We propose LauraTSE, an Auto-Regressive Decoder-Only Language Model for Target Speaker Extraction (TSE) based on the LauraGPT backbone. It employs a small-scale auto-regressive decoder-only language model which takes the continuous representations for both the mixture and the reference speeches and produces the first few layers of the target speech's discrete codec representations. In addition, a one-step encoder-only language model reconstructs the sum of the predicted codec embeddings using both the mixture and the reference information. Our approach achieves superior or comparable performance to existing generative and discriminative TSE models. To the best of our knowledge, LauraTSE is the first single-task TSE model to leverage an auto-regressive decoder-only language model as the backbone.
Large Language Models (LLMs) can encode complex relationships in their latent spaces, yet harnessing them for optimization under uncertainty remains challenging. We address this gap with a novel architecture that reframes LLM finetuning as Gaussian process (GP) marginal likelihood optimization via deep kernel methods. We introduce LLM-based deep kernels, jointly optimized with GPs to preserve the benefits of both - LLMs to provide a rich and flexible input space for Bayesian optimization and - GPs to model this space with predictive uncertainty for more efficient sampling. Applied to Buchwald-Hartwig reaction optimization, our method nearly doubles the discovery rate of high-performing reactions compared to static LLM embeddings (from 24% to 43% coverage of the top 5% reactions in just 50 optimization iterations). We also observe a 14% improvement over domain-specific representations without requiring specialized features. Extensive empirical evaluation across 19 benchmarks - ranging from general chemistry to reaction and molecular property optimization - demonstrates our method's robustness, generality, and consistent improvements across: (1) tasks, (2) LLM architectures (encoder, decoder, encoder-decoder), (3) pretraining domains (chemistry-related or general-purpose) and (4) hyperparameter settings (tuned once on a single dataset). Finally, we explain these improvements: joint LLM-GP optimization through marginal likelihood implicitly performs contrastive learning, aligning representations to produce (1) better-structured embedding spaces, (2) improved uncertainty calibration, and (3) more efficient sampling - without requiring any external loss. This work provides both practical advances in sample-efficient optimization and insights into what makes effective Bayesian optimization.
Accurate surgical instrument segmentation is essential in cataract surgery for tasks such as skill assessment and workflow optimization. However, limited annotated data makes it difficult to develop fully automatic models. Prompt-based methods like SAM2 offer flexibility yet remain highly sensitive to the point prompt placement, often leading to inconsistent segmentations. We address this issue by introducing RP-SAM2, which incorporates a novel shift block and a compound loss function to stabilize point prompts. Our approach reduces annotator reliance on precise point positioning while maintaining robust segmentation capabilities. Experiments on the Cataract1k dataset demonstrate that RP-SAM2 improves segmentation accuracy, with a 2% mDSC gain, a 21.36% reduction in mHD95, and decreased variance across random single-point prompt results compared to SAM2. Additionally, on the CaDIS dataset, pseudo masks generated by RP-SAM2 for fine-tuning SAM2's mask decoder outperformed those generated by SAM2. These results highlight RP-SAM2 as a practical, stable and reliable solution for semi-automatic instrument segmentation in data-constrained medical settings. The code is available at https://github.com/BioMedIA-MBZUAI/RP-SAM2.
Continual learning in large language models (LLMs) is prone to catastrophic forgetting, where adapting to new tasks significantly degrades performance on previously learned ones. Existing methods typically rely on low-rank, parameter-efficient updates that limit the model's expressivity and introduce additional parameters per task, leading to scalability issues. To address these limitations, we propose a novel continual full fine-tuning approach leveraging adaptive singular value decomposition (SVD). Our method dynamically identifies task-specific low-rank parameter subspaces and constrains updates to be orthogonal to critical directions associated with prior tasks, thus effectively minimizing interference without additional parameter overhead or storing previous task gradients. We evaluate our approach extensively on standard continual learning benchmarks using both encoder-decoder (T5-Large) and decoder-only (LLaMA-2 7B) models, spanning diverse tasks including classification, generation, and reasoning. Empirically, our method achieves state-of-the-art results, up to 7% higher average accuracy than recent baselines like O-LoRA, and notably maintains the model's general linguistic capabilities, instruction-following accuracy, and safety throughout the continual learning process by reducing forgetting to near-negligible levels. Our adaptive SVD framework effectively balances model plasticity and knowledge retention, providing a practical, theoretically grounded, and computationally scalable solution for continual learning scenarios in large language models.
High-resolution segmentation is critical for precise disease diagnosis by extracting micro-imaging information from medical images. Existing transformer-based encoder-decoder frameworks have demonstrated remarkable versatility and zero-shot performance in medical segmentation. While beneficial, they usually require huge memory costs when handling large-size segmentation mask predictions, which are expensive to apply to real-world scenarios. To address this limitation, we propose a memory-efficient framework for high-resolution medical image segmentation, called HRMedSeg. Specifically, we first devise a lightweight gated vision transformer (LGViT) as our image encoder to model long-range dependencies with linear complexity. Then, we design an efficient cross-multiscale decoder (ECM-Decoder) to generate high-resolution segmentation masks. Moreover, we utilize feature distillation during pretraining to unleash the potential of our proposed model. Extensive experiments reveal that HRMedSeg outperforms state-of-the-arts in diverse high-resolution medical image segmentation tasks. In particular, HRMedSeg uses only 0.59GB GPU memory per batch during fine-tuning, demonstrating low training costs. Besides, when HRMedSeg meets the Segment Anything Model (SAM), our HRMedSegSAM takes 0.61% parameters of SAM-H. The code is available at https://github.com/xq141839/HRMedSeg.
In this work, we introduce implicit Finite Operator Learning (iFOL) for the continuous and parametric solution of partial differential equations (PDEs) on arbitrary geometries. We propose a physics-informed encoder-decoder network to establish the mapping between continuous parameter and solution spaces. The decoder constructs the parametric solution field by leveraging an implicit neural field network conditioned on a latent or feature code. Instance-specific codes are derived through a PDE encoding process based on the second-order meta-learning technique. In training and inference, a physics-informed loss function is minimized during the PDE encoding and decoding. iFOL expresses the loss function in an energy or weighted residual form and evaluates it using discrete residuals derived from standard numerical PDE methods. This approach results in the backpropagation of discrete residuals during both training and inference. iFOL features several key properties: (1) its unique loss formulation eliminates the need for the conventional encode-process-decode pipeline previously used in operator learning with conditional neural fields for PDEs; (2) it not only provides accurate parametric and continuous fields but also delivers solution-to-parameter gradients without requiring additional loss terms or sensitivity analysis; (3) it can effectively capture sharp discontinuities in the solution; and (4) it removes constraints on the geometry and mesh, making it applicable to arbitrary geometries and spatial sampling (zero-shot super-resolution capability). We critically assess these features and analyze the network's ability to generalize to unseen samples across both stationary and transient PDEs. The overall performance of the proposed method is promising, demonstrating its applicability to a range of challenging problems in computational mechanics.
Epilepsy is a common neurological disorder that affects around 65 million people worldwide. Detecting seizures quickly and accurately is vital, given the prevalence and severity of the associated complications. Recently, deep learning-based automated seizure detection methods have emerged as solutions; however, most existing methods require extensive post-processing and do not effectively handle the crucial long-range patterns in EEG data. In this work, we propose SeizureTransformer, a simple model comprised of (i) a deep encoder comprising 1D convolutions (ii) a residual CNN stack and a transformer encoder to embed previous output into high-level representation with contextual information, and (iii) streamlined decoder which converts these features into a sequence of probabilities, directly indicating the presence or absence of seizures at every time step. Extensive experiments on public and private EEG seizure detection datasets demonstrate that our model significantly outperforms existing approaches (ranked in the first place in the 2025 "seizure detection challenge" organized in the International Conference on Artificial Intelligence in Epilepsy and Other Neurological Disorders), underscoring its potential for real-time, precise seizure detection.
Vision Transformers (ViTs) have shown remarkable performance and scalability across various computer vision tasks. To apply single-scale ViTs to image segmentation, existing methods adopt a convolutional adapter to generate multi-scale features, a pixel decoder to fuse these features, and a Transformer decoder that uses the fused features to make predictions. In this paper, we show that the inductive biases introduced by these task-specific components can instead be learned by the ViT itself, given sufficiently large models and extensive pre-training. Based on these findings, we introduce the Encoder-only Mask Transformer (EoMT), which repurposes the plain ViT architecture to conduct image segmentation. With large-scale models and pre-training, EoMT obtains a segmentation accuracy similar to state-of-the-art models that use task-specific components. At the same time, EoMT is significantly faster than these methods due to its architectural simplicity, e.g., up to 4x faster with ViT-L. Across a range of model sizes, EoMT demonstrates an optimal balance between segmentation accuracy and prediction speed, suggesting that compute resources are better spent on scaling the ViT itself rather than adding architectural complexity. Code: https://www.tue-mps.org/eomt/.
We introduce a novel visual tokenization framework that embeds a provable PCA-like structure into the latent token space. While existing visual tokenizers primarily optimize for reconstruction fidelity, they often neglect the structural properties of the latent space -- a critical factor for both interpretability and downstream tasks. Our method generates a 1D causal token sequence for images, where each successive token contributes non-overlapping information with mathematically guaranteed decreasing explained variance, analogous to principal component analysis. This structural constraint ensures the tokenizer extracts the most salient visual features first, with each subsequent token adding diminishing yet complementary information. Additionally, we identified and resolved a semantic-spectrum coupling effect that causes the unwanted entanglement of high-level semantic content and low-level spectral details in the tokens by leveraging a diffusion decoder. Experiments demonstrate that our approach achieves state-of-the-art reconstruction performance and enables better interpretability to align with the human vision system. Moreover, auto-regressive models trained on our token sequences achieve performance comparable to current state-of-the-art methods while requiring fewer tokens for training and inference.
Reliable high-definition (HD) map construction is crucial for the driving safety of autonomous vehicles. Although recent studies demonstrate improved performance, their generalization capability across unfamiliar driving scenes remains unexplored. To tackle this issue, we propose UIGenMap, an uncertainty-instructed structure injection approach for generalizable HD map vectorization, which concerns the uncertainty resampling in statistical distribution and employs explicit instance features to reduce excessive reliance on training data. Specifically, we introduce the perspective-view (PV) detection branch to obtain explicit structural features, in which the uncertainty-aware decoder is designed to dynamically sample probability distributions considering the difference in scenes. With probabilistic embedding and selection, UI2DPrompt is proposed to construct PV-learnable prompts. These PV prompts are integrated into the map decoder by designed hybrid injection to compensate for neglected instance structures. To ensure real-time inference, a lightweight Mimic Query Distillation is designed to learn from PV prompts, which can serve as an efficient alternative to the flow of PV branches. Extensive experiments on challenging geographically disjoint (geo-based) data splits demonstrate that our UIGenMap achieves superior performance, with +5.7 mAP improvement on the nuScenes dataset. Source code will be available at https://github.com/xiaolul2/UIGenMap.
Multi-organ segmentation holds paramount significance in many clinical tasks. In practice, compared to large fully annotated datasets, multiple small datasets are often more accessible and organs are not labelled consistently. Normally, an individual model is trained for each of these datasets, which is not an effective way of using data for model learning. It remains challenging to train a single model that can robustly learn from several partially labelled datasets due to label conflict and data imbalance problems. We propose MO-CTranS: a single model that can overcome such problems. MO-CTranS contains a CNN-based encoder and a Transformer-based decoder, which are connected in a multi-resolution manner. Task-specific tokens are introduced in the decoder to help differentiate label discrepancies. Our method was evaluated and compared to several baseline models and state-of-the-art (SOTA) solutions on abdominal MRI datasets that were acquired in different views (i.e. axial and coronal) and annotated for different organs (i.e. liver, kidney, spleen). Our method achieved better performance (most were statistically significant) than the compared methods. Github link: https://github.com/naisops/MO-CTranS.
In multi-class unsupervised anomaly detection(MUAD), reconstruction-based methods learn to map input images to normal patterns to identify anomalous pixels. However, this strategy easily falls into the well-known "learning shortcut" issue when decoders fail to capture normal patterns and reconstruct both normal and abnormal samples naively. To address that, we propose to learn the input features in global and local manners, forcing the network to memorize the normal patterns more comprehensively. Specifically, we design a two-branch decoder block, named Omni-block. One branch corresponds to global feature learning, where we serialize two self-attention blocks but replace the query and (key, value) with learnable tokens, respectively, thus capturing global features of normal patterns concisely and thoroughly. The local branch comprises depth-separable convolutions, whose locality enables effective and efficient learning of local features for normal patterns. By stacking Omni-blocks, we build a framework, Omni-AD, to learn normal patterns of different granularity and reconstruct them progressively. Comprehensive experiments on public anomaly detection benchmarks show that our method outperforms state-of-the-art approaches in MUAD. Code is available at https://github.com/easyoo/Omni-AD.git
Generative Information Retrieval (GenIR) is a novel paradigm in which a transformer encoder-decoder model predicts document rankings based on a query in an end-to-end fashion. These GenIR models have received significant attention due to their simple retrieval architecture while maintaining high retrieval effectiveness. However, in contrast to established retrieval architectures like cross-encoders or bi-encoders, their internal computations remain largely unknown. Therefore, this work studies the internal retrieval process of GenIR models by applying methods based on mechanistic interpretability, such as patching and vocabulary projections. By replacing the GenIR encoder with one trained on fewer documents, we demonstrate that the decoder is the primary component responsible for successful retrieval. Our patching experiments reveal that not all components in the decoder are crucial for the retrieval process. More specifically, we find that a pass through the decoder can be divided into three stages: (I) the priming stage, which contributes important information for activating subsequent components in later layers; (II) the bridging stage, where cross-attention is primarily active to transfer query information from the encoder to the decoder; and (III) the interaction stage, where predominantly MLPs are active to predict the document identifier. Our findings indicate that interaction between query and document information occurs only in the last stage. We hope our results promote a better understanding of GenIR models and foster future research to overcome the current challenges associated with these models.
Many methods have been proposed for removing batch effects and aligning single-cell RNA (scRNA) datasets. However, performance is typically evaluated based on multiple parameters and few datasets, creating challenges in assessing which method is best for aligning data at scale. Here, we introduce the K-Neighbors Intersection (KNI) score, a single score that both penalizes batch effects and measures accuracy at cross-dataset cell-type label prediction alongside carefully curated small (scMARK) and large (scREF) benchmarks comprising 11 and 46 human scRNA studies respectively, where we have standardized author labels. Using the KNI score, we evaluate and optimize approaches for cross-dataset single-cell RNA integration. We introduce Batch Adversarial single-cell Variational Inference (BA-scVI), as a new variant of scVI that uses adversarial training to penalize batch-effects in the encoder and decoder, and show this approach outperforms other methods. In the resulting aligned space, we find that the granularity of cell-type groupings is conserved, supporting the notion that whole-organism cell-type maps can be created by a single model without loss of information.
Node importance estimation, a classical problem in network analysis, underpins various web applications. Previous methods either exploit intrinsic topological characteristics, e.g., graph centrality, or leverage additional information, e.g., data heterogeneity, for node feature enhancement. However, these methods follow the supervised learning setting, overlooking the fact that ground-truth node-importance data are usually partially labeled in practice. In this work, we propose the first semi-supervised node importance estimation framework, i.e., EASING, to improve learning quality for unlabeled data in heterogeneous graphs. Different from previous approaches, EASING explicitly captures uncertainty to reflect the confidence of model predictions. To jointly estimate the importance values and uncertainties, EASING incorporates DJE, a deep encoder-decoder neural architecture. DJE introduces distribution modeling for graph nodes, where the distribution representations derive both importance and uncertainty estimates. Additionally, DJE facilitates effective pseudo-label generation for the unlabeled data to enrich the training samples. Based on labeled and pseudo-labeled data, EASING develops effective semi-supervised heteroscedastic learning with varying node uncertainty regularization. Extensive experiments on three real-world datasets highlight the superior performance of EASING compared to competing methods. Codes are available via https://github.com/yankai-chen/EASING.
Recently, 3D Gaussian Splatting (3DGS) has emerged as a prominent framework for novel view synthesis, providing high fidelity and rapid rendering speed. However, the substantial data volume of 3DGS and its attributes impede its practical utility, requiring compression techniques for reducing memory cost. Nevertheless, the unorganized shape of 3DGS leads to difficulties in compression. To formulate unstructured attributes into normative distribution, we propose a well-structured tri-plane to encode Gaussian attributes, leveraging the distribution of attributes for compression. To exploit the correlations among adjacent Gaussians, K-Nearest Neighbors (KNN) is used when decoding Gaussian distribution from the Tri-plane. We also introduce Gaussian position information as a prior of the position-sensitive decoder. Additionally, we incorporate an adaptive wavelet loss, aiming to focus on the high-frequency details as iterations increase. Our approach has achieved results that are comparable to or surpass that of SOTA 3D Gaussians Splatting compression work in extensive experiments across multiple datasets. The codes are released at https://github.com/timwang2001/TC-GS.
TerraTorch is a fine-tuning and benchmarking toolkit for Geospatial Foundation Models built on PyTorch Lightning and tailored for satellite, weather, and climate data. It integrates domain-specific data modules, pre-defined tasks, and a modular model factory that pairs any backbone with diverse decoder heads. These components allow researchers and practitioners to fine-tune supported models in a no-code fashion by simply editing a training configuration. By consolidating best practices for model development and incorporating the automated hyperparameter optimization extension Iterate, TerraTorch reduces the expertise and time required to fine-tune or benchmark models on new Earth Observation use cases. Furthermore, TerraTorch directly integrates with GEO-Bench, allowing for systematic and reproducible benchmarking of Geospatial Foundation Models. TerraTorch is open sourced under Apache 2.0, available at https://github.com/IBM/terratorch, and can be installed via pip install terratorch.
Relation extraction (RE) is a standard information extraction task playing a major role in downstream applications such as knowledge discovery and question answering. Although decoder-only large language models are excelling in generative tasks, smaller encoder models are still the go to architecture for RE. In this paper, we revisit fine-tuning such smaller models using a novel dual-encoder architecture with a joint contrastive and cross-entropy loss. Unlike previous methods that employ a fixed linear layer for predicate representations, our approach uses a second encoder to compute instance-specific predicate representations by infusing them with real entity spans from corresponding input instances. We conducted experiments on two biomedical RE datasets and two general domain datasets. Our approach achieved F1 score improvements ranging from 1% to 2% over state-of-the-art methods with a simple but elegant formulation. Ablation studies justify the importance of various components built into the proposed architecture.
Online Action Detection (OAD) detects actions in streaming videos using past observations. State-of-the-art OAD approaches model past observations and their interactions with an anticipated future. The past is encoded using short- and long-term memories to capture immediate and long-range dependencies, while anticipation compensates for missing future context. We identify a training-inference discrepancy in existing OAD methods that hinders learning effectiveness. The training uses varying lengths of short-term memory, while inference relies on a full-length short-term memory. As a remedy, we propose a Context-enhanced Memory-Refined Transformer (CMeRT). CMeRT introduces a context-enhanced encoder to improve frame representations using additional near-past context. It also features a memory-refined decoder to leverage near-future generation to enhance performance. CMeRT achieves state-of-the-art in online detection and anticipation on THUMOS'14, CrossTask, and EPIC-Kitchens-100.
The perception system for autonomous driving generally requires to handle multiple diverse sub-tasks. However, current algorithms typically tackle individual sub-tasks separately, which leads to low efficiency when aiming at obtaining full-perception results. Some multi-task learning methods try to unify multiple tasks with one model, but do not solve the conflicts in multi-task learning. In this paper, we introduce M3Net, a novel multimodal and multi-task network that simultaneously tackles detection, segmentation, and 3D occupancy prediction for autonomous driving and achieves superior performance than single task model. M3Net takes multimodal data as input and multiple tasks via query-token interactions. To enhance the integration of multi-modal features for multi-task learning, we first propose the Modality-Adaptive Feature Integration (MAFI) module, which enables single-modality features to predict channel-wise attention weights for their high-performing tasks, respectively. Based on integrated features, we then develop task-specific query initialization strategies to accommodate the needs of detection/segmentation and 3D occupancy prediction. Leveraging the properly initialized queries, a shared decoder transforms queries and BEV features layer-wise, facilitating multi-task learning. Furthermore, we propose a Task-oriented Channel Scaling (TCS) module in the decoder to mitigate conflicts between optimizing for different tasks. Additionally, our proposed multi-task querying and TCS module support both Transformer-based decoder and Mamba-based decoder, demonstrating its flexibility to different architectures. M3Net achieves state-of-the-art multi-task learning performance on the nuScenes benchmarks.