Trichomoniasis is a common infectious disease with high incidence caused by the parasite Trichomonas vaginalis, increasing the risk of getting HIV in humans if left untreated. Automated detection of Trichomonas vaginalis from microscopic images can provide vital information for the diagnosis of trichomoniasis. However, accurate Trichomonas vaginalis segmentation (TVS) is a challenging task due to the high appearance similarity between the Trichomonas and other cells (e.g., leukocyte), the large appearance variation caused by their motility, and, most importantly, the lack of large-scale annotated data for deep model training. To address these challenges, we elaborately collected the first large-scale Microscopic Image dataset of Trichomonas Vaginalis, named TVMI3K, which consists of 3,158 images covering Trichomonas of various appearances in diverse backgrounds, with high-quality annotations including object-level mask labels, object boundaries, and challenging attributes. Besides, we propose a simple yet effective baseline, termed TVNet, to automatically segment Trichomonas from microscopic images, including high-resolution fusion and foreground-background attention modules. Extensive experiments demonstrate that our model achieves superior segmentation performance and outperforms various cutting-edge object detection models both quantitatively and qualitatively, making it a promising framework to promote future research in TVS tasks. The dataset and results will be publicly available at: https://github.com/CellRecog/cellRecog.
Therapeutic antibody development has become an increasingly popular approach for drug development. To date, antibody therapeutics are largely developed using large scale experimental screens of antibody libraries containing hundreds of millions of antibody sequences. The high cost and difficulty of developing therapeutic antibodies create a pressing need for computational methods to predict antibody properties and create bespoke designs. However, the relationship between antibody sequence and activity is a complex physical process and traditional iterative design approaches rely on large scale assays and random mutagenesis. Deep learning methods have emerged as a promising way to learn antibody property predictors, but predicting antibody properties and target-specific activities depends critically on the choice of antibody representations and data linking sequences to properties is often limited. Existing works have not yet investigated the value, limitations and opportunities of these methods in application to antibody-based drug discovery. In this paper, we present results on a novel SARS-CoV-2 antibody binding dataset and an additional benchmark dataset. We compare three classes of models: conventional statistical sequence models, supervised learning on each dataset independently, and fine-tuning an antibody specific pre-trained language model. Experimental results suggest that self-supervised pretraining of feature representation consistently offers significant improvement in over previous approaches. We also investigate the impact of data size on the model performance, and discuss challenges and opportunities that the machine learning community can address to advance in silico engineering and design of therapeutic antibodies.
Contrast-enhanced T1 (T1ce) is one of the most essential magnetic resonance imaging (MRI) modalities for diagnosing and analyzing brain tumors, especially gliomas. In clinical practice, common MRI modalities such as T1, T2, and fluid attenuation inversion recovery are relatively easy to access while T1ce is more challenging considering the additional cost and potential risk of allergies to the contrast agent. Therefore, it is of great clinical necessity to develop a method to synthesize T1ce from other common modalities. Current paired image translation methods typically have the issue of requiring a large amount of paired data and do not focus on specific regions of interest, e.g., the tumor region, in the synthesization process. To address these issues, we propose a Difficulty-perceived common-to-T1ce Semi-Supervised multimodal MRI Synthesis network (DS3-Net), involving both paired and unpaired data together with dual-level knowledge distillation. DS3-Net predicts a difficulty map to progressively promote the synthesis task. Specifically, a pixelwise constraint and a patchwise contrastive constraint are guided by the predicted difficulty map. Through extensive experiments on the publiclyavailable BraTS2020 dataset, DS3-Net outperforms its supervised counterpart in each respect. Furthermore, with only 5% paired data, the proposed DS3-Net achieves competitive performance with state-of-theart image translation methods utilizing 100% paired data, delivering an average SSIM of 0.8947 and an average PSNR of 23.60.
Joint channel estimation and signal detection (JCESD) is crucial in orthogonal frequency division multiplexing (OFDM) systems, but traditional algorithms perform poorly in low signal-to-noise ratio (SNR) scenarios. Deep learning (DL) methods have been investigated, but concerns regarding computational expense and lack of validation in low-SNR settings remain. Hence, the development of a robust and low-complexity model that can deliver excellent performance across a wide range of SNRs is highly desirable. In this paper, we aim to establish a benchmark where traditional algorithms and DL methods are validated on different channel models, Doppler, and SNR settings, particularly focusing on the semi-blind setting. In particular, we propose a new DL model where the backbone network is formed by unrolling the iterative algorithm, and the hyperparameters are estimated by hypernetworks. Additionally, we adapt a lightweight DenseNet to the task of JCESD for comparison. We evaluate different methods in three aspects: generalization in terms of bit error rate (BER), robustness, and complexity. Our results indicate that DL approaches outperform traditional algorithms in the challenging low-SNR setting, while the iterative algorithm performs better in high-SNR settings. Furthermore, the iterative algorithm is more robust in the presence of carrier frequency offset, whereas DL methods excel when signals are corrupted by asymmetric Gaussian noise.
Panoptic Scene Graph Generation (PSG) aims to generate a comprehensive graph-structure representation based on panoptic segmentation masks. Despite remarkable progress in PSG, almost all existing methods neglect the importance of shape-aware features, which inherently focus on the contours and boundaries of objects. To bridge this gap, we propose a model-agnostic Curricular shApe-aware FEature (CAFE) learning strategy for PSG. Specifically, we incorporate shape-aware features (i.e., mask features and boundary features) into PSG, moving beyond reliance solely on bbox features. Furthermore, drawing inspiration from human cognition, we propose to integrate shape-aware features in an easy-to-hard manner. To achieve this, we categorize the predicates into three groups based on cognition learning difficulty and correspondingly divide the training process into three stages. Each stage utilizes a specialized relation classifier to distinguish specific groups of predicates. As the learning difficulty of predicates increases, these classifiers are equipped with features of ascending complexity. We also incorporate knowledge distillation to retain knowledge acquired in earlier stages. Due to its model-agnostic nature, CAFE can be seamlessly incorporated into any PSG model. Extensive experiments and ablations on two PSG tasks under both robust and zero-shot PSG have attested to the superiority and robustness of our proposed CAFE, which outperforms existing state-of-the-art methods by a large margin.
Open-vocabulary scene graph generation (OVSGG) extends traditional SGG by recognizing novel objects and relationships beyond predefined categories, leveraging the knowledge from pre-trained large-scale models. Existing OVSGG methods always adopt a two-stage pipeline: 1) \textit{Infusing knowledge} into large-scale models via pre-training on large datasets; 2) \textit{Transferring knowledge} from pre-trained models with fully annotated scene graphs during supervised fine-tuning. However, due to a lack of explicit interaction modeling, these methods struggle to distinguish between interacting and non-interacting instances of the same object category. This limitation induces critical issues in both stages of OVSGG: it generates noisy pseudo-supervision from mismatched objects during knowledge infusion, and causes ambiguous query matching during knowledge transfer. To this end, in this paper, we propose an inter\textbf{AC}tion-\textbf{C}entric end-to-end OVSGG framework (\textbf{ACC}) in an interaction-driven paradigm to minimize these mismatches. For \textit{interaction-centric knowledge infusion}, ACC employs a bidirectional interaction prompt for robust pseudo-supervision generation to enhance the model's interaction knowledge. For \textit{interaction-centric knowledge transfer}, ACC first adopts interaction-guided query selection that prioritizes pairing interacting objects to reduce interference from non-interacting ones. Then, it integrates interaction-consistent knowledge distillation to bolster robustness by pushing relational foreground away from the background while retaining general knowledge. Extensive experimental results on three benchmarks show that ACC achieves state-of-the-art performance, demonstrating the potential of interaction-centric paradigms for real-world applications.
Teddy Koker, Keegan Quigley, Eric Taw et al. · mit
The calculation of electron density distribution using density functional theory (DFT) in materials and molecules is central to the study of their quantum and macro-scale properties, yet accurate and efficient calculation remains a long-standing challenge. We introduce ChargE3Net, an E(3)-equivariant graph neural network for predicting electron density in atomic systems. ChargE3Net enables the learning of higher-order equivariant feature to achieve high predictive accuracy and model expressivity. We show that ChargE3Net exceeds the performance of prior work on diverse sets of molecules and materials. When trained on the massive dataset of over 100K materials in the Materials Project database, our model is able to capture the complexity and variability in the data, leading to a significant 26.7% reduction in self-consistent iterations when used to initialize DFT calculations on unseen materials. Furthermore, we show that non-self-consistent DFT calculations using our predicted charge densities yield near-DFT performance on electronic and thermodynamic property prediction at a fraction of the computational cost. Further analysis attributes the greater predictive accuracy to improved modeling of systems with high angular variations. These results illuminate a pathway towards a machine learning-accelerated ab initio calculations for materials discovery.
Video dubbing aims to generate high-fidelity speech that is precisely temporally aligned with the visual content. Existing methods still suffer from limitations in speech naturalness and audio-visual synchronization, and are limited to monolingual settings. To address these challenges, we propose SyncVoice, a vision-augmented video dubbing framework built upon a pretrained text-to-speech (TTS) model. By fine-tuning the TTS model on audio-visual data, we achieve strong audiovisual consistency. We propose a Dual Speaker Encoder to effectively mitigate inter-language interference in cross-lingual speech synthesis and explore the application of video dubbing in video translation scenarios. Experimental results show that SyncVoice achieves high-fidelity speech generation with strong synchronization performance, demonstrating its potential in video dubbing tasks.
Medical image datasets often exhibit long-tailed distributions due to the inherent challenges in medical data collection and annotation. In long-tailed contexts, some common disease categories account for most of the data, while only a few samples are available in the rare disease categories, resulting in poor performance of deep learning methods. To address this issue, previous approaches have employed class re-sampling or re-weighting techniques, which often encounter challenges such as overfitting to tail classes or difficulties in optimization during training. In this work, we propose a novel approach, namely \textbf{S}aliency-guided and \textbf{P}atch-based \textbf{Mix}up (SPMix) for long-tailed skin cancer image classification. Specifically, given a tail-class image and a head-class image, we generate a new tail-class image by mixing them under the guidance of saliency mapping, which allows for preserving and augmenting the discriminative features of the tail classes without any interference of the head-class features. Extensive experiments are conducted on the ISIC2018 dataset, demonstrating the superiority of SPMix over existing state-of-the-art methods.
The fifth Oriental Language Recognition (OLR) Challenge focuses on language recognition in a variety of complex environments to promote its development. The OLR 2020 Challenge includes three tasks: (1) cross-channel language identification, (2) dialect identification, and (3) noisy language identification. We choose Cavg as the principle evaluation metric, and the Equal Error Rate (EER) as the secondary metric. There were 58 teams participating in this challenge and one third of the teams submitted valid results. Compared with the best baseline, the Cavg values of Top 1 system for the three tasks were relatively reduced by 82%, 62% and 48%, respectively. This paper describes the three tasks, the database profile, and the final results. We also outline the novel approaches that improve the performance of language recognition systems most significantly, such as the utilization of auxiliary information.
This paper proposes an additive phoneme-aware margin softmax (APM-Softmax) loss to train the multi-task learning network with phonetic information for language recognition. In additive margin softmax (AM-Softmax) loss, the margin is set as a constant during the entire training for all training samples, and that is a suboptimal method since the recognition difficulty varies in training samples. In additive angular margin softmax (AAM-Softmax) loss, the additional angular margin is set as a costant as well. In this paper, we propose an APM-Softmax loss for language recognition with phoneitc multi-task learning, in which the additive phoneme-aware margin is automatically tuned for different training samples. More specifically, the margin of language recognition is adjusted according to the results of phoneme recognition. Experiments are reported on Oriental Language Recognition (OLR) datasets, and the proposed method improves AM-Softmax loss and AAM-Softmax loss in different language recognition testing conditions.
Under noisy environments, to achieve the robust performance of speaker recognition is still a challenging task. Motivated by the promising performance of multi-task training in a variety of image processing tasks, we explore the potential of multi-task adversarial training for learning a noise-robust speaker embedding. In this paper we present a novel framework which consists of three components: an encoder that extracts noise-robust speaker embedding; a classifier that classifies the speakers; a discriminator that discriminates the noise type of the speaker embedding. Besides, we propose a training strategy using the training accuracy as an indicator to stabilize the multi-class adversarial optimization process. We conduct our experiments on the English and Mandarin corpus and the experimental results demonstrate that our proposed multi-task adversarial training method could greatly outperform the other methods without adversarial training in noisy environments. Furthermore, experiments indicate that our method is also able to improve the speaker verification performance the clean condition.
In this letter, an effective image saliency detection method is proposed by constructing some novel spaces to model the background and redefine the distance of the salient patches away from the background. Concretely, given the backgroundness prior, eigendecomposition is utilized to create four spaces of background-based distribution (SBD) to model the background, in which a more appropriate metric (Mahalanobis distance) is quoted to delicately measure the saliency of every image patch away from the background. After that, a coarse saliency map is obtained by integrating the four adjusted Mahalanobis distance maps, each of which is formed by the distances between all the patches and background in the corresponding SBD. To be more discriminative, the coarse saliency map is further enhanced into the posterior probability map within Bayesian perspective. Finally, the final saliency map is generated by properly refining the posterior probability map with geodesic distance. Experimental results on two usual datasets show that the proposed method is effective compared with the state-of-the-art algorithms.