Daily Papers

It has been observed that the input space of deep neural network classifiers can exhibit `fragmentation', where the model function rapidly changes class as the input space is traversed. The severity of this fragmentation tends to follow the double descent curve, achieving a maximum at the interpolation regime. We study this phenomenon in the context of image classification and ask whether fragmentation could be predictive of generalization performance. Using a fragmentation-based complexity measure, we show this to be possible by achieving good performance on the PGDL (Predicting Generalization in Deep Learning) benchmark. In addition, we report on new observations related to fragmentation, namely (i) fragmentation is not limited to the input space but occurs in the hidden representations as well, (ii) fragmentation follows the trends in the validation error throughout training, and (iii) fragmentation is not a direct result of increased weight norms. Together, this indicates that fragmentation is a phenomenon worth investigating further when studying the generalization ability of deep neural networks.

As with many other problems, real-world regression is plagued by the presence of noisy labels, an inevitable issue that demands our attention. Fortunately, much real-world data often exhibits an intrinsic property of continuously ordered correlations between labels and features, where data points with similar labels are also represented with closely related features. In response, we propose a novel approach named ConFrag, where we collectively model the regression data by transforming them into disjoint yet contrasting fragmentation pairs. This enables the training of more distinctive representations, enhancing the ability to select clean samples. Our ConFrag framework leverages a mixture of neighboring fragments to discern noisy labels through neighborhood agreement among expert feature extractors. We extensively perform experiments on six newly curated benchmark datasets of diverse domains, including age prediction, price prediction, and music production year estimation. We also introduce a metric called Error Residual Ratio (ERR) to better account for varying degrees of label noise. Our approach consistently outperforms fourteen state-of-the-art baselines, being robust against symmetric and random Gaussian label noise.

High-resolution inputs enable Large Vision-Language Models (LVLMs) to discern finer visual details, enhancing their comprehension capabilities. To reduce the training and computation costs caused by high-resolution input, one promising direction is to use sliding windows to slice the input into uniform patches, each matching the input size of the well-trained vision encoder. Although efficient, this slicing strategy leads to the fragmentation of original input, i.e., the continuity of contextual information and spatial geometry is lost across patches, adversely affecting performance in cross-patch context perception and position-specific tasks. To overcome these shortcomings, we introduce HiRes-LLaVA, a novel framework designed to efficiently process any size of high-resolution input without altering the original contextual and geometric information. HiRes-LLaVA comprises two innovative components: (i) a SliceRestore adapter that reconstructs sliced patches into their original form, efficiently extracting both global and local features via down-up-sampling and convolution layers, and (ii) a Self-Mining Sampler to compresses the vision tokens based on themselves, preserving the original context and positional information while reducing training overhead. To assess the ability of handling context fragmentation, we construct a new benchmark, EntityGrid-QA, consisting of edge-related and position-related tasks. Our comprehensive experiments demonstrate the superiority of HiRes-LLaVA on both existing public benchmarks and on EntityGrid-QA, particularly on document-oriented tasks, establishing new standards for handling high-resolution inputs.

The incorporation of high-resolution visual input equips multimodal large language models (MLLMs) with enhanced visual perception capabilities for real-world tasks. However, most existing high-resolution MLLMs rely on a cropping-based approach to process images, which leads to fragmented visual encoding and a sharp increase in redundant tokens. To tackle these issues, we propose the FALCON model. FALCON introduces a novel visual register technique to simultaneously: 1) Eliminate redundant tokens at the stage of visual encoding. To directly address the visual redundancy present in the output of vision encoder, we propose a Register-based Representation Compacting (ReCompact) mechanism. This mechanism introduces a set of learnable visual registers designed to adaptively aggregate essential information while discarding redundancy. It enables the encoder to produce a more compact visual representation with a minimal number of output tokens, thus eliminating the need for an additional compression module. 2) Ensure continuity in visual encoding. To address the potential encoding errors caused by fragmented visual inputs, we develop a Register Interactive Attention (ReAtten) module. This module facilitates effective and efficient information exchange across sub-images by enabling interactions between visual registers. It ensures the continuity of visual semantics throughout the encoding. We conduct comprehensive experiments with FALCON on high-resolution benchmarks across a wide range of scenarios. FALCON demonstrates superior performance with a remarkable 9-fold reduction in visual tokens.

Generalist robot policies trained on large-scale datasets such as Open X-Embodiment (OXE) demonstrate strong performance across a wide range of tasks. However, they often struggle to generalize beyond the distribution of their training data. In this paper, we investigate the underlying cause of this limited generalization capability. We identify shortcut learning -- the reliance on task-irrelevant features -- as a key impediment to generalization. Through comprehensive theoretical and empirical analysis, we uncover two primary contributors to shortcut learning: (1) limited diversity within individual sub-datasets, and (2) significant distributional disparities across sub-datasets, leading to dataset fragmentation. These issues arise from the inherent structure of large-scale datasets like OXE, which are typically composed of multiple sub-datasets collected independently across varied environments and embodiments. Our findings provide critical insights into dataset collection strategies that can reduce shortcut learning and enhance the generalization ability of generalist robot policies. Moreover, in scenarios where acquiring new large-scale data is impractical, we demonstrate that carefully selected robotic data augmentation strategies can effectively reduce shortcut learning in existing offline datasets, thereby improving generalization capabilities of generalist robot policies, e.g., pi_0, in both simulation and real-world environments. More information at https://lucky-light-sun.github.io/proj/shortcut-learning-in-grps/.

Proteins perform nearly all cellular functions and constitute most drug targets, making their analysis fundamental to understanding human biology in health and disease. Tandem mass spectrometry (MS^2) is the major analytical technique in proteomics that identifies peptides by ionizing them, fragmenting them, and using the resulting mass spectra to identify and quantify proteins in biological samples. In MS^2 analysis, peptide fragment ion probability prediction plays a critical role, enhancing the accuracy of peptide identification from mass spectra as a complement to the intensity information. Current approaches rely on global statistics of fragmentation, which assumes that a fragment's probability is uniform across all peptides. Nevertheless, this assumption is oversimplified from a biochemical principle point of view and limits accurate prediction. To address this gap, we present Pep2Prob, the first comprehensive dataset and benchmark designed for peptide-specific fragment ion probability prediction. The proposed dataset contains fragment ion probability statistics for 608,780 unique precursors (each precursor is a pair of peptide sequence and charge state), summarized from more than 183 million high-quality, high-resolution, HCD MS^2 spectra with validated peptide assignments and fragmentation annotations. We establish baseline performance using simple statistical rules and learning-based methods, and find that models leveraging peptide-specific information significantly outperform previous methods using only global fragmentation statistics. Furthermore, performance across benchmark models with increasing capacities suggests that the peptide-fragmentation relationship exhibits complex nonlinearities requiring sophisticated machine learning approaches.

The increasing population of objects in geostationary orbit has raised concerns about the potential risks posed by debris clouds resulting from fragmentation. The short-term evolution and associated hazards of debris generated by collisions in the geostationary region is investigated in this study. The initial distribution of two debris clouds is modeled using a single probability density function.The combined distribution of the evolved clouds is determined by solving boundary value problems.The risks associated with these debris clouds are evaluated by calculating the instantaneous impact rate and cumulative collision probability.The probability of collisions with millimeter-sized fragments may increase to 1% within 36 hours, while the probability of collisions with fragments 5 cm or larger is approximately 10^{-5}.These findings underscore the vulnerability of the geostationary region to space traffic accidents.

While language models are increasingly utilized in materials science, typical models rely on frequency-centric tokenization methods originally developed for natural language processing. However, these methods frequently produce excessive fragmentation and semantic loss, failing to maintain the structural and semantic integrity of material concepts. To address this issue, we propose MATTER, a novel tokenization approach that integrates material knowledge into tokenization. Based on MatDetector trained on our materials knowledge base and a re-ranking method prioritizing material concepts in token merging, MATTER maintains the structural integrity of identified material concepts and prevents fragmentation during tokenization, ensuring their semantic meaning remains intact. The experimental results demonstrate that MATTER outperforms existing tokenization methods, achieving an average performance gain of 4% and 2% in the generation and classification tasks, respectively. These results underscore the importance of domain knowledge for tokenization strategies in scientific text processing. Our code is available at https://github.com/yerimoh/MATTER

Tissue segmentation is a routine preprocessing step to reduce the computational cost of whole slide image (WSI) analysis by excluding background regions. Traditional image processing techniques are commonly used for tissue segmentation, but often require manual adjustments to parameter values for atypical cases, fail to exclude all slide and scanning artifacts from the background, and are unable to segment adipose tissue. Pen marking artifacts in particular can be a potential source of bias for subsequent analyses if not removed. In addition, several applications require the separation of individual cross-sections, which can be challenging due to tissue fragmentation and adjacent positioning. To address these problems, we develop a convolutional neural network for tissue and pen marking segmentation using a dataset of 200 H&E stained WSIs. For separating tissue cross-sections, we propose a novel post-processing method based on clustering predicted centroid locations of the cross-sections in a 2D histogram. On an independent test set, the model achieved a mean Dice score of 0.981pm0.033 for tissue segmentation and a mean Dice score of 0.912pm0.090 for pen marking segmentation. The mean absolute difference between the number of annotated and separated cross-sections was 0.075pm0.350. Our results demonstrate that the proposed model can accurately segment H&E stained tissue cross-sections and pen markings in WSIs while being robust to many common slide and scanning artifacts. The model with trained model parameters and post-processing method are made publicly available as a Python package called SlideSegmenter.

Segmentation of the coronary artery is an important task for the quantitative analysis of coronary computed tomography angiography (CCTA) images and is being stimulated by the field of deep learning. However, the complex structures with tiny and narrow branches of the coronary artery bring it a great challenge. Coupled with the medical image limitations of low resolution and poor contrast, fragmentations of segmented vessels frequently occur in the prediction. Therefore, a geometry-based cascaded segmentation method is proposed for the coronary artery, which has the following innovations: 1) Integrating geometric deformation networks, we design a cascaded network for segmenting the coronary artery and vectorizing results. The generated meshes of the coronary artery are continuous and accurate for twisted and sophisticated coronary artery structures, without fragmentations. 2) Different from mesh annotations generated by the traditional marching cube method from voxel-based labels, a finer vectorized mesh of the coronary artery is reconstructed with the regularized morphology. The novel mesh annotation benefits the geometry-based segmentation network, avoiding bifurcation adhesion and point cloud dispersion in intricate branches. 3) A dataset named CCA-200 is collected, consisting of 200 CCTA images with coronary artery disease. The ground truths of 200 cases are coronary internal diameter annotations by professional radiologists. Extensive experiments verify our method on our collected dataset CCA-200 and public ASOCA dataset, with a Dice of 0.778 on CCA-200 and 0.895 on ASOCA, showing superior results. Especially, our geometry-based model generates an accurate, intact and smooth coronary artery, devoid of any fragmentations of segmented vessels.