Accurate 3D shape representation is essential in engineering applications such as design, optimization, and simulation. In practice, engineering workflows require structured, part-aware representations, as objects are inherently designed as assemblies of distinct components. However, most existing methods either model shapes holistically or decompose them without predefined part structures, limiting their applicability in real-world design tasks. We propose PartSDF, a supervised implicit representation framework that explicitly models composite shapes with independent, controllable parts while maintaining shape consistency. Despite its simple single-decoder architecture, PartSDF outperforms both supervised and unsupervised baselines in reconstruction and generation tasks. We further demonstrate its effectiveness as a structured shape prior for engineering applications, enabling precise control over individual components while preserving overall coherence. Code available at https://github.com/cvlab-epfl/PartSDF.
Generative models are spearheading recent progress in deep learning, showcasing strong promise for trajectory sampling in dynamical systems as well. However, whereas latent space modeling paradigms have transformed image and video generation, similar approaches are more difficult for most dynamical systems. Such systems -- from chemical molecule structures to collective human behavior -- are described by interactions of entities, making them inherently linked to connectivity patterns, entity conservation, and the traceability of entities over time. Our approach, LaM-SLidE (Latent Space Modeling of Spatial Dynamical Systems via Linked Entities), bridges the gap between: (1) keeping the traceability of individual entities in a latent system representation, and (2) leveraging the efficiency and scalability of recent advances in image and video generation, where pre-trained encoder and decoder enable generative modeling directly in latent space. The core idea of LaM-SLidE is the introduction of identifier representations (IDs) that enable the retrieval of entity properties and entity composition from latent system representations, thus fostering traceability. Experimentally, across different domains, we show that LaM-SLidE performs favorably in terms of speed, accuracy, and generalizability. Code is available at https://github.com/ml-jku/LaM-SLidE .
Molecules have various computational representations, including numerical descriptors, strings, graphs, point clouds, and surfaces. Each representation method enables the application of various machine learning methodologies from linear regression to graph neural networks paired with large language models. To complement existing representations, we introduce the representation of molecules through vector-valued functions, or $n$-dimensional vector fields, that are parameterized by neural networks, which we denote molecular neural fields. Unlike surface representations, molecular neural fields capture external features and the hydrophobic core of macromolecules such as proteins. Compared to discrete graph or point representations, molecular neural fields are compact, resolution independent and inherently suited for interpolation in spatial and temporal dimensions. These properties inherited by molecular neural fields lend themselves to tasks including the generation of molecules based on their desired shape, structure, and composition, and the resolution-independent interpolation between molecular conformations in space and time. Here, we provide a framework and proofs-of-concept for molecular neural fields, namely, the parametrization and superresolution reconstruction of a protein-ligand complex using an auto-decoder architecture and the embedding of molecular volumes in latent space using an auto-encoder architecture.
Reduced Order Modeling is of paramount importance for efficiently inferring high-dimensional spatio-temporal fields in parametric contexts, enabling computationally tractable parametric analyses, uncertainty quantification and control. However, conventional dimensionality reduction techniques are typically limited to known and constant parameters, inefficient for nonlinear and chaotic dynamics, and uninformed to the actual system behavior. In this work, we propose sensor-driven SHallow REcurrent Decoder networks for Reduced Order Modeling (SHRED-ROM). Specifically, we consider the composition of a long short-term memory network, which encodes the temporal dynamics of limited sensor data in multiple scenarios, and a shallow decoder, which reconstructs the corresponding high-dimensional states. SHRED-ROM is a robust decoding-only strategy that circumvents the numerically unstable approximation of an inverse which is required by encoding-decoding schemes. To enhance computational efficiency and memory usage, the full-order state snapshots are reduced by, e.g., proper orthogonal decomposition, allowing for compressive training of the networks with minimal hyperparameter tuning. Through applications on chaotic and nonlinear fluid dynamics, we show that SHRED-ROM (i) accurately reconstructs the state dynamics for new parameter values starting from limited fixed or mobile sensors, independently on sensor placement, (ii) can cope with both physical, geometrical and time-dependent parametric dependencies, while being agnostic to their actual values, (iii) can accurately estimate unknown parameters, and (iv) can deal with different data sources, such as high-fidelity simulations, coupled fields and videos.
Current image tampering localization methods primarily rely on Convolutional Neural Networks (CNNs) and Transformers. While CNNs suffer from limited local receptive fields, Transformers offer global context modeling at the expense of quadratic computational complexity. Recently, the state space model Mamba has emerged as a competitive alternative, enabling linear-complexity global dependency modeling. Inspired by it, we propose a lightweight and effective FORensic network based on vision MAmba (ForMa) for blind image tampering localization. Firstly, ForMa captures multi-scale global features that achieves efficient global dependency modeling through linear complexity. Then the pixel-wise localization map is generated by a lightweight decoder, which employs a parameter-free pixel shuffle layer for upsampling. Additionally, a noise-assisted decoding strategy is proposed to integrate complementary manipulation traces from tampered images, boosting decoder sensitivity to forgery cues. Experimental results on 10 standard datasets demonstrate that ForMa achieves state-of-the-art generalization ability and robustness, while maintaining the lowest computational complexity. Code is available at https://github.com/multimediaFor/ForMa.
The deployment of advanced deep learning models for medical image segmentation is often constrained by the requirement for extensively annotated datasets. Weakly-supervised learning, which allows less precise labels, has become a promising solution to this challenge. Building on this approach, we propose QMaxViT-Unet+, a novel framework for scribble-supervised medical image segmentation. This framework is built on the U-Net architecture, with the encoder and decoder replaced by Multi-Axis Vision Transformer (MaxViT) blocks. These blocks enhance the model's ability to learn local and global features efficiently. Additionally, our approach integrates a query-based Transformer decoder to refine features and an edge enhancement module to compensate for the limited boundary information in the scribble label. We evaluate the proposed QMaxViT-Unet+ on four public datasets focused on cardiac structures, colorectal polyps, and breast cancer: ACDC, MS-CMRSeg, SUN-SEG, and BUSI. Evaluation metrics include the Dice similarity coefficient (DSC) and the 95th percentile of Hausdorff distance (HD95). Experimental results show that QMaxViT-Unet+ achieves 89.1\% DSC and 1.316mm HD95 on ACDC, 88.4\% DSC and 2.226mm HD95 on MS-CMRSeg, 71.4\% DSC and 4.996mm HD95 on SUN-SEG, and 69.4\% DSC and 50.122mm HD95 on BUSI. These results demonstrate that our method outperforms existing approaches in terms of accuracy, robustness, and efficiency while remaining competitive with fully-supervised learning approaches. This makes it ideal for medical image analysis, where high-quality annotations are often scarce and require significant effort and expense. The code is available at: https://github.com/anpc849/QMaxViT-Unet
This paper introduces the Large Memory Model (LM2), a decoder-only Transformer architecture enhanced with an auxiliary memory module that aims to address the limitations of standard Transformers in multi-step reasoning, relational argumentation, and synthesizing information distributed over long contexts. The proposed LM2 incorporates a memory module that acts as a contextual representation repository, interacting with input tokens via cross attention and updating through gating mechanisms. To preserve the Transformers general-purpose capabilities, LM2 maintains the original information flow while integrating a complementary memory pathway. Experimental results on the BABILong benchmark demonstrate that the LM2model outperforms both the memory-augmented RMT model by 37.1% and the baseline Llama-3.2 model by 86.3% on average across tasks. LM2 exhibits exceptional capabilities in multi-hop inference, numerical reasoning, and large-context question-answering. On the MMLU dataset, it achieves a 5.0% improvement over a pre-trained vanilla model, demonstrating that its memory module does not degrade performance on general tasks. Further, in our analysis, we explore the memory interpretability, effectiveness of memory modules, and test-time behavior. Our findings emphasize the importance of explicit memory in enhancing Transformer architectures.
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.
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
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.
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.
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.
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
Recently, large language model (LLM) based text-to-speech (TTS) systems have gradually become the mainstream in the industry due to their high naturalness and powerful zero-shot voice cloning capabilities.Here, we introduce the IndexTTS system, which is mainly based on the XTTS and Tortoise model. We add some novel improvements. Specifically, in Chinese scenarios, we adopt a hybrid modeling method that combines characters and pinyin, making the pronunciations of polyphonic characters and long-tail characters controllable. We also performed a comparative analysis of the Vector Quantization (VQ) with Finite-Scalar Quantization (FSQ) for codebook utilization of acoustic speech tokens. To further enhance the effect and stability of voice cloning, we introduce a conformer-based speech conditional encoder and replace the speechcode decoder with BigVGAN2. Compared with XTTS, it has achieved significant improvements in naturalness, content consistency, and zero-shot voice cloning. As for the popular TTS systems in the open-source, such as Fish-Speech, CosyVoice2, FireRedTTS and F5-TTS, IndexTTS has a relatively simple training process, more controllable usage, and faster inference speed. Moreover, its performance surpasses that of these systems. Our demos are available at https://index-tts.github.io.
MedSAM, a medical foundation model derived from the SAM architecture, has demonstrated notable success across diverse medical domains. However, its clinical application faces two major challenges: the dependency on labor-intensive manual prompt generation, which imposes a significant burden on clinicians, and the absence of semantic labeling in the generated segmentation masks for organs or lesions, limiting its practicality for non-expert users. To address these limitations, we propose AutoMedSAM, an end-to-end framework derived from SAM, designed to enhance usability and segmentation performance. AutoMedSAM retains MedSAM's image encoder and mask decoder structure while introducing a novel diffusion-based class prompt encoder. The diffusion-based encoder employs a dual-decoder structure to collaboratively generate prompt embeddings guided by sparse and dense prompt definitions. These embeddings enhance the model's ability to understand and process clinical imagery autonomously. With this encoder, AutoMedSAM leverages class prompts to embed semantic information into the model's predictions, transforming MedSAM's semi-automated pipeline into a fully automated workflow. Furthermore, AutoMedSAM employs an uncertainty-aware joint optimization strategy during training to effectively inherit MedSAM's pre-trained knowledge while improving generalization by integrating multiple loss functions. Experimental results across diverse datasets demonstrate that AutoMedSAM achieves superior performance while broadening its applicability to both clinical settings and non-expert users. Code is available at https://github.com/HP-ML/AutoPromptMedSAM.git.
Prompt caching in large language models (LLMs) results in data-dependent timing variations: cached prompts are processed faster than non-cached prompts. These timing differences introduce the risk of side-channel timing attacks. For example, if the cache is shared across users, an attacker could identify cached prompts from fast API response times to learn information about other users' prompts. Because prompt caching may cause privacy leakage, transparency around the caching policies of API providers is important. To this end, we develop and conduct statistical audits to detect prompt caching in real-world LLM API providers. We detect global cache sharing across users in seven API providers, including OpenAI, resulting in potential privacy leakage about users' prompts. Timing variations due to prompt caching can also result in leakage of information about model architecture. Namely, we find evidence that OpenAI's embedding model is a decoder-only Transformer, which was previously not publicly known.
Large Language Models (LLMs) are discovered to suffer from accurately retrieving key information. To address this, we propose Mask-Enhanced Autoregressive Prediction (MEAP), a simple yet effective training paradigm that seamlessly integrates Masked Language Modeling (MLM) into Next-Token Prediction (NTP) to enhance the latter's in-context retrieval capabilities. Specifically, MEAP first randomly masks a small fraction of input tokens and then directly performs the standard next-token prediction autoregressive using a decoder-only Transformer. MEAP eliminates the need for bidirectional attention or encoder-decoder architectures for MLM, incurring no additional computational overhead during pre-training or inference. Intensive experiments demonstrate that MEAP substantially outperforms NTP on key information retrieval and long-context reasoning tasks, while performing on par or better on commonsense reasoning tasks. The benefits of MEAP also extend to supervised fine-tuning, where it shows remarkable advantages in lost-in-the-middle scenarios, outperforming NTP by 11.77 percentage points. Our analysis indicates that MEAP's effectiveness arises from its ability to promote more distinguishable attention scores by concentrating on a reduced set of non-masked tokens. This mechanism improves the model's focus on task-relevant signals while mitigating the influence of peripheral context. These findings position MEAP as a promising training paradigm for large language models.
Recent advances in large language models (LLMs) have shown remarkable performance across diverse tasks. However, these models are typically deployed with fixed weights, which limits their ability to adapt dynamically to the variability inherent in real-world data during inference. This paper introduces ChamaleonLLM, a novel framework that enables inference-time adaptation of LLMs by leveraging batch-aware clustering and on-the-fly generation of low-rank updates. Unlike traditional fine-tuning approaches such as Low-Rank Adaptation (LoRA) or methods that rely on a fixed set of pre-learned uniforms (changeable masks), our method dynamically generates adaptive modifications to the decoder weights based on the aggregated statistics of clustered batches. By intelligently grouping similar inputs and computing context-aware low-rank updates via a hyper-network, ChamaleonLLM achieves significant performance gains, outperforming conventional LoRA methods while eliminating the overhead of maintaining multiple expert models. Our experiments highlight the potential of our approach to serve as a versatile and highly adaptive solution for language model inference. ChamaleonLLM is open-sourced to ensure the reproducibility of our experiments: https://anonymous.4open.science/r/ChamaleonLLM/