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.
In this challenge, we explored text-based food hazard prediction with long tail distributed classes. The task was divided into two subtasks: (1) predicting whether a web text implies one of ten food-hazard categories and identifying the associated food category, and (2) providing a more fine-grained classification by assigning a specific label to both the hazard and the product. Our findings highlight that large language model-generated synthetic data can be highly effective for oversampling long-tail distributions. Furthermore, we find that fine-tuned encoder-only, encoder-decoder, and decoder-only systems achieve comparable maximum performance across both subtasks. During this challenge, we gradually released (under CC BY-NC-SA 4.0) a novel set of 6,644 manually labeled food-incident reports.
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.
Data center networks (DCNs) require a low-cost, low-power optical transceiver to handle increased traffic from generative artificial intelligence, video streaming services, and more. Improving the required signal-to-noise ratio (RSNR) by digital signal processing such as forward error correction (FEC) mitigates the requirements for electrical and optical components. The optical transceivers in DCNs exploit a low-complexity soft-decision (SD) FEC, consisting of short block-length linear error-correcting codes and a low-complexity SD decoder (SDD), such as a Chase decoder and ordered statistical decoding. The low complexity SDD efficiently approaches a maximum likelihood decoding (MLD). However, the decoding performance of MLD is limited by its finite block length. In this paper, we describe the detail of our proposed channel-polarized multilevel coding with iterative decoding (CP-MLC-ID), which improves the decoding performance. The 19.5$\%$-OH CP-MLC-ID 128-bit extended Bose-Chaudhuri-Hocquenghem (eBCH) and KP4 codes outperform the concatenated eBCH and KP4 codes with a net coding gain of 0.25 and 0.40 dB for the same and double the number of SDDs, respectively. We also investigate the dependency of the decoding performance on the size of a bit interleaver. The performance degradation of CP-MLC-ID using an 8-bit interleaver is about 0.1 dB compared to using the large-bit interleaver. Our results indicate that even a weak connection by exclusive-OR between codewords improves the decoding performance, compared to simple concatenated codes in the DCNs.
Purpose: To characterize the 3D structural phenotypes of the optic nerve head (ONH) in patients with glaucoma, high myopia, and concurrent high myopia and glaucoma, and to evaluate their variations across these conditions. Participants: A total of 685 optical coherence tomography (OCT) scans from 754 subjects of Singapore-Chinese ethnicity, including 256 healthy (H), 94 highly myopic (HM), 227 glaucomatous (G), and 108 highly myopic with glaucoma (HMG) cases. Methods: We segmented the retinal and connective tissues from OCT volumes and their boundary edges were converted into 3D point clouds. To classify the 3D point clouds into four ONH conditions, i.e., H, HM, G, and HMG, a specialized ensemble network was developed, consisting of an encoder to transform high-dimensional input data into a compressed latent vector, a decoder to reconstruct point clouds from the latent vector, and a classifier to categorize the point clouds into the four ONH conditions. Results: The classification network achieved high accuracy, distinguishing H, HM, G, and HMG classes with a micro-average AUC of 0.92 $\pm$ 0.03 on an independent test set. The decoder effectively reconstructed point clouds, achieving a Chamfer loss of 0.013 $\pm$ 0.002. Dimensionality reduction clustered ONHs into four distinct groups, revealing structural variations such as changes in retinal and connective tissue thickness, tilting and stretching of the disc and scleral canal opening, and alterations in optic cup morphology, including shallow or deep excavation, across the four conditions. Conclusions: This study demonstrated that ONHs exhibit distinct structural signatures across H, HM, G, and HMG conditions. The findings further indicate that ONH morphology provides sufficient information for classification into distinct clusters, with principal components capturing unique structural patterns within each group.
We introduce Gene42, a novel family of Genomic Foundation Models (GFMs) designed to manage context lengths of up to 192,000 base pairs (bp) at a single-nucleotide resolution. Gene42 models utilize a decoder-only (LLaMA-style) architecture with a dense self-attention mechanism. Initially trained on fixed-length sequences of 4,096 bp, our models underwent continuous pretraining to extend the context length to 192,000 bp. This iterative extension allowed for the comprehensive processing of large-scale genomic data and the capture of intricate patterns and dependencies within the human genome. Gene42 is the first dense attention model capable of handling such extensive long context lengths in genomics, challenging state-space models that often rely on convolutional operators among other mechanisms. Our pretrained models exhibit notably low perplexity values and high reconstruction accuracy, highlighting their strong ability to model genomic data. Extensive experiments on various genomic benchmarks have demonstrated state-of-the-art performance across multiple tasks, including biotype classification, regulatory region identification, chromatin profiling prediction, variant pathogenicity prediction, and species classification. The models are publicly available at huggingface.co/inceptionai.
Skills have been introduced to offline reinforcement learning (RL) as temporal abstractions to tackle complex, long-horizon tasks, promoting consistent behavior and enabling meaningful exploration. While skills in offline RL are predominantly modeled within a continuous latent space, the potential of discrete skill spaces remains largely underexplored. In this paper, we propose a compact discrete skill space for offline RL tasks supported by state-of-the-art transformer-based encoder and diffusion-based decoder. Coupled with a high-level policy trained via offline RL techniques, our method establishes a hierarchical RL framework where the trained diffusion decoder plays a pivotal role. Empirical evaluations show that the proposed algorithm, Discrete Diffusion Skill (DDS), is a powerful offline RL method. DDS performs competitively on Locomotion and Kitchen tasks and excels on long-horizon tasks, achieving at least a 12 percent improvement on AntMaze-v2 benchmarks compared to existing offline RL approaches. Furthermore, DDS offers improved interpretability, training stability, and online exploration compared to previous skill-based methods.
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.
In this digital world, people freely express their emotions using different social media platforms. As a result, modeling and integrating emotion-understanding models are vital for various human-computer interaction tasks such as decision-making, product and customer feedback analysis, political promotions, marketing research, and social media monitoring. As users express different emotions simultaneously in a single instance, annotating emotions in a multilabel setting such as the EthioEmo (Belay et al., 2025) dataset effectively captures this dynamic. Additionally, incorporating intensity, or the degree of emotion, is crucial, as emotions can significantly differ in their expressive strength and impact. This intensity is significant for assessing whether further action is necessary in decision-making processes, especially concerning negative emotions in applications such as healthcare and mental health studies. To enhance the EthioEmo dataset, we include annotations for the intensity of each labeled emotion. Furthermore, we evaluate various state-of-the-art encoder-only Pretrained Language Models (PLMs) and decoder-only Large Language Models (LLMs) to provide comprehensive benchmarking.
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.
Transformer-based time series forecasting has recently gained strong interest due to the ability of transformers to model sequential data. Most of the state-of-the-art architectures exploit either temporal or inter-channel dependencies, limiting their effectiveness in multivariate time-series forecasting where both types of dependencies are crucial. We propose Sentinel, a full transformer-based architecture composed of an encoder able to extract contextual information from the channel dimension, and a decoder designed to capture causal relations and dependencies across the temporal dimension. Additionally, we introduce a multi-patch attention mechanism, which leverages the patching process to structure the input sequence in a way that can be naturally integrated into the transformer architecture, replacing the multi-head splitting process. Extensive experiments on standard benchmarks demonstrate that Sentinel, because of its ability to "monitor" both the temporal and the inter-channel dimension, achieves better or comparable performance with respect to state-of-the-art approaches.
Modeling cardiovascular anatomies poses a significant challenge due to their complex, irregular structures and inherent pathological conditions. Numerical simulations, while accurate, are often computationally expensive, limiting their practicality in clinical settings. Traditional machine learning methods, on the other hand, often struggle with some major hurdles, including high dimensionality of the inputs, inability to effectively work with irregular grids, and preserving the time dependencies of responses in dynamic problems. In response to these challenges, we propose a geometry adaptive waveformer model to predict blood flow dynamics in the cardiovascular system. The framework is primarily composed of three components: a geometry encoder, a geometry decoder, and a waveformer. The encoder transforms input defined on the irregular domain to a regular domain using a graph operator-based network and signed distance functions. The waveformer operates on the transformed field on the irregular grid. Finally, the decoder reverses this process, transforming the output from the regular grid back to the physical space. We evaluate the efficacy of the approach on different sets of cardiovascular data.
In recent years, vision transformers with text decoder have demonstrated remarkable performance on Scene Text Recognition (STR) due to their ability to capture long-range dependencies and contextual relationships with high learning capacity. However, the computational and memory demands of these models are significant, limiting their deployment in resource-constrained applications. To address this challenge, we propose an efficient and accurate STR system. Specifically, we focus on improving the efficiency of encoder models by introducing a cascaded-transformers structure. This structure progressively reduces the vision token size during the encoding step, effectively eliminating redundant tokens and reducing computational cost. Our experimental results confirm that our STR system achieves comparable performance to state-of-the-art baselines while substantially decreasing computational requirements. In particular, for large-models, the accuracy remains same, 92.77 to 92.68, while computational complexity is almost halved with our structure.
Most Video-Large Language Models (Video-LLMs) adopt an encoder-decoder framework, where a vision encoder extracts frame-wise features for processing by a language model. However, this approach incurs high computational costs, introduces resolution biases, and struggles to capture fine-grained multimodal interactions. To overcome these limitations, we propose ELVA, an encoder-free Video-LLM that directly models nuanced video-language interactions without relying on a vision encoder. ELVA employs token merging to construct a bottom-up hierarchical representation and incorporates a video guidance supervisor for direct spatiotemporal representation learning. Additionally, a hybrid-resolution mechanism strategically integrates high- and low-resolution frames as inputs to achieve an optimal balance between performance and efficiency. With only 7M publicly available video-text pairs, ELVA achieves performance on par with encoder-based Video-LLMs while reducing FLOPs by up to 95\% and inference latency by 92\%, offering a scalable and efficient solution for real-time video understanding.
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.
Recently, 3D Gaussian Splatting (3DGS) has shown encouraging performance for open vocabulary scene understanding tasks. However, previous methods cannot distinguish 3D instance-level information, which usually predicts a heatmap between the scene feature and text query. In this paper, we propose PanoGS, a novel and effective 3D panoptic open vocabulary scene understanding approach. Technically, to learn accurate 3D language features that can scale to large indoor scenarios, we adopt the pyramid tri-plane to model the latent continuous parametric feature space and use a 3D feature decoder to regress the multi-view fused 2D feature cloud. Besides, we propose language-guided graph cuts that synergistically leverage reconstructed geometry and learned language cues to group 3D Gaussian primitives into a set of super-primitives. To obtain 3D consistent instance, we perform graph clustering based segmentation with SAM-guided edge affinity computation between different super-primitives. Extensive experiments on widely used datasets show better or more competitive performance on 3D panoptic open vocabulary scene understanding. Project page: \href{https://zju3dv.github.io/panogs}{https://zju3dv.github.io/panogs}.
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.
Contrastive learning in self-supervised settings primarily focuses on pre-training encoders, while decoders are typically introduced and trained separately for downstream dense prediction tasks. This conventional approach, however, overlooks the potential benefits of jointly pre-training both the encoder and decoder. In this paper, we propose DeCon: a framework-agnostic adaptation to convert an encoder-only self-supervised learning (SSL) contrastive approach to an efficient encoder-decoder framework that can be pre-trained in a contrastive manner. We first update the existing architecture to accommodate a decoder and its respective contrastive loss. We then introduce a weighted encoder-decoder contrastive loss with non-competing objectives that facilitates the joint encoder-decoder architecture pre-training. We adapt two established contrastive SSL frameworks tailored for dense prediction tasks, achieve new state-of-the-art results in COCO object detection and instance segmentation, and match state-of-the-art performance on Pascal VOC semantic segmentation. We show that our approach allows for pre-training a decoder and enhances the representation power of the encoder and its performance in dense prediction tasks. This benefit holds across heterogeneous decoder architectures between pre-training and fine-tuning and persists in out-of-domain, limited-data scenarios.