Does the intrinsic curvature of complex networks hold the key to unveiling graph anomalies that conventional approaches overlook? Reconstruction-based graph anomaly detection (GAD) methods overlook such geometric outliers, focusing only on structural and attribute-level anomalies. To this end, we propose CurvGAD - a mixed-curvature graph autoencoder that introduces the notion of curvature-based geometric anomalies. CurvGAD introduces two parallel pipelines for enhanced anomaly interpretability: (1) Curvature-equivariant geometry reconstruction, which focuses exclusively on reconstructing the edge curvatures using a mixed-curvature, Riemannian encoder and Gaussian kernel-based decoder; and (2) Curvature-invariant structure and attribute reconstruction, which decouples structural and attribute anomalies from geometric irregularities by regularizing graph curvature under discrete Ollivier-Ricci flow, thereby isolating the non-geometric anomalies. By leveraging curvature, CurvGAD refines the existing anomaly classifications and identifies new curvature-driven anomalies. Extensive experimentation over 10 real-world datasets (both homophilic and heterophilic) demonstrates an improvement of up to 6.5% over state-of-the-art GAD methods.
Multiple instance learning (MIL)-based framework has become the mainstream for processing the whole slide image (WSI) with giga-pixel size and hierarchical image context in digital pathology. However, these methods heavily depend on a substantial number of bag-level labels and solely learn from the original slides, which are easily affected by variations in data distribution. Recently, vision language model (VLM)-based methods introduced the language prior by pre-training on large-scale pathological image-text pairs. However, the previous text prompt lacks the consideration of pathological prior knowledge, therefore does not substantially boost the model's performance. Moreover, the collection of such pairs and the pre-training process are very time-consuming and source-intensive.To solve the above problems, we propose a dual-scale vision-language multiple instance learning (ViLa-MIL) framework for whole slide image classification. Specifically, we propose a dual-scale visual descriptive text prompt based on the frozen large language model (LLM) to boost the performance of VLM effectively. To transfer the VLM to process WSI efficiently, for the image branch, we propose a prototype-guided patch decoder to aggregate the patch features progressively by grouping similar patches into the same prototype; for the text branch, we introduce a context-guided text decoder to enhance the text features by incorporating the multi-granular image contexts. Extensive studies on three multi-cancer and multi-center subtyping datasets demonstrate the superiority of ViLa-MIL.
Decoder-only language models have the ability to dynamically switch between various computational tasks based on input prompts. Despite many successful applications of prompting, there is very limited understanding of the internal mechanism behind such flexibility. In this work, we investigate how different prompting methods affect the geometry of representations in these models. Employing a framework grounded in statistical physics, we reveal that various prompting techniques, while achieving similar performance, operate through distinct representational mechanisms for task adaptation. Our analysis highlights the critical role of input distribution samples and label semantics in few-shot in-context learning. We also demonstrate evidence of synergistic and interfering interactions between different tasks on the representational level. Our work contributes to the theoretical understanding of large language models and lays the groundwork for developing more effective, representation-aware prompting strategies.
Decoder-only transformers lead to a step-change in capability of large language models. However, opinions are mixed as to whether they are really planning or reasoning. A path to making progress in this direction is to study the model's behavior in a setting with carefully controlled data. Then interpret the learned representations and reverse-engineer the computation performed internally. We study decoder-only transformer language models trained from scratch to predict shortest paths on simple, connected and undirected graphs. In this setting, the representations and the dynamics learned by the model are interpretable. We present three major results: (1) Two-layer decoder-only language models can learn to predict shortest paths on simple, connected graphs containing up to 10 nodes. (2) Models learn a graph embedding that is correlated with the spectral decomposition of the line graph. (3) Following the insights, we discover a novel approximate path-finding algorithm Spectral Line Navigator (SLN) that finds shortest path by greedily selecting nodes in the space of spectral embedding of the line graph.
The hemorrhagic lesion segmentation plays a critical role in ophthalmic diagnosis, directly influencing early disease detection, treatment planning, and therapeutic efficacy evaluation. However, the task faces significant challenges due to lesion morphological variability, indistinct boundaries, and low contrast with background tissues. To improve diagnostic accuracy and treatment outcomes, developing advanced segmentation techniques remains imperative. This paper proposes an adversarial learning-based dynamic architecture adjustment approach that integrates hierarchical U-shaped encoder-decoder, residual blocks, attention mechanisms, and ASPP modules. By dynamically optimizing feature fusion, our method enhances segmentation performance. Experimental results demonstrate a Dice coefficient of 0.6802, IoU of 0.5602, Recall of 0.766, Precision of 0.6525, and Accuracy of 0.9955, effectively addressing the challenges in fundus image hemorrhage segmentation.[* Corresponding author.]
Medical images are often high-resolution and lose important detail if downsampled, making pixel-level methods such as semantic segmentation much less efficient if performed on a low-dimensional image. We propose a low-rank Matryoshka projection and a hybrid segmenting architecture that preserves important information while retaining sufficient pixel geometry for pixel-level tasks. We design the Matryoshka Autoencoder (MatAE-U-Net) which combines the hierarchical encoding of the Matryoshka Autoencoder with the spatial reconstruction capabilities of a U-Net decoder, leveraging multi-scale feature extraction and skip connections to enhance accuracy and generalisation. We apply it to the problem of segmenting the left ventricle (LV) in echocardiographic images using the Stanford EchoNet-D dataset, including 1,000 standardised video-mask pairs of cardiac ultrasound videos resized to 112x112 pixels. The MatAE-UNet model achieves a Mean IoU of 77.68\%, Mean Pixel Accuracy of 97.46\%, and Dice Coefficient of 86.91\%, outperforming the baseline U-Net, which attains a Mean IoU of 74.70\%, Mean Pixel Accuracy of 97.31\%, and Dice Coefficient of 85.20\%. The results highlight the potential of using the U-Net in the recursive Matroshka latent space for imaging problems with low-contrast such as echocardiographic analysis.
Extracting lane topology from perspective views (PV) is crucial for planning and control in autonomous driving. This approach extracts potential drivable trajectories for self-driving vehicles without relying on high-definition (HD) maps. However, the unordered nature and weak long-range perception of the DETR-like framework can result in misaligned segment endpoints and limited topological prediction capabilities. Inspired by the learning of contextual relationships in language models, the connectivity relations in roads can be characterized as explicit topology sequences. In this paper, we introduce Topo2Seq, a novel approach for enhancing topology reasoning via topology sequences learning. The core concept of Topo2Seq is a randomized order prompt-to-sequence learning between lane segment decoder and topology sequence decoder. The dual-decoder branches simultaneously learn the lane topology sequences extracted from the Directed Acyclic Graph (DAG) and the lane graph containing geometric information. Randomized order prompt-to-sequence learning extracts unordered key points from the lane graph predicted by the lane segment decoder, which are then fed into the prompt design of the topology sequence decoder to reconstruct an ordered and complete lane graph. In this way, the lane segment decoder learns powerful long-range perception and accurate topological reasoning from the topology sequence decoder. Notably, topology sequence decoder is only introduced during training and does not affect the inference efficiency. Experimental evaluations on the OpenLane-V2 dataset demonstrate the state-of-the-art performance of Topo2Seq in topology reasoning.
Mass spectrometry plays a fundamental role in elucidating the structures of unknown molecules and subsequent scientific discoveries. One formulation of the structure elucidation task is the conditional de novo generation of molecular structure given a mass spectrum. Toward a more accurate and efficient scientific discovery pipeline for small molecules, we present DiffMS, a formula-restricted encoder-decoder generative network that achieves state-of-the-art performance on this task. The encoder utilizes a transformer architecture and models mass spectra domain knowledge such as peak formulae and neutral losses, and the decoder is a discrete graph diffusion model restricted by the heavy-atom composition of a known chemical formula. To develop a robust decoder that bridges latent embeddings and molecular structures, we pretrain the diffusion decoder with fingerprint-structure pairs, which are available in virtually infinite quantities, compared to structure-spectrum pairs that number in the tens of thousands. Extensive experiments on established benchmarks show that DiffMS outperforms existing models on de novo molecule generation. We provide several ablations to demonstrate the effectiveness of our diffusion and pretraining approaches and show consistent performance scaling with increasing pretraining dataset size. DiffMS code is publicly available at https://github.com/coleygroup/DiffMS.
Recent advancements in neural audio codecs have enabled the use of tokenized audio representations in various audio generation tasks, such as text-to-speech, text-to-audio, and text-to-music generation. Leveraging this approach, we propose TokenSynth, a novel neural synthesizer that utilizes a decoder-only transformer to generate desired audio tokens from MIDI tokens and CLAP (Contrastive Language-Audio Pretraining) embedding, which has timbre-related information. Our model is capable of performing instrument cloning, text-to-instrument synthesis, and text-guided timbre manipulation without any fine-tuning. This flexibility enables diverse sound design and intuitive timbre control. We evaluated the quality of the synthesized audio, the timbral similarity between synthesized and target audio/text, and synthesis accuracy (i.e., how accurately it follows the input MIDI) using objective measures. TokenSynth demonstrates the potential of leveraging advanced neural audio codecs and transformers to create powerful and versatile neural synthesizers. The source code, model weights, and audio demos are available at: https://github.com/KyungsuKim42/tokensynth
Remote sensing image captioning aims to generate descriptive text from remote sensing images, typically employing an encoder-decoder framework. In this setup, a convolutional neural network (CNN) extracts feature representations from the input image, which then guide the decoder in a sequence-to-sequence caption generation process. Although much research has focused on refining the decoder, the quality of image representations from the encoder remains crucial for accurate captioning. This paper introduces a novel approach that integrates features from two distinct CNN based encoders, capturing complementary information to enhance caption generation. Additionally, we propose a weighted averaging technique to combine the outputs of all GRUs in the stacked decoder. Furthermore, a comparison-based beam search strategy is incorporated to refine caption selection. The results demonstrate that our fusion-based approach, along with the enhanced stacked decoder, significantly outperforms both the transformer-based state-of-the-art model and other LSTM-based baselines.
Hallucinated facts in large language models (LLMs) have recently been shown to obey a statistical lower bound determined by the monofact rate (related to the classical Good-Turing missing mass estimator) minus model miscalibration (Kalai & Vempala, 2024). We present the first empirical investigation of this three-way relationship in classical n-gram models and fine-tuned encoder-decoder Transformers. By generating training data from Pareto distributions with varying shape parameters, we systematically control the monofact rates and establish its positive relationship with hallucination. To bridge theory and practice, we derive an empirical analog of the hallucination bound by replacing the population miscalibration term (Section 2.1) with an empirical bin-wise KL divergence and confirm its practical viability. We then introduce selective upweighting -- a simple yet effective technique that strategically repeats as little as 5% of training examples -- to deliberately inject miscalibration into the model. This intervention reduces hallucination by up to 40%, challenging universal deduplication policies. Our experiments reveal a critical trade-off: selective upweighting maintains pre-injection levels of accuracy while substantially reducing hallucination, whereas standard training gradually improves accuracy but fails to address persistently high hallucination, indicating an inherent tension in optimization objectives.
Molecular communication (MC) provides a foundational framework for information transmission in the Internet of Bio-Nano Things (IoBNT), where efficiency and reliability are crucial. However, the inherent limitations of molecular channels, such as low transmission rates, noise, and intersymbol interference (ISI), limit their ability to support complex data transmission. This paper proposes an end-to-end semantic learning framework designed to optimize task-oriented molecular communication, with a focus on biomedical diagnostic tasks under resource-constrained conditions. The proposed framework employs a deep encoder-decoder architecture to efficiently extract, quantize, and decode semantic features, prioritizing taskrelevant semantic information to enhance diagnostic classification performance. Additionally, a probabilistic channel network is introduced to approximate molecular propagation dynamics, enabling gradient-based optimization for end-to-end learning. Experimental results demonstrate that the proposed semantic framework improves diagnostic accuracy by at least 25% compared to conventional JPEG compression with LDPC coding methods under resource-constrained communication scenarios.
Advancements in computer vision technology have facilitated the extensive deployment of intelligent transportation systems and visual surveillance systems across various applications, including autonomous driving, public safety, and environmental monitoring. However, adverse weather conditions such as haze, rain, snow, and more complex mixed degradation can significantly degrade image quality. The degradation compromises the accuracy and reliability of these systems across various scenarios. To tackle the challenge of developing adaptable models for scene restoration, we introduce the unified scene recovery network (USRNet), capable of handling multiple types of image degradation. The USRNet features a sophisticated architecture consisting of a scene encoder, an attention-driven node independent learning mechanism (NILM), an edge decoder, and a scene restoration module. The scene encoder, powered by advanced residual blocks, extracts deep features from degraded images in a progressive manner, ensuring thorough encoding of degradation information. To enhance the USRNet's adaptability in diverse weather conditions, we introduce NILM, which enables the network to learn and respond to different scenarios with precision, thereby increasing its robustness. The edge decoder is designed to extract edge features with precision, which is essential for maintaining image sharpness. Experimental results demonstrate that USRNet surpasses existing methods in handling complex imaging degradations, thereby improving the accuracy and reliability of visual systems across diverse scenarios. The code resources for this work can be accessed in https://github.com/LouisYxLu/USRNet.
Existing encoder-free vision-language models (VLMs) are rapidly narrowing the performance gap with their encoder-based counterparts, highlighting the promising potential for unified multimodal systems with structural simplicity and efficient deployment. We systematically clarify the performance gap between VLMs using pre-trained vision encoders, discrete tokenizers, and minimalist visual layers from scratch, deeply excavating the under-examined characteristics of encoder-free VLMs. We develop efficient strategies for encoder-free VLMs that rival mainstream encoder-based ones. After an in-depth investigation, we launch EVEv2.0, a new and improved family of encoder-free VLMs. We show that: (i) Properly decomposing and hierarchically associating vision and language within a unified model reduces interference between modalities. (ii) A well-designed training strategy enables effective optimization for encoder-free VLMs. Through extensive evaluation, our EVEv2.0 represents a thorough study for developing a decoder-only architecture across modalities, demonstrating superior data efficiency and strong vision-reasoning capability. Code is publicly available at: https://github.com/baaivision/EVE.
In recent years, deep learning with Convolutional Neural Networks (CNNs) has achieved remarkable results in the field of HMER (Handwritten Mathematical Expression Recognition). However, it remains challenging to improve performance with limited labeled training data. This paper presents, for the first time, a simple yet effective semi-supervised HMER framework by introducing dual-branch semi-supervised learning. Specifically, we simplify the conventional deep co-training from consistency regularization to cross-supervised learning, where the prediction of one branch is used as a pseudo-label to supervise the other branch directly end-to-end. Considering that the learning of the two branches tends to converge in the later stages of model optimization, we also incorporate a weak-to-strong strategy by applying different levels of augmentation to each branch, which behaves like expanding the training data and improving the quality of network training. Meanwhile, We propose a novel module, Global Dynamic Counting Module(GDCM), to enhance the performance of the HMER decoder, which alleviates recognition inaccuracies in long-distance formula recognition and the occurrence of repeated characters. We release our code at https://github.com/chenkehua/SemiHMER.
Historically, LLMs have been trained using either autoregressive (AR) or masked language modeling (MLM) objectives, with AR models gaining dominance in recent years. However, AR models are inherently incapable of masked infilling, which is the ability to predict masked tokens between past and future context. In contrast, MLM models suffer from intrinsic computational inefficiencies during both training and inference that hinder their scalability. This work introduces MARIA (Masked and Autoregressive Infilling Architecture), a novel approach that leverages the strengths of both paradigms to achieve state-of-the-art masked infilling performance. MARIA combines a pre-trained MLM and AR model by training a linear decoder that takes their concatenated hidden states as input. This minimal modification enables the AR model to perform infilling while retaining its inherent advantages in terms of faster inference with KV caching. Our results demonstrate that MARIA significantly outperforms existing methods, namely discrete diffusion models, on masked infilling tasks.
This study investigates continual fine-tuning strategies for deep learning in online longitudinal electroencephalography (EEG) motor imagery (MI) decoding within a causal setting involving a large user group and multiple sessions per participant. We are the first to explore such strategies across a large user group, as longitudinal adaptation is typically studied in the single-subject setting with a single adaptation strategy, which limits the ability to generalize findings. First, we examine the impact of different fine-tuning approaches on decoder performance and stability. Building on this, we integrate online test-time adaptation (OTTA) to adapt the model during deployment, complementing the effects of prior fine-tuning. Our findings demonstrate that fine-tuning that successively builds on prior subject-specific information improves both performance and stability, while OTTA effectively adapts the model to evolving data distributions across consecutive sessions, enabling calibration-free operation. These results offer valuable insights and recommendations for future research in longitudinal online MI decoding and highlight the importance of combining domain adaptation strategies for improving BCI performance in real-world applications. Clinical Relevance: Our investigation enables more stable and efficient long-term motor imagery decoding, which is critical for neurorehabilitation and assistive technologies.
Interpreting the internal mechanisms of large language models (LLMs) is crucial for improving their trustworthiness and utility. Prior work has primarily focused on mapping individual neurons to discrete semantic concepts. However, such mappings struggle to handle the inherent polysemanticity in LLMs, where individual neurons encode multiple, distinct concepts. Through a comprehensive analysis of both encoder and decoder-based LLMs across diverse datasets, we observe that even highly salient neurons, identified via various attribution techniques for specific semantic concepts, consistently exhibit polysemantic behavior. Importantly, activation magnitudes for fine-grained concepts follow distinct, often Gaussian-like distributions with minimal overlap. This observation motivates a shift from neuron attribution to range-based interpretation. We hypothesize that interpreting and manipulating neuron activation ranges would enable more precise interpretability and targeted interventions in LLMs. To validate our hypothesis, we introduce NeuronLens, a novel range-based interpretation and manipulation framework that provides a finer view of neuron activation distributions to localize concept attribution within a neuron. Extensive empirical evaluations demonstrate that NeuronLens significantly reduces unintended interference, while maintaining precise manipulation of targeted concepts, outperforming neuron attribution.
Non-autoregressive (NAR) generative models are valuable because they can handle diverse conditional generation tasks in a more principled way than their autoregressive (AR) counterparts, which are constrained by sequential dependency requirements. Recent advancements in NAR models, such as diffusion language models, have demonstrated superior performance in unconditional generation compared to AR models (e.g., GPTs) of similar sizes. However, such improvements do not always lead to improved conditional generation performance. We show that a key reason for this gap is the difficulty in generalizing to conditional probability queries unseen during training. As a result, strong unconditional generation performance does not guarantee high-quality conditional generation. This paper proposes Tractable Transformers (Tracformer), a Transformer-based generative model that is more robust to different conditional generation tasks. Unlike existing models that rely solely on global contextual features derived from full inputs, Tracformers incorporate a sparse Transformer encoder to capture both local and global contextual information. This information is routed through a decoder for conditional generation. Empirical results demonstrate that Tracformers achieve state-of-the-art conditional generation performance on text modeling compared to recent diffusion and AR model baselines.
Motivation: Proteins are of great significance in living organisms. However, understanding their functions encounters numerous challenges, such as insufficient integration of multimodal information, a large number of training parameters, limited flexibility of classification-based methods, and the lack of systematic evaluation metrics for protein Q&A systems. To tackle these issues, we propose the Prot2Chat framework. Results: We modified ProteinMPNN to encode protein sequence and structural information in a unified way. We used a large language model (LLM) to encode questions into vectors and developed a protein-text adapter to compress protein information into virtual tokens based on these vectors, achieving the early fusion of text and protein information. Finally, the same LLM reads the virtual tokens and the questions to generate answers. To optimize training efficiency, we froze the encoder and employed Low-Rank Adaptation (LoRA) techniques for the LLM. Experiments on two datasets show that both automated metrics and expert evaluations demonstrate the superior performance of our model, and zero-shot prediction results highlight its generalization ability. The models and codes are available at https://github.com/ wangzc1233/Prot2Chat. Contact: [email omitted] or [email omitted] Key words: Protein Q&A, Early-Fusion, LLM