The task of understanding and interpreting the complex information encoded within genomic sequences remains a grand challenge in biological research and clinical applications. In this context, recent advancements in large language model research have led to the development of both encoder-only and decoder-only foundation models designed to decode intricate information in DNA sequences. However, several issues persist, particularly regarding the efficient management of long-range dependencies inherent in genomic sequences, the effective representation of nucleotide variations, and the considerable computational costs associated with large model architectures and extensive pretraining datasets. Current genomic foundation models often face a critical tradeoff: smaller models with mediocre performance versus large models with improved performance. To address these challenges, we introduce dnaGrinder, a unique and efficient genomic foundation model. dnaGrinder excels at managing long-range dependencies within genomic sequences while minimizing computational costs without compromising performance. It achieves results that are not just comparable but often superior to leading DNA models such as Nucleotide Transformer and DNABERT-2. Furthermore, dnaGrinder is designed for easy fine-tuning on workstation-grade GPUs, accommodating input lengths exceeding 17,000 tokens. On a single high-performance GPU, it supports sequences longer than 140,000 tokens, making it a highly efficient and accessible tool for both basic biological research and clinical applications.
Biomarker discovery is vital in advancing personalized medicine, offering insights into disease diagnosis, prognosis, and therapeutic efficacy. Traditionally, the identification and validation of biomarkers heavily depend on extensive experiments and statistical analyses. These approaches are time-consuming, demand extensive domain expertise, and are constrained by the complexity of biological systems. These limitations motivate us to ask: Can we automatically identify the effective biomarker subset without substantial human efforts? Inspired by the success of generative AI, we think that the intricate knowledge of biomarker identification can be compressed into a continuous embedding space, thus enhancing the search for better biomarkers. Thus, we propose a new biomarker identification framework with two important modules:1) training data preparation and 2) embedding-optimization-generation. The first module uses a multi-agent system to automatically collect pairs of biomarker subsets and their corresponding prediction accuracy as training data. These data establish a strong knowledge base for biomarker identification. The second module employs an encoder-evaluator-decoder learning paradigm to compress the knowledge of the collected data into a continuous space. Then, it utilizes gradient-based search techniques and autoregressive-based reconstruction to efficiently identify the optimal subset of biomarkers. Finally, we conduct extensive experiments on three real-world datasets to show the efficiency, robustness, and effectiveness of our method.
Video anomaly detection (VAD) is a crucial task in video analysis and surveillance within computer vision. Currently, VAD is gaining attention with memory techniques that store the features of normal frames. The stored features are utilized for frame reconstruction, identifying an abnormality when a significant difference exists between the reconstructed and input frames. However, this approach faces several challenges due to the simultaneous optimization required for both the memory and encoder-decoder model. These challenges include increased optimization difficulty, complexity of implementation, and performance variability depending on the memory size. To address these challenges,we propose an effective memory method for VAD, called VideoPatchCore. Inspired by PatchCore, our approach introduces a structure that prioritizes memory optimization and configures three types of memory tailored to the characteristics of video data. This method effectively addresses the limitations of existing memory-based methods, achieving good performance comparable to state-of-the-art methods. Furthermore, our method requires no training and is straightforward to implement, making VAD tasks more accessible. Our code is available online at github.com/SkiddieAhn/Paper-VideoPatchCore.
Semi-supervised change detection (SSCD) utilizes partially labeled data and a large amount of unlabeled data to detect changes. However, the transformer-based SSCD network does not perform as well as the convolution-based SSCD network due to the lack of labeled data. To overcome this limitation, we introduce a new decoder called Cross Branch Feature Fusion CBFF, which combines the strengths of both local convolutional branch and global transformer branch. The convolutional branch is easy to learn and can produce high-quality features with a small amount of labeled data. The transformer branch, on the other hand, can extract global context features but is hard to learn without a lot of labeled data. Using CBFF, we build our SSCD model based on a strong-to-weak consistency strategy. Through comprehensive experiments on WHU-CD and LEVIR-CD datasets, we have demonstrated the superiority of our method over seven state-of-the-art SSCD methods.
The performance of deep learning based edge detector has far exceeded that of humans, but the huge computational cost and complex training strategy hinder its further development and application. In this paper, we eliminate these complexities with a vanilla encoder-decoder based detector. Firstly, we design a bilateral encoder to decouple the extraction process of location features and semantic features. Since the location branch no longer provides cues for the semantic branch, the richness of features can be further compressed, which is the key to make our model more compact. We propose a cascaded feature fusion decoder, where the location features are progressively refined by semantic features. The refined location features are the only basis for generating the edge map. The coarse original location features and semantic features are avoided from direct contact with the final result. So the noise in the location features and the location error in the semantic features can be suppressed in the generated edge map. The proposed New Baseline for Edge Detection (NBED) achieves superior performance consistently across multiple edge detection benchmarks, even compared with those methods with huge computational cost and complex training strategy. The ODS of NBED on BSDS500 is 0.838, achieving state-of-the-art performance. Our study shows that what really matters in the current edge detection is high-quality features, and we can make the encoder-decoder based detector great again even without complex training strategies and huge computational cost. The code is available at https://github.com/Li-yachuan/NBED.
In recent years, digital watermarking techniques based on deep learning have been widely studied. To achieve both imperceptibility and robustness of image watermarks, most current methods employ convolutional neural networks to build robust watermarking frameworks. However, despite the success of CNN-based watermarking models, they struggle to achieve robustness against geometric attacks due to the limitations of convolutional neural networks in capturing global and long-range relationships. To address this limitation, we propose a robust watermarking framework based on the Swin Transformer, named RoWSFormer. Specifically, we design the Locally-Channel Enhanced Swin Transformer Block as the core of both the encoder and decoder. This block utilizes the self-attention mechanism to capture global and long-range information, thereby significantly improving adaptation to geometric distortions. Additionally, we construct the Frequency-Enhanced Transformer Block to extract frequency domain information, which further strengthens the robustness of the watermarking framework. Experimental results demonstrate that our RoWSFormer surpasses existing state-of-the-art watermarking methods. For most non-geometric attacks, RoWSFormer improves the PSNR by 3 dB while maintaining the same extraction accuracy. In the case of geometric attacks (such as rotation, scaling, and affine transformations), RoWSFormer achieves over a 6 dB improvement in PSNR, with extraction accuracy exceeding 97\%.
U-Net is currently the most widely used architecture for medical image segmentation. Benefiting from its unique encoder-decoder architecture and skip connections, it can effectively extract features from input images to segment target regions. The commonly used U-Net is typically based on convolutional operations or Transformers, modeling the dependencies between local or global information to accomplish medical image analysis tasks. However, convolutional layers, fully connected layers, and attention mechanisms used in this process introduce a significant number of parameters, often requiring the stacking of network layers to model complex nonlinear relationships, which can impact the training process. To address these issues, we propose TransUKAN. Specifically, we have improved the KAN to reduce memory usage and computational load. On this basis, we explored an effective combination of KAN, Transformer, and U-Net structures. This approach enhances the model's capability to capture nonlinear relationships by introducing only a small number of additional parameters and compensates for the Transformer structure's deficiency in local information extraction. We validated TransUKAN on multiple medical image segmentation tasks. Experimental results demonstrate that TransUKAN achieves excellent performance with significantly reduced parameters. The code will be available athttps://github.com/wuyanlin-wyl/TransUKAN.
Visual localization plays an important role in the applications of Augmented Reality (AR), which enable AR devices to obtain their 6-DoF pose in the pre-build map in order to render virtual content in real scenes. However, most existing approaches can not perform novel view rendering and require large storage capacities for maps. To overcome these limitations, we propose an efficient visual localization method capable of high-quality rendering with fewer parameters. Specifically, our approach leverages 3D Gaussian primitives as the scene representation. To ensure precise 2D-3D correspondences for pose estimation, we develop an unbiased 3D scene-specific descriptor decoder for Gaussian primitives, distilled from a constructed feature volume. Additionally, we introduce a salient 3D landmark selection algorithm that selects a suitable primitive subset based on the saliency score for localization. We further regularize key Gaussian primitives to prevent anisotropic effects, which also improves localization performance. Extensive experiments on two widely used datasets demonstrate that our method achieves superior or comparable rendering and localization performance to state-of-the-art implicit-based visual localization approaches. Project page: \href{https://zju3dv.github.io/splatloc}{https://zju3dv.github.io/splatloc}.
Recent studies have showcased remarkable capabilities of decoder-only models in many NLP tasks, including translation. Yet, the machine translation field has been largely dominated by encoder-decoder models based on the Transformer architecture. As a consequence, scaling laws of encoder-decoder models for neural machine translation have already been well studied, but decoder-only models have received less attention. This work explores the scaling laws of decoder-only models on the multilingual and multidomain translation task. We trained a collection of six decoder-only models, ranging from 70M to 7B parameters, on a sentence-level, multilingual and multidomain dataset. We conducted a series of experiments showing that the loss of decoder-only models can be estimated using a scaling law similar to the one discovered for large language models, but we also show that this scaling law has difficulties to generalize to too large models or to a different data distribution. We also study different scaling methods and show that scaling the depth and the width of a model lead to similar test loss improvements, but with different impact on the model's efficiency.
Language Models (LMs) recently incorporate mixture-of-experts layers consisting of a router and a collection of experts to scale up their parameter count given a fixed computational budget. Building on previous efforts indicating that token-expert assignments are predominantly influenced by token identities and positions, we trace routing decisions of similarity-annotated text pairs to evaluate the context sensitivity of learned token-expert assignments. We observe that routing in encoder layers mainly depends on (semantic) associations, but contextual cues provide an additional layer of refinement. Conversely, routing in decoder layers is more variable and markedly less sensitive to context.
Multilingual automatic speech recognition (ASR) in the medical domain serves as a foundational task for various downstream applications such as speech translation, spoken language understanding, and voice-activated assistants. This technology improves patient care by enabling efficient communication across language barriers, alleviating specialized workforce shortages, and facilitating improved diagnosis and treatment, particularly during pandemics. In this work, we introduce MultiMed, the first multilingual medical ASR dataset, along with the first collection of small-to-large end-to-end medical ASR models, spanning five languages: Vietnamese, English, German, French, and Mandarin Chinese. To our best knowledge, MultiMed stands as the world's largest medical ASR dataset across all major benchmarks: total duration, number of recording conditions, number of accents, and number of speaking roles. Furthermore, we present the first multilinguality study for medical ASR, which includes reproducible empirical baselines, a monolinguality-multilinguality analysis, Attention Encoder Decoder (AED) vs Hybrid comparative study and a linguistic analysis. We present practical ASR end-to-end training schemes optimized for a fixed number of trainable parameters that are common in industry settings. All code, data, and models are available online: https://github.com/leduckhai/MultiMed/tree/master/MultiMed.
Current common interactions with language models is through full inference. This approach may not necessarily align with the model's internal knowledge. Studies show discrepancies between prompts and internal representations. Most focus on sentence understanding. We study the discrepancy of word semantics understanding in internal and external mismatch across Encoder-only, Decoder-only, and Encoder-Decoder pre-trained language models.
We present Uni-DVPS, a unified model for Depth-aware Video Panoptic Segmentation (DVPS) that jointly tackles distinct vision tasks, i.e., video panoptic segmentation, monocular depth estimation, and object tracking. In contrast to the prior works that adopt diverged decoder networks tailored for each task, we propose an architecture with a unified Transformer decoder network. We design a single Transformer decoder network for multi-task learning to increase shared operations to facilitate the synergies between tasks and exhibit high efficiency. We also observe that our unified query learns instance-aware representation guided by multi-task supervision, which encourages query-based tracking and obviates the need for training extra tracking module. We validate our architectural design choices with experiments on Cityscapes-DVPS and SemKITTI-DVPS datasets. The performances of all tasks are jointly improved, and we achieve state-of-the-art results on DVPQ metric for both datasets.
Small language models (SLMs), despite their widespread adoption in modern smart devices, have received significantly less academic attention compared to their large language model (LLM) counterparts, which are predominantly deployed in data centers and cloud environments. While researchers continue to improve the capabilities of LLMs in the pursuit of artificial general intelligence, SLM research aims to make machine intelligence more accessible, affordable, and efficient for everyday tasks. Focusing on transformer-based, decoder-only language models with 100M-5B parameters, we survey 59 state-of-the-art open-source SLMs, analyzing their technical innovations across three axes: architectures, training datasets, and training algorithms. In addition, we evaluate their capabilities in various domains, including commonsense reasoning, in-context learning, mathematics, and coding. To gain further insight into their on-device runtime costs, we benchmark their inference latency and memory footprints. Through in-depth analysis of our benchmarking data, we offer valuable insights to advance research in this field.
This project, titled "Machine Translation with Large Language Models: Decoder-only vs. Encoder-Decoder," aims to develop a multilingual machine translation (MT) model. Focused on Indian regional languages, especially Telugu, Tamil, and Malayalam, the model seeks to enable accurate and contextually appropriate translations across diverse language pairs. By comparing Decoder-only and Encoder-Decoder architectures, the project aims to optimize translation quality and efficiency, advancing cross-linguistic communication tools.The primary objective is to develop a model capable of delivering high-quality translations that are accurate and contextually appropriate. By leveraging large language models, specifically comparing the effectiveness of Decoder-only and Encoder-Decoder architectures, the project seeks to optimize translation performance and efficiency across multilingual contexts. Through rigorous experimentation and analysis, this project aims to advance the field of machine translation, contributing valuable insights into the effectiveness of different model architectures and paving the way for enhanced cross-linguistic communication tools.
The transducer model trained based on sequence-level criterion requires a lot of memory due to the generation of the large probability matrix. We proposed a lightweight transducer model based on frame-level criterion, which uses the results of the CTC forced alignment algorithm to determine the label for each frame. Then the encoder output can be combined with the decoder output at the corresponding time, rather than adding each element output by the encoder to each element output by the decoder as in the transducer. This significantly reduces memory and computation requirements. To address the problem of imbalanced classification caused by excessive blanks in the label, we decouple the blank and non-blank probabilities and truncate the gradient of the blank classifier to the main network. Experiments on the AISHELL-1 demonstrate that this enables the lightweight transducer to achieve similar results to transducer. Additionally, we use richer information to predict the probability of blank, achieving superior results to transducer.
In recent years, encoder-decoder networks have focused on expanding receptive fields and incorporating multi-scale context to capture global features for objects of varying sizes. However, as networks deepen, they often discard fine spatial details, impairing precise object localization. Additionally, conventional decoders' use of interpolation for upsampling leads to a loss of global context, diminishing edge segmentation accuracy. To address the above problems, we propose a novel parallel multi-resolution encoder-decoder network, namely PMR-Net for short. First, we design a parallel multi-resolution encoder and a multi-resolution context encoder. The parallel multi-resolution encoder can extract and fuse multi-scale fine-grained local features in parallel for input images with different resolutions. The multi-resolution context encoder fuses the global context semantic features of different receptive fields from different encoder branches to maintain effectively the integrity of global information. Secondly, we design a parallel multi-resolution decoder symmetrical to the structure of parallel multi-resolution encoder. The decoder can continuously supplement the global context features of low-resolution branches to the feature maps of high-resolution branches, and effectively solve the problem of global context feature loss caused by upsampling operation in the decoding process. Extensive experiment results demonstrate that our proposed PMR-Net can achieve more accurate segmentation results than state-of-the-art methods on five public available datasets. Moreover, PMR-Net is also a flexible network framework, which can meet the requirements of different scenarios by adjusting the number of network layers and the number of parallel encoder-decoder branches.
Recently, while significant progress has been made in remote sensing image change captioning, existing methods fail to filter out areas unrelated to actual changes, making models susceptible to irrelevant features. In this article, we propose a novel multimodal framework for remote sensing image change captioning, guided by Key Change Features and Instruction-tuned (KCFI). This framework aims to fully leverage the intrinsic knowledge of large language models through visual instructions and enhance the effectiveness and accuracy of change features using pixel-level change detection tasks. Specifically, KCFI includes a ViTs encoder for extracting bi-temporal remote sensing image features, a key feature perceiver for identifying critical change areas, a pixel-level change detection decoder to constrain key change features, and an instruction-tuned decoder based on a large language model. Moreover, to ensure that change description and change detection tasks are jointly optimized, we employ a dynamic weight-averaging strategy to balance the losses between the two tasks. We also explore various feature combinations for visual fine-tuning instructions and demonstrate that using only key change features to guide the large language model is the optimal choice. To validate the effectiveness of our approach, we compare it against several state-of-the-art change captioning methods on the LEVIR-CC dataset, achieving the best performance. Our code will be available at https://github.com/yangcong356/KCFI.git.
In this work, we significantly enhance masked particle modeling (MPM), a self-supervised learning scheme for constructing highly expressive representations of unordered sets relevant to developing foundation models for high-energy physics. In MPM, a model is trained to recover the missing elements of a set, a learning objective that requires no labels and can be applied directly to experimental data. We achieve significant performance improvements over previous work on MPM by addressing inefficiencies in the implementation and incorporating a more powerful decoder. We compare several pre-training tasks and introduce new reconstruction methods that utilize conditional generative models without data tokenization or discretization. We show that these new methods outperform the tokenized learning objective from the original MPM on a new test bed for foundation models for jets, which includes using a wide variety of downstream tasks relevant to jet physics, such as classification, secondary vertex finding, and track identification.
Open-vocabulary video visual relationship detection aims to expand video visual relationship detection beyond annotated categories by detecting unseen relationships between both seen and unseen objects in videos. Existing methods usually use trajectory detectors trained on closed datasets to detect object trajectories, and then feed these trajectories into large-scale pre-trained vision-language models to achieve open-vocabulary classification. Such heavy dependence on the pre-trained trajectory detectors limits their ability to generalize to novel object categories, leading to performance degradation. To address this challenge, we propose to unify object trajectory detection and relationship classification into an end-to-end open-vocabulary framework. Under this framework, we propose a relationship-aware open-vocabulary trajectory detector. It primarily consists of a query-based Transformer decoder, where the visual encoder of CLIP is distilled for frame-wise open-vocabulary object detection, and a trajectory associator. To exploit relationship context during trajectory detection, a relationship query is embedded into the Transformer decoder, and accordingly, an auxiliary relationship loss is designed to enable the decoder to perceive the relationships between objects explicitly. Moreover, we propose an open-vocabulary relationship classifier that leverages the rich semantic knowledge of CLIP to discover novel relationships. To adapt CLIP well to relationship classification, we design a multi-modal prompting method that employs spatio-temporal visual prompting for visual representation and vision-guided language prompting for language input. Extensive experiments on two public datasets, VidVRD and VidOR, demonstrate the effectiveness of our framework. Our framework is also applied to a more difficult cross-dataset scenario to further demonstrate its generalization ability.