the use of our compact and flexible achromatic metafiber for fiber-optic confocal imaging, capable of creating in-focus sharp images under broadband light illumination. These results may unleash the full potential of fiber meta-optics for widespread applications including hyperspectral endoscopic imaging, femtosecond laser-assisted treatment, deep tissue imaging, wavelength-multiplexing fiber-optic communications, fiber sensing, and fiber lasers.

physics.optics↗

arXiv2021

Optical vortices in nanophotonics

In the last two decades, optical vortices carried by twisted light wavefronts have attracted a great deal of interest, providing not only new physical insights into light-matter interactions, but also a transformative platform for boosting optical information capacity. Meanwhile, advances in nanoscience and nanotechnology lead to the emerging field of nanophotonics, offering an unprecedented level of light manipulation via nanostructured materials and devices. Many exciting ideas and concepts come up when optical vortices meet nanophotonic devices. Here, we provide a mini review on recent achievements made in nanophotonics for the generation and detection of optical vortices and some of their applications.

physics.optics↗