arXiv subjects

Fei Deng

Publications and source records attributed to Fei Deng.

At least 37 records · Page 2Linked to original sources

arXiv2025

Normalization and selecting non-differentially expressed genes improve machine learning modelling of cross-platform transcriptomic data

Normalization is a critical step in quantitative analyses of biological processes. Recent works show that cross-platform integration and normalization enable machine learning (ML) training on RNA microarray and RNA-seq data, but no independent datasets were used in their studies. Therefore, it is unclear how to improve ML modelling performance on independent RNA array and RNA-seq based datasets. Inspired by the house-keeping genes that are commonly used in experimental biology, this study tests the hypothesis that non-differentially expressed genes (NDEG) may improve normalization of transcriptomic data and subsequently cross-platform modelling performance of ML models. Microarray and RNA-seq datasets of the TCGA breast cancer were used as independent training and test datasets, respectively, to classify the molecular subtypes of breast cancer. NDEG (p>0.85) and differentially expressed genes (DEG, p<0.05) were selected based on the p values of ANOVA analysis and used for subsequent data normalization and classification, respectively. Models trained based on data from one platform were used for testing on the other platform. Our data show that NDEG and DEG gene selection could effectively improve the model classification performance. Normalization methods based on parametric statistical analysis were inferior to those based on nonparametric statistics. In this study, the LOG_QN and LOG_QNZ normalization methods combined with the neural network classification model seem to achieve better performance. Therefore, NDEG-based normalization appears useful for cross-platform testing on completely independent datasets. However, more studies are required to examine whether NDEG-based normalization can improve ML classification performance in other datasets and other omic data types.

q-bio.QM↗

arXiv2024

Slot State Space Models

Recent State Space Models (SSMs) such as S4, S5, and Mamba have shown remarkable computational benefits in long-range temporal dependency modeling. However, in many sequence modeling problems, the underlying process is inherently modular and it is of interest to have inductive biases that mimic this modular structure. In this paper, we introduce SlotSSMs, a novel framework for incorporating independent mechanisms into SSMs to preserve or encourage separation of information. Unlike conventional SSMs that maintain a monolithic state vector, SlotSSMs maintains the state as a collection of multiple vectors called slots. Crucially, the state transitions are performed independently per slot with sparse interactions across slots implemented via the bottleneck of self-attention. In experiments, we evaluate our model in object-centric learning, 3D visual reasoning, and long-context video understanding tasks, which involve modeling multiple objects and their long-range temporal dependencies. We find that our proposed design offers substantial performance gains over existing sequence modeling methods. Project page is available at https://slotssms.github.io/

cs.AI↗

arXiv2024

SiamSeg: Self-Training with Contrastive Learning for Unsupervised Domain Adaptation Semantic Segmentation in Remote Sensing

Semantic segmentation of remote sensing (RS) images is a challenging yet essential task with broad applications. While deep learning, particularly supervised learning with large-scale labeled datasets, has significantly advanced this field, the acquisition of high-quality labeled data remains costly and time-intensive. Unsupervised domain adaptation (UDA) provides a promising alternative by enabling models to learn from unlabeled target domain data while leveraging labeled source domain data. Recent self-training (ST) approaches employing pseudo-label generation have shown potential in mitigating domain discrepancies. However, the application of ST to RS image segmentation remains underexplored. Factors such as variations in ground sampling distance, imaging equipment, and geographic diversity exacerbate domain shifts, limiting model performance across domains. In that case, existing ST methods, due to significant domain shifts in cross-domain RS images, often underperform. To address these challenges, we propose integrating contrastive learning into UDA, enhancing the model's ability to capture semantic information in the target domain by maximizing the similarity between augmented views of the same image. This additional supervision improves the model's representational capacity and segmentation performance in the target domain. Extensive experiments conducted on RS datasets, including Potsdam, Vaihingen, and LoveDA, demonstrate that our method, SimSeg, outperforms existing approaches, achieving state-of-the-art results. Visualization and quantitative analyses further validate SimSeg's superior ability to learn from the target domain. The code is publicly available at https://github.com/woldier/SiamSeg.

cs.CV↗

arXiv2024

SeisFusion: Constrained Diffusion Model with Input Guidance for 3D Seismic Data Interpolation and Reconstruction

Geographical, physical, or economic constraints often result in missing traces within seismic data, making the reconstruction of complete seismic data a crucial step in seismic data processing. Traditional methods for seismic data reconstruction require the selection of multiple empirical parameters and struggle to handle large-scale continuous missing data. With the development of deep learning, various neural networks have demonstrated powerful reconstruction capabilities. However, these convolutional neural networks represent a point-to-point reconstruction approach that may not cover the entire distribution of the dataset. Consequently, when dealing with seismic data featuring complex missing patterns, such networks may experience varying degrees of performance degradation. In response to this challenge, we propose a novel diffusion model reconstruction framework tailored for 3D seismic data. To constrain the results generated by the diffusion model, we introduce conditional supervision constraints into the diffusion model, constraining the generated data of the diffusion model based on the input data to be reconstructed. We introduce a 3D neural network architecture into the diffusion model, successfully extending the 2D diffusion model to 3D space. Additionally, we refine the model's generation process by incorporating missing data into the generation process, resulting in reconstructions with higher consistency. Through ablation studies determining optimal parameter values, our method exhibits superior reconstruction accuracy when applied to both field datasets and synthetic datasets, effectively addressing a wide range of complex missing patterns. Our implementation is available at https://github.com/WAL-l/SeisFusion.

cs.LG↗

arXiv2024

Parrot: Pareto-optimal Multi-Reward Reinforcement Learning Framework for Text-to-Image Generation

Recent works have demonstrated that using reinforcement learning (RL) with multiple quality rewards can improve the quality of generated images in text-to-image (T2I) generation. However, manually adjusting reward weights poses challenges and may cause over-optimization in certain metrics. To solve this, we propose Parrot, which addresses the issue through multi-objective optimization and introduces an effective multi-reward optimization strategy to approximate Pareto optimal. Utilizing batch-wise Pareto optimal selection, Parrot automatically identifies the optimal trade-off among different rewards. We use the novel multi-reward optimization algorithm to jointly optimize the T2I model and a prompt expansion network, resulting in significant improvement of image quality and also allow to control the trade-off of different rewards using a reward related prompt during inference. Furthermore, we introduce original prompt-centered guidance at inference time, ensuring fidelity to user input after prompt expansion. Extensive experiments and a user study validate the superiority of Parrot over several baselines across various quality criteria, including aesthetics, human preference, text-image alignment, and image sentiment.

cs.CV↗

arXiv2024

PlanDQ: Hierarchical Plan Orchestration via D-Conductor and Q-Performer

Despite the recent advancements in offline RL, no unified algorithm could achieve superior performance across a broad range of tasks. Offline \textit{value function learning}, in particular, struggles with sparse-reward, long-horizon tasks due to the difficulty of solving credit assignment and extrapolation errors that accumulates as the horizon of the task grows.~On the other hand, models that can perform well in long-horizon tasks are designed specifically for goal-conditioned tasks, which commonly perform worse than value function learning methods on short-horizon, dense-reward scenarios. To bridge this gap, we propose a hierarchical planner designed for offline RL called PlanDQ. PlanDQ incorporates a diffusion-based planner at the high level, named D-Conductor, which guides the low-level policy through sub-goals. At the low level, we used a Q-learning based approach called the Q-Performer to accomplish these sub-goals. Our experimental results suggest that PlanDQ can achieve superior or competitive performance on D4RL continuous control benchmark tasks as well as AntMaze, Kitchen, and Calvin as long-horizon tasks.

cs.LG↗

arXiv2024

EEGDiR: Electroencephalogram denoising network for temporal information storage and global modeling through Retentive Network

Electroencephalogram (EEG) signals play a pivotal role in clinical medicine, brain research, and neurological disease studies. However, susceptibility to various physiological and environmental artifacts introduces noise in recorded EEG data, impeding accurate analysis of underlying brain activity. Denoising techniques are crucial to mitigate this challenge. Recent advancements in deep learningbased approaches exhibit substantial potential for enhancing the signal-to-noise ratio of EEG data compared to traditional methods. In the realm of large-scale language models (LLMs), the Retentive Network (Retnet) infrastructure, prevalent for some models, demonstrates robust feature extraction and global modeling capabilities. Recognizing the temporal similarities between EEG signals and natural language, we introduce the Retnet from natural language processing to EEG denoising. This integration presents a novel approach to EEG denoising, opening avenues for a profound understanding of brain activities and accurate diagnosis of neurological diseases. Nonetheless, direct application of Retnet to EEG denoising is unfeasible due to the one-dimensional nature of EEG signals, while natural language processing deals with two-dimensional data. To facilitate Retnet application to EEG denoising, we propose the signal embedding method, transforming one-dimensional EEG signals into two dimensions for use as network inputs. Experimental results validate the substantial improvement in denoising effectiveness achieved by the proposed method.

eess.SP↗

arXiv2024

WiTUnet: A U-Shaped Architecture Integrating CNN and Transformer for Improved Feature Alignment and Local Information Fusion

Low-dose computed tomography (LDCT) has become the technology of choice for diagnostic medical imaging, given its lower radiation dose compared to standard CT, despite increasing image noise and potentially affecting diagnostic accuracy. To address this, advanced deep learning-based LDCT denoising algorithms have been developed, primarily using Convolutional Neural Networks (CNNs) or Transformer Networks with the Unet architecture. This architecture enhances image detail by integrating feature maps from the encoder and decoder via skip connections. However, current methods often overlook enhancements to the Unet architecture itself, focusing instead on optimizing encoder and decoder structures. This approach can be problematic due to the significant differences in feature map characteristics between the encoder and decoder, where simple fusion strategies may not effectively reconstruct images.In this paper, we introduce WiTUnet, a novel LDCT image denoising method that utilizes nested, dense skip pathways instead of traditional skip connections to improve feature integration. WiTUnet also incorporates a windowed Transformer structure to process images in smaller, non-overlapping segments, reducing computational load. Additionally, the integration of a Local Image Perception Enhancement (LiPe) module in both the encoder and decoder replaces the standard multi-layer perceptron (MLP) in Transformers, enhancing local feature capture and representation. Through extensive experimental comparisons, WiTUnet has demonstrated superior performance over existing methods in key metrics such as Peak Signal-to-Noise Ratio (PSNR), Structural Similarity (SSIM), and Root Mean Square Error (RMSE), significantly improving noise removal and image quality.

cs.CV↗

arXiv2024

PRDP: Proximal Reward Difference Prediction for Large-Scale Reward Finetuning of Diffusion Models

Reward finetuning has emerged as a promising approach to aligning foundation models with downstream objectives. Remarkable success has been achieved in the language domain by using reinforcement learning (RL) to maximize rewards that reflect human preference. However, in the vision domain, existing RL-based reward finetuning methods are limited by their instability in large-scale training, rendering them incapable of generalizing to complex, unseen prompts. In this paper, we propose Proximal Reward Difference Prediction (PRDP), enabling stable black-box reward finetuning for diffusion models for the first time on large-scale prompt datasets with over 100K prompts. Our key innovation is the Reward Difference Prediction (RDP) objective that has the same optimal solution as the RL objective while enjoying better training stability. Specifically, the RDP objective is a supervised regression objective that tasks the diffusion model with predicting the reward difference of generated image pairs from their denoising trajectories. We theoretically prove that the diffusion model that obtains perfect reward difference prediction is exactly the maximizer of the RL objective. We further develop an online algorithm with proximal updates to stably optimize the RDP objective. In experiments, we demonstrate that PRDP can match the reward maximization ability of well-established RL-based methods in small-scale training. Furthermore, through large-scale training on text prompts from the Human Preference Dataset v2 and the Pick-a-Pic v1 dataset, PRDP achieves superior generation quality on a diverse set of complex, unseen prompts whereas RL-based methods completely fail.

cs.LG↗

arXiv2024

Simple Hierarchical Planning with Diffusion

Diffusion-based generative methods have proven effective in modeling trajectories with offline datasets. However, they often face computational challenges and can falter in generalization, especially in capturing temporal abstractions for long-horizon tasks. To overcome this, we introduce the Hierarchical Diffuser, a simple, fast, yet surprisingly effective planning method combining the advantages of hierarchical and diffusion-based planning. Our model adopts a "jumpy" planning strategy at the higher level, which allows it to have a larger receptive field but at a lower computational cost -- a crucial factor for diffusion-based planning methods, as we have empirically verified. Additionally, the jumpy sub-goals guide our low-level planner, facilitating a fine-tuning stage and further improving our approach's effectiveness. We conducted empirical evaluations on standard offline reinforcement learning benchmarks, demonstrating our method's superior performance and efficiency in terms of training and planning speed compared to the non-hierarchical Diffuser as well as other hierarchical planning methods. Moreover, we explore our model's generalization capability, particularly on how our method improves generalization capabilities on compositional out-of-distribution tasks.

cs.LG↗

arXiv2023

CF-NeRF: Camera Parameter Free Neural Radiance Fields with Incremental Learning

Neural Radiance Fields (NeRF) have demonstrated impressive performance in novel view synthesis. However, NeRF and most of its variants still rely on traditional complex pipelines to provide extrinsic and intrinsic camera parameters, such as COLMAP. Recent works, like NeRFmm, BARF, and L2G-NeRF, directly treat camera parameters as learnable and estimate them through differential volume rendering. However, these methods work for forward-looking scenes with slight motions and fail to tackle the rotation scenario in practice. To overcome this limitation, we propose a novel \underline{c}amera parameter \underline{f}ree neural radiance field (CF-NeRF), which incrementally reconstructs 3D representations and recovers the camera parameters inspired by incremental structure from motion (SfM). Given a sequence of images, CF-NeRF estimates the camera parameters of images one by one and reconstructs the scene through initialization, implicit localization, and implicit optimization. To evaluate our method, we use a challenging real-world dataset NeRFBuster which provides 12 scenes under complex trajectories. Results demonstrate that CF-NeRF is robust to camera rotation and achieves state-of-the-art results without providing prior information and constraints.

cs.CV↗

arXiv2023

Facing Off World Model Backbones: RNNs, Transformers, and S4

World models are a fundamental component in model-based reinforcement learning (MBRL). To perform temporally extended and consistent simulations of the future in partially observable environments, world models need to possess long-term memory. However, state-of-the-art MBRL agents, such as Dreamer, predominantly employ recurrent neural networks (RNNs) as their world model backbone, which have limited memory capacity. In this paper, we seek to explore alternative world model backbones for improving long-term memory. In particular, we investigate the effectiveness of Transformers and Structured State Space Sequence (S4) models, motivated by their remarkable ability to capture long-range dependencies in low-dimensional sequences and their complementary strengths. We propose S4WM, the first world model compatible with parallelizable SSMs including S4 and its variants. By incorporating latent variable modeling, S4WM can efficiently generate high-dimensional image sequences through latent imagination. Furthermore, we extensively compare RNN-, Transformer-, and S4-based world models across four sets of environments, which we have tailored to assess crucial memory capabilities of world models, including long-term imagination, context-dependent recall, reward prediction, and memory-based reasoning. Our findings demonstrate that S4WM outperforms Transformer-based world models in terms of long-term memory, while exhibiting greater efficiency during training and imagination. These results pave the way for the development of stronger MBRL agents.

cs.LG↗

arXiv2023

Object-Centric Slot Diffusion

The recent success of transformer-based image generative models in object-centric learning highlights the importance of powerful image generators for handling complex scenes. However, despite the high expressiveness of diffusion models in image generation, their integration into object-centric learning remains largely unexplored in this domain. In this paper, we explore the feasibility and potential of integrating diffusion models into object-centric learning and investigate the pros and cons of this approach. We introduce Latent Slot Diffusion (LSD), a novel model that serves dual purposes: it is the first object-centric learning model to replace conventional slot decoders with a latent diffusion model conditioned on object slots, and it is also the first unsupervised compositional conditional diffusion model that operates without the need for supervised annotations like text. Through experiments on various object-centric tasks, including the first application of the FFHQ dataset in this field, we demonstrate that LSD significantly outperforms state-of-the-art transformer-based decoders, particularly in more complex scenes, and exhibits superior unsupervised compositional generation quality. In addition, we conduct a preliminary investigation into the integration of pre-trained diffusion models in LSD and demonstrate its effectiveness in real-world image segmentation and generation. Project page is available at https://latentslotdiffusion.github.io

cs.CV↗

arXiv2023

Constructive Assimilation: Boosting Contrastive Learning Performance through View Generation Strategies

Transformations based on domain expertise (expert transformations), such as random-resized-crop and color-jitter, have proven critical to the success of contrastive learning techniques such as SimCLR. Recently, several attempts have been made to replace such domain-specific, human-designed transformations with generated views that are learned. However for imagery data, so far none of these view-generation methods has been able to outperform expert transformations. In this work, we tackle a different question: instead of replacing expert transformations with generated views, can we constructively assimilate generated views with expert transformations? We answer this question in the affirmative and propose a view generation method and a simple, effective assimilation method that together improve the state-of-the-art by up to ~3.6% on three different datasets. Importantly, we conduct a detailed empirical study that systematically analyzes a range of view generation and assimilation methods and provides a holistic picture of the efficacy of learned views in contrastive representation learning.

cs.CV↗

arXiv2022

SphereDepth: Panorama Depth Estimation from Spherical Domain

The panorama image can simultaneously demonstrate complete information of the surrounding environment and has many advantages in virtual tourism, games, robotics, etc. However, the progress of panorama depth estimation cannot completely solve the problems of distortion and discontinuity caused by the commonly used projection methods. This paper proposes SphereDepth, a novel panorama depth estimation method that predicts the depth directly on the spherical mesh without projection preprocessing. The core idea is to establish the relationship between the panorama image and the spherical mesh and then use a deep neural network to extract features on the spherical domain to predict depth. To address the efficiency challenges brought by the high-resolution panorama data, we introduce two hyper-parameters for the proposed spherical mesh processing framework to balance the inference speed and accuracy. Validated on three public panorama datasets, SphereDepth achieves comparable results with the state-of-the-art methods of panorama depth estimation. Benefiting from the spherical domain setting, SphereDepth can generate a high-quality point cloud and significantly alleviate the issues of distortion and discontinuity.

cs.CV↗

arXiv2022

Rethinking Disparity: A Depth Range Free Multi-View Stereo Based on Disparity

Existing learning-based multi-view stereo (MVS) methods rely on the depth range to build the 3D cost volume and may fail when the range is too large or unreliable. To address this problem, we propose a disparity-based MVS method based on the epipolar disparity flow (E-flow), called DispMVS, which infers the depth information from the pixel movement between two views. The core of DispMVS is to construct a 2D cost volume on the image plane along the epipolar line between each pair (between the reference image and several source images) for pixel matching and fuse uncountable depths triangulated from each pair by multi-view geometry to ensure multi-view consistency. To be robust, DispMVS starts from a randomly initialized depth map and iteratively refines the depth map with the help of the coarse-to-fine strategy. Experiments on DTUMVS and Tanks\&Temple datasets show that DispMVS is not sensitive to the depth range and achieves state-of-the-art results with lower GPU memory.

cs.CV↗

arXiv2022

Illiterate DALL-E Learns to Compose

Although DALL-E has shown an impressive ability of composition-based systematic generalization in image generation, it requires the dataset of text-image pairs and the compositionality is provided by the text. In contrast, object-centric representation models like the Slot Attention model learn composable representations without the text prompt. However, unlike DALL-E its ability to systematically generalize for zero-shot generation is significantly limited. In this paper, we propose a simple but novel slot-based autoencoding architecture, called SLATE, for combining the best of both worlds: learning object-centric representations that allows systematic generalization in zero-shot image generation without text. As such, this model can also be seen as an illiterate DALL-E model. Unlike the pixel-mixture decoders of existing object-centric representation models, we propose to use the Image GPT decoder conditioned on the slots for capturing complex interactions among the slots and pixels. In experiments, we show that this simple and easy-to-implement architecture not requiring a text prompt achieves significant improvement in in-distribution and out-of-distribution (zero-shot) image generation and qualitatively comparable or better slot-attention structure than the models based on mixture decoders.

cs.CV↗

arXiv2021

DreamerPro: Reconstruction-Free Model-Based Reinforcement Learning with Prototypical Representations

Top-performing Model-Based Reinforcement Learning (MBRL) agents, such as Dreamer, learn the world model by reconstructing the image observations. Hence, they often fail to discard task-irrelevant details and struggle to handle visual distractions. To address this issue, previous work has proposed to contrastively learn the world model, but the performance tends to be inferior in the absence of distractions. In this paper, we seek to enhance robustness to distractions for MBRL agents. Specifically, we consider incorporating prototypical representations, which have yielded more accurate and robust results than contrastive approaches in computer vision. However, it remains elusive how prototypical representations can benefit temporal dynamics learning in MBRL, since they treat each image independently without capturing temporal structures. To this end, we propose to learn the prototypes from the recurrent states of the world model, thereby distilling temporal structures from past observations and actions into the prototypes. The resulting model, DreamerPro, successfully combines Dreamer with prototypes, making large performance gains on the DeepMind Control suite both in the standard setting and when there are complex background distractions. Code available at https://github.com/fdeng18/dreamer-pro .

cs.LG↗