Modern deep neural networks have achieved great successes in medical image analysis. However, the features captured by convolutional neural networks (CNNs) or Transformers tend to be optimized for pixel intensities and neglect key anatomical structures such as connected components and loops. In this paper, we propose a persistent homology guided approach (PHG-Net) that explores topological features of objects for medical image classification. For an input image, we first compute its cubical persistence diagram and extract topological features into a vector representation using a small neural network (called the PH module). The extracted topological features are then incorporated into the feature map generated by CNN or Transformer for feature fusion. The PH module is lightweight and capable of integrating topological features into any CNN or Transformer architectures in an end-to-end fashion. We evaluate our PHG-Net on three public datasets and demonstrate its considerable improvements on the target classification tasks over state-of-the-art methods.
Benefiting from the advancements in deep learning, various genomic analytical techniques, such as survival analysis, classification of tumors and their subtypes, and exploration of specific pathways, have significantly enhanced our understanding of the biological mechanisms driving cancer. However, the overfitting issue, arising from the limited number of patient samples, poses a challenge in improving the accuracy of genome analysis by deepening the neural network. Furthermore, it remains uncertain whether novel approaches such as the sparsely gated mixture of expert (MOE) and self-attention mechanisms can improve the accuracy of genomic analysis. In this paper, we introduce a novel sparsely gated RNA-seq analysis framework called Gene-MOE. This framework exploits the potential of the MOE layers and the proposed mixture of attention expert (MOAE) layers to enhance the analysis accuracy. Additionally, it addresses overfitting challenges by integrating pan-cancer information from 33 distinct cancer types through pre-training.We pre-trained Gene-MOE on TCGA pan-cancer RNA-seq dataset with 33 cancer types. Subsequently, we conducted experiments involving cancer classification and survival analysis based on the pre-trained Gene-MOE. According to the survival analysis results on 14 cancer types, Gene-MOE outperformed state-of-the-art models on 12 cancer types. Through detailed feature analysis, we found that the Gene-MOE model could learn rich feature representations of high-dimensional genes. According to the classification results, the total accuracy of the classification model for 33 cancer classifications reached 95.8%, representing the best performance compared to state-of-the-art models. These results indicate that Gene-MOE holds strong potential for use in cancer classification and survival analysis.
Due to the depth degradation effect in residual connections, many efficient Vision Transformers models that rely on stacking layers for information exchange often fail to form sufficient information mixing, leading to unnatural visual perception. To address this issue, in this paper, we propose Aggregated Attention, a biomimetic design-based token mixer that simulates biological foveal vision and continuous eye movement while enabling each token on the feature map to have a global perception. Furthermore, we incorporate learnable tokens that interact with conventional queries and keys, which further diversifies the generation of affinity matrices beyond merely relying on the similarity between queries and keys. Our approach does not rely on stacking for information exchange, thus effectively avoiding depth degradation and achieving natural visual perception. Additionally, we propose Convolutional GLU, a channel mixer that bridges the gap between GLU and SE mechanism, which empowers each token to have channel attention based on its nearest neighbor image features, enhancing local modeling capability and model robustness. We combine aggregated attention and convolutional GLU to create a new visual backbone called TransNeXt. Extensive experiments demonstrate that our TransNeXt achieves state-of-the-art performance across multiple model sizes. At a resolution of $224^2$, TransNeXt-Tiny attains an ImageNet accuracy of 84.0%, surpassing ConvNeXt-B with 69% fewer parameters. Our TransNeXt-Base achieves an ImageNet accuracy of 86.2% and an ImageNet-A accuracy of 61.6% at a resolution of $384^2$, a COCO object detection mAP of 57.1, and an ADE20K semantic segmentation mIoU of 54.7.
We propose a dual-stream multi-scale vision transformer (DS-MSHViT) architecture that processes RGB and optical flow inputs for efficient sewer defect classification. Unlike existing methods that combine the predictions of two separate networks trained on each modality, we jointly train a single network with two branches for RGB and motion. Our key idea is to use self-attention regularization to harness the complementary strengths of the RGB and motion streams. The motion stream alone struggles to generate accurate attention maps, as motion images lack the rich visual features present in RGB images. To facilitate this, we introduce an attention consistency loss between the dual streams. By leveraging motion cues through a self-attention regularizer, we align and enhance RGB attention maps, enabling the network to concentrate on pertinent input regions. We evaluate our data on a public dataset as well as cross-validate our model performance in a novel dataset. Our method outperforms existing models that utilize either convolutional neural networks (CNNs) or multi-scale hybrid vision transformers (MSHViTs) without employing attention regularization between the two streams.
Deep learning approaches exhibit promising performances on various text tasks. However, they are still struggling on medical text classification since samples are often extremely imbalanced and scarce. Different from existing mainstream approaches that focus on supplementary semantics with external medical information, this paper aims to rethink the data challenges in medical texts and present a novel framework-agnostic algorithm called Text2Tree that only utilizes internal label hierarchy in training deep learning models. We embed the ICD code tree structure of labels into cascade attention modules for learning hierarchy-aware label representations. Two new learning schemes, Similarity Surrogate Learning (SSL) and Dissimilarity Mixup Learning (DML), are devised to boost text classification by reusing and distinguishing samples of other labels following the label representation hierarchy, respectively. Experiments on authoritative public datasets and real-world medical records show that our approach stably achieves superior performances over classical and advanced imbalanced classification methods.
Multi-label classification (MLC) refers to the problem of tagging a given instance with a set of relevant labels. Most existing MLC methods are based on the assumption that the correlation of two labels in each label pair is symmetric, which is violated in many real-world scenarios. Moreover, most existing methods design learning processes associated with the number of labels, which makes their computational complexity a bottleneck when scaling up to large-scale output space. To tackle these issues, we propose a novel method named Scalable Label Distribution Learning (SLDL) for multi-label classification which can describe different labels as distributions in a latent space, where the label correlation is asymmetric and the dimension is independent of the number of labels. Specifically, SLDL first converts labels into continuous distributions within a low-dimensional latent space and leverages the asymmetric metric to establish the correlation between different labels. Then, it learns the mapping from the feature space to the latent space, resulting in the computational complexity is no longer related to the number of labels. Finally, SLDL leverages a nearest-neighbor-based strategy to decode the latent representations and obtain the final predictions. Extensive experiments illustrate that SLDL achieves very competitive classification performances with little computational consumption.
Missing data is a common problem in practical data science settings. Various imputation methods have been developed to deal with missing data. However, even though the labels are available in the training data in many situations, the common practice of imputation usually only relies on the input and ignores the label. We propose Classification Based on MissForest Imputation (CBMI), a classification strategy that initializes the predicted test label with missing values and stacks the label with the input for imputation, allowing the label and the input to be imputed simultaneously. In addition, we propose the imputation using labels (IUL) algorithm, an imputation strategy that stacks the label into the input and illustrates how it can significantly improve the imputation quality. Experiments show that CBMI has classification accuracy when the test set contains missing data, especially for imbalanced data and categorical data. Moreover, for both the regression and classification, IUL consistently shows significantly better results than imputation based on only the input data.
While performance of many text classification tasks has been recently improved due to Pre-trained Language Models (PLMs), in this paper we show that they still suffer from a performance gap when the underlying distribution of topics changes. For example, a genre classifier trained on \textit{political} topics often fails when tested on documents about \textit{sport} or \textit{medicine}. In this work, we quantify this phenomenon empirically with a large corpus and a large set of topics. Consequently, we verify that domain transfer remains challenging both for classic PLMs, such as BERT, and for modern large models, such as GPT-3. We also suggest and successfully test a possible remedy: after augmenting the training dataset with topically-controlled synthetic texts, the F1 score improves by up to 50\% for some topics, nearing on-topic training results, while others show little to no improvement. While our empirical results focus on genre classification, our methodology is applicable to other classification tasks such as gender, authorship, or sentiment classification. The code and data to replicate the experiments are available at https://github.com/dminus1/genre
The dissection of hyperspectral images into intrinsic components through hyperspectral intrinsic image decomposition (HIID) enhances the interpretability of hyperspectral data, providing a foundation for more accurate classification outcomes. However, the classification performance of HIID is constrained by the model's representational ability. To address this limitation, this study rethinks hyperspectral intrinsic image decomposition for classification tasks by introducing deep feature embedding. The proposed framework, HyperDID, incorporates the Environmental Feature Module (EFM) and Categorical Feature Module (CFM) to extract intrinsic features. Additionally, a Feature Discrimination Module (FDM) is introduced to separate environment-related and category-related features. Experimental results across three commonly used datasets validate the effectiveness of HyperDID in improving hyperspectral image classification performance. This novel approach holds promise for advancing the capabilities of hyperspectral image analysis by leveraging deep feature embedding principles. The implementation of the proposed method could be accessed soon at https://github.com/shendu-sw/HyperDID for the sake of reproducibility.
Among the many tasks that Large Language Models (LLMs) have revolutionized is text classification. Current text classification paradigms, however, rely solely on the output of the final layer in the LLM, with the rich information contained in internal neurons largely untapped. In this study, we present SPIN: a model-agnostic framework that sparsifies and integrates internal neurons of intermediate layers of LLMs for text classification. Specifically, SPIN sparsifies internal neurons by linear probing-based salient neuron selection layer by layer, avoiding noise from unrelated neurons and ensuring efficiency. The cross-layer salient neurons are then integrated to serve as multi-layered features for the classification head. Extensive experimental results show our proposed SPIN significantly improves text classification accuracy, efficiency, and interpretability.
We conduct an extensive study on using near-term quantum computers for a task in the domain of computational biology. By constructing quantum models based on parameterised quantum circuits we perform sequence classification on a task relevant to the design of therapeutic proteins, and find competitive performance with classical baselines of similar scale. To study the effect of noise, we run some of the best-performing quantum models with favourable resource requirements on emulators of state-of-the-art noisy quantum processors. We then apply error mitigation methods to improve the signal. We further execute these quantum models on the Quantinuum H1-1 trapped-ion quantum processor and observe very close agreement with noiseless exact simulation. Finally, we perform feature attribution methods and find that the quantum models indeed identify sensible relationships, at least as well as the classical baselines. This work constitutes the first proof-of-concept application of near-term quantum computing to a task critical to the design of therapeutic proteins, opening the route toward larger-scale applications in this and related fields, in line with the hardware development roadmaps of near-term quantum technologies.
Dataset pruning aims to construct a coreset capable of achieving performance comparable to the original, full dataset. Most existing dataset pruning methods rely on snapshot-based criteria to identify representative samples, often resulting in poor generalization across various pruning and cross-architecture scenarios. Recent studies have addressed this issue by expanding the scope of training dynamics considered, including factors such as forgetting event and probability change, typically using an averaging approach. However, these works struggle to integrate a broader range of training dynamics without overlooking well-generalized samples, which may not be sufficiently highlighted in an averaging manner. In this study, we propose a novel dataset pruning method termed as Temporal Dual-Depth Scoring (TDDS), to tackle this problem. TDDS utilizes a dual-depth strategy to achieve a balance between incorporating extensive training dynamics and identifying representative samples for dataset pruning. In the first depth, we estimate the series of each sample's individual contributions spanning the training progress, ensuring comprehensive integration of training dynamics. In the second depth, we focus on the variability of the sample-wise contributions identified in the first depth to highlight well-generalized samples. Extensive experiments conducted on CIFAR and ImageNet datasets verify the superiority of TDDS over previous SOTA methods. Specifically on CIFAR-100, our method achieves 54.51% accuracy with only 10% training data, surpassing random selection by 7.83% and other comparison methods by at least 12.69%.
Classifying patterns of known classes and rejecting ambiguous and novel (also called as out-of-distribution (OOD)) inputs are involved in open world pattern recognition. Deep neural network models usually excel in closed-set classification while performs poorly in rejecting OOD inputs. To tackle this problem, numerous methods have been designed to perform open set recognition (OSR) or OOD rejection/detection tasks. Previous methods mostly take post-training score transformation or hybrid models to ensure low scores on OOD inputs while separating known classes. In this paper, we attempt to build a unified framework for building open set classifiers for both classification and OOD rejection. We formulate the open set recognition of $ K $-known-class as a $ (K+1) $-class classification problem with model trained on known-class samples only. By decomposing the $ K $-class problem into $ K $ one-versus-all (OVA) binary classification tasks and binding some parameters, we show that combining the scores of OVA classifiers can give $ (K+1) $-class posterior probabilities, which enables classification and OOD rejection in a unified framework. To maintain the closed-set classification accuracy of the OVA trained classifier, we propose a hybrid training strategy combining OVA loss and multi-class cross-entropy loss. We implement the OVA framework and hybrid training strategy on the recently proposed convolutional prototype network and prototype classifier on vision transformer (ViT) backbone. Experiments on popular OSR and OOD detection datasets demonstrate that the proposed framework, using a single multi-class classifier, yields competitive performance in closed-set classification, OOD detection, and misclassification detection.
While graph neural networks have achieved state-of-the-art performances in many real-world tasks including graph classification and node classification, recent works have demonstrated they are also extremely vulnerable to adversarial attacks. Most previous works have focused on attacking node classification networks under impractical white-box scenarios. In this work, we will propose a non-targeted Hard Label Black Box Node Injection Attack on Graph Neural Networks, which to the best of our knowledge, is the first of its kind. Under this setting, more real world tasks can be studied because our attack assumes no prior knowledge about (1): the model architecture of the GNN we are attacking; (2): the model's gradients; (3): the output logits of the target GNN model. Our attack is based on an existing edge perturbation attack, from which we restrict the optimization process to formulate a node injection attack. In the work, we will evaluate the performance of the attack using three datasets, COIL-DEL, IMDB-BINARY, and NCI1.
Sound Source Localization (SSL) involves estimating the Direction of Arrival (DOA) of sound sources. Since the DOA estimation output space is continuous, regression might be more suitable for DOA, offering higher precision. However, in practice, classification often outperforms regression, exhibiting greater robustness to interference. Conversely, classification's drawback is inherent quantization error. Within the classification paradigm, the DOA output space is discretized into intervals, each treated as a class. These classes show strong inter-class correlations, being inherently ordered, with higher similarity as intervals grow closer. Nevertheless, this has not been fully exploited. To address this, we propose an Unbiased Label Distribution (ULD) to eliminate quantization error in training targets. Furthermore, we tailor two loss functions for the soft label family: Negative Log Absolute Error (NLAE) and Mean Squared Error without activation (MSE(wo)). Finally, we introduce Weighted Adjacent Decoding (WAD) to overcome quantization error during model prediction decoding. Experimental results demonstrate our approach surpasses classification quantization limits, achieving state-of-the-art performance. Our code and supplementary materials are available at https://github.com/linfeng-feng/ULD.
Formally verifying audio classification systems is essential to ensure accurate signal classification across real-world applications like surveillance, automotive voice commands, and multimedia content management, preventing potential errors with serious consequences. Drawing from recent research, this study advances the utilization of star-set-based formal verification, extended through reachability analysis, tailored explicitly for Long Short-Term Memory architectures and their Convolutional variations within the audio classification domain. By conceptualizing the classification process as a sequence of set operations, the star set-based reachability approach streamlines the exploration of potential operational states attainable by the system. The paper serves as an encompassing case study, validating and verifying sequence audio classification analytics within real-world contexts. It accentuates the necessity for robustness verification to ensure precise and dependable predictions, particularly in light of the impact of noise on the accuracy of output classifications.
Group fairness is a central research topic in text classification, where reaching fair treatment between sensitive groups (e.g. women vs. men) remains an open challenge. This paper presents a novel method for mitigating biases in neural text classification, agnostic to the model architecture. Considering the difficulty to distinguish fair from unfair information in a text encoder, we take inspiration from adversarial training to induce Wasserstein independence between representations learned to predict our target label and the ones learned to predict some sensitive attribute. Our approach provides two significant advantages. Firstly, it does not require annotations of sensitive attributes in both testing and training data. This is more suitable for real-life scenarios compared to existing methods that require annotations of sensitive attributes at train time. Second, our approach exhibits a comparable or better fairness-accuracy trade-off compared to existing methods.
Advancing loss function design is pivotal for optimizing neural network training and performance. This work introduces Random Linear Projections (RLP) loss, a novel approach that enhances training efficiency by leveraging geometric relationships within the data. Distinct from traditional loss functions that target minimizing pointwise errors, RLP loss operates by minimizing the distance between sets of hyperplanes connecting fixed-size subsets of feature-prediction pairs and feature-label pairs. Our empirical evaluations, conducted across benchmark datasets and synthetic examples, demonstrate that neural networks trained with RLP loss outperform those trained with traditional loss functions, achieving improved performance with fewer data samples, and exhibiting greater robustness to additive noise. We provide theoretical analysis supporting our empirical findings.
We propose a method for the classification of objects that are structured as random trees. Our aim is to model a distribution over the node label assignments in settings where the tree data structure is associated with node attributes (typically high dimensional embeddings). The tree topology is not predetermined and none of the label assignments are present during inference. Other methods that produce a distribution over node label assignment in trees (or more generally in graphs) either assume conditional independence of the label assignment, operate on a fixed graph topology, or require part of the node labels to be observed. Our method defines a Markov Network with the corresponding topology of the random tree and an associated Gibbs distribution. We parameterize the Gibbs distribution with a Graph Neural Network that operates on the random tree and the node embeddings. This allows us to estimate the likelihood of node assignments for a given random tree and use MCMC to sample from the distribution of node assignments. We evaluate our method on the tasks of node classification in trees on the Stanford Sentiment Treebank dataset. Our method outperforms the baselines on this dataset, demonstrating its effectiveness for modeling joint distributions of node labels in random trees.
This paper proposes a novel method of classifying malware into families using high-resolution greyscale images and multiple instance learning to overcome adversarial binary enlargement. Current methods of visualisation-based malware classification largely rely on lossy transformations of inputs such as resizing to handle the large, variable-sized images. Through empirical analysis and experimentation, it is shown that these approaches cause crucial information loss that can be exploited. The proposed solution divides the images into patches and uses embedding-based multiple instance learning with a convolutional neural network and an attention aggregation function for classification. The implementation is evaluated on the Microsoft Malware Classification dataset and achieves accuracies of up to $96.6\%$ on adversarially enlarged samples compared to the baseline of $22.8\%$. The Python code is available online at https://github.com/timppeters/MIL-Malware-Images .