Improving Molecular Graph Generation with Flow Matching and Optimal Transport

Generating molecular graphs is crucial in drug design and discovery but remains challenging due to the complex interdependencies between nodes and edges. While diffusion models have demonstrated their potentiality in molecular graph design, they often suffer from unstable training and inefficient sampling. To enhance generation performance and training stability, we propose GGFlow, a discrete flow matching generative model incorporating optimal transport for molecular graphs and it incorporates an edge-augmented graph transformer to enable the direct communications among chemical bounds. Additionally, GGFlow introduces a novel goal-guided generation framework to control the generative trajectory of our model, aiming to design novel molecular structures with the desired properties. GGFlow demonstrates superior performance on both unconditional and conditional molecule generation tasks, outperforming existing baselines and underscoring its effectiveness and potential for wider application.

A Nested Graph Reinforcement Learning-based Decision-making Strategy for Eco-platooning

Platooning technology is renowned for its precise vehicle control, traffic flow optimization, and energy efficiency enhancement. However, in large-scale mixed platoons, vehicle heterogeneity and unpredictable traffic conditions lead to virtual bottlenecks. These bottlenecks result in reduced traffic throughput and increased energy consumption within the platoon. To address these challenges, we introduce a decision-making strategy based on nested graph reinforcement learning. This strategy improves collaborative decision-making, ensuring energy efficiency and alleviating congestion. We propose a theory of nested traffic graph representation that maps dynamic interactions between vehicles and platoons in non-Euclidean spaces. By incorporating spatio-temporal weighted graph into a multi-head attention mechanism, we further enhance the model's capacity to process both local and global data. Additionally, we have developed a nested graph reinforcement learning framework to enhance the self-iterative learning capabilities of platooning. Using the I-24 dataset, we designed and conducted comparative algorithm experiments, generalizability testing, and permeability ablation experiments, thereby validating the proposed strategy's effectiveness. Compared to the baseline, our strategy increases throughput by 10% and decreases energy use by 9%. Specifically, increasing the penetration rate of CAVs significantly enhances traffic throughput, though it also increases energy consumption.

Improving Representation of High-frequency Components for Medical Foundation Models

Foundation models have recently attracted significant attention for their impressive generalizability across diverse downstream tasks. However, these models are demonstrated to exhibit great limitations in representing high-frequency components and fine-grained details. In many medical imaging tasks, the precise representation of such information is crucial due to the inherently intricate anatomical structures, sub-visual features, and complex boundaries involved. Consequently, the limited representation of prevalent foundation models can result in significant performance degradation or even failure in these tasks. To address these challenges, we propose a novel pretraining strategy, named Frequency-advanced Representation Autoencoder (Frepa). Through high-frequency masking and low-frequency perturbation combined with adversarial learning, Frepa encourages the encoder to effectively represent and preserve high-frequency components in the image embeddings. Additionally, we introduce an innovative histogram-equalized image masking strategy, extending the Masked Autoencoder approach beyond ViT to other architectures such as Swin Transformer and convolutional networks. We develop Frepa across nine medical modalities and validate it on 32 downstream tasks for both 2D images and 3D volume data. Without fine-tuning, Frepa can outperform other self-supervised pretraining methods and, in some cases, even surpasses task-specific trained models. This improvement is particularly significant for tasks involving fine-grained details, such as achieving up to a +15% increase in DSC for retina vessel segmentation and a +7% increase in IoU for lung nodule detection. Further experiments quantitatively reveal that Frepa enables superior high-frequency representations and preservation in the embeddings, underscoring its potential for developing more generalized and universal medical image foundation models.

ScholarChemQA: Unveiling the Power of Language Models in Chemical Research Question Answering

Question Answering (QA) effectively evaluates language models' reasoning and knowledge depth. While QA datasets are plentiful in areas like general domain and biomedicine, academic chemistry is less explored. Chemical QA plays a crucial role in both education and research by effectively translating complex chemical information into readily understandable format. Addressing this gap, we introduce ScholarChemQA, a large-scale QA dataset constructed from chemical papers. This dataset reflects typical real-world challenges, including an imbalanced data distribution and a substantial amount of unlabeled data that can be potentially useful. Correspondingly, we introduce a QAMatch model, specifically designed to effectively answer chemical questions by fully leveraging our collected data. We first address the issue of imbalanced label distribution by re-weighting the instance-wise loss based on the inverse frequency of each class, ensuring minority classes are not dominated by majority ones during optimization. Next, we utilize the unlabeled data to enrich the learning process, generating a variety of augmentations based on a SoftMix operation and ensuring their predictions align with the same target, i.e., pseudo-labels. To ensure the quality of the pseudo-labels, we propose a calibration procedure aimed at closely aligning the pseudo-label estimates of individual samples with a desired ground truth distribution. Experiments show that our QAMatch significantly outperforms the recent similar-scale baselines and Large Language Models (LLMs) not only on our ScholarChemQA dataset but also on four benchmark datasets. We hope our benchmark and model can facilitate and promote more research on chemical QA.

Trustworthy Contrast-enhanced Brain MRI Synthesis

Contrast-enhanced brain MRI (CE-MRI) is a valuable diagnostic technique but may pose health risks and incur high costs. To create safer alternatives, multi-modality medical image translation aims to synthesize CE-MRI images from other available modalities. Although existing methods can generate promising predictions, they still face two challenges, i.e., exhibiting over-confidence and lacking interpretability on predictions. To address the above challenges, this paper introduces TrustI2I, a novel trustworthy method that reformulates multi-to-one medical image translation problem as a multimodal regression problem, aiming to build an uncertainty-aware and reliable system. Specifically, our method leverages deep evidential regression to estimate prediction uncertainties and employs an explicit intermediate and late fusion strategy based on the Mixture of Normal Inverse Gamma (MoNIG) distribution, enhancing both synthesis quality and interpretability. Additionally, we incorporate uncertainty calibration to improve the reliability of uncertainty. Validation on the BraTS2018 dataset demonstrates that our approach surpasses current methods, producing higher-quality images with rational uncertainty estimation.

MBA-Net: SAM-driven Bidirectional Aggregation Network for Ovarian Tumor Segmentation

Accurate segmentation of ovarian tumors from medical images is crucial for early diagnosis, treatment planning, and patient management. However, the diverse morphological characteristics and heterogeneous appearances of ovarian tumors pose significant challenges to automated segmentation methods. In this paper, we propose MBA-Net, a novel architecture that integrates the powerful segmentation capabilities of the Segment Anything Model (SAM) with domain-specific knowledge for accurate and robust ovarian tumor segmentation. MBA-Net employs a hybrid encoder architecture, where the encoder consists of a prior branch, which inherits the SAM encoder to capture robust segmentation priors, and a domain branch, specifically designed to extract domain-specific features. The bidirectional flow of information between the two branches is facilitated by the robust feature injection network (RFIN) and the domain knowledge integration network (DKIN), enabling MBA-Net to leverage the complementary strengths of both branches. We extensively evaluate MBA-Net on the public multi-modality ovarian tumor ultrasound dataset and the in-house multi-site ovarian tumor MRI dataset. Our proposed method consistently outperforms state-of-the-art segmentation approaches. Moreover, MBA-Net demonstrates superior generalization capability across different imaging modalities and clinical sites.

Personalized Federated Continual Learning via Multi-granularity Prompt

Personalized Federated Continual Learning (PFCL) is a new practical scenario that poses greater challenges in sharing and personalizing knowledge. PFCL not only relies on knowledge fusion for server aggregation at the global spatial-temporal perspective but also needs model improvement for each client according to the local requirements. Existing methods, whether in Personalized Federated Learning (PFL) or Federated Continual Learning (FCL), have overlooked the multi-granularity representation of knowledge, which can be utilized to overcome Spatial-Temporal Catastrophic Forgetting (STCF) and adopt generalized knowledge to itself by coarse-to-fine human cognitive mechanisms. Moreover, it allows more effectively to personalized shared knowledge, thus serving its own purpose. To this end, we propose a novel concept called multi-granularity prompt, i.e., coarse-grained global prompt acquired through the common model learning process, and fine-grained local prompt used to personalize the generalized representation. The former focuses on efficiently transferring shared global knowledge without spatial forgetting, and the latter emphasizes specific learning of personalized local knowledge to overcome temporal forgetting. In addition, we design a selective prompt fusion mechanism for aggregating knowledge of global prompts distilled from different clients. By the exclusive fusion of coarse-grained knowledge, we achieve the transmission and refinement of common knowledge among clients, further enhancing the performance of personalization. Extensive experiments demonstrate the effectiveness of the proposed method in addressing STCF as well as improving personalized performance. Our code now is available at https://github.com/SkyOfBeginning/FedMGP.

Evidential Concept Embedding Models: Towards Reliable Concept Explanations for Skin Disease Diagnosis

Due to the high stakes in medical decision-making, there is a compelling demand for interpretable deep learning methods in medical image analysis. Concept Bottleneck Models (CBM) have emerged as an active interpretable framework incorporating human-interpretable concepts into decision-making. However, their concept predictions may lack reliability when applied to clinical diagnosis, impeding concept explanations' quality. To address this, we propose an evidential Concept Embedding Model (evi-CEM), which employs evidential learning to model the concept uncertainty. Additionally, we offer to leverage the concept uncertainty to rectify concept misalignments that arise when training CBMs using vision-language models without complete concept supervision. With the proposed methods, we can enhance concept explanations' reliability for both supervised and label-efficient settings. Furthermore, we introduce concept uncertainty for effective test-time intervention. Our evaluation demonstrates that evi-CEM achieves superior performance in terms of concept prediction, and the proposed concept rectification effectively mitigates concept misalignments for label-efficient training. Our code is available at https://github.com/obiyoag/evi-CEM.

Flexible and Adaptable Summarization via Expertise Separation

A proficient summarization model should exhibit both flexibility -- the capacity to handle a range of in-domain summarization tasks, and adaptability -- the competence to acquire new knowledge and adjust to unseen out-of-domain tasks. Unlike large language models (LLMs) that achieve this through parameter scaling, we propose a more parameter-efficient approach in this study. Our motivation rests on the principle that the general summarization ability to capture salient information can be shared across different tasks, while the domain-specific summarization abilities need to be distinct and tailored. Concretely, we propose MoeSumm, a Mixture-of-Expert Summarization architecture, which utilizes a main expert for gaining the general summarization capability and deputy experts that selectively collaborate to meet specific summarization task requirements. We further propose a max-margin loss to stimulate the separation of these abilities. Our model's distinct separation of general and domain-specific summarization abilities grants it with notable flexibility and adaptability, all while maintaining parameter efficiency. MoeSumm achieves flexibility by managing summarization across multiple domains with a single model, utilizing a shared main expert and selected deputy experts. It exhibits adaptability by tailoring deputy experts to cater to out-of-domain few-shot and zero-shot scenarios. Experimental results on 11 datasets show the superiority of our model compared with recent baselines and LLMs. We also provide statistical and visual evidence of the distinct separation of the two abilities in MoeSumm (https://github.com/iriscxy/MoE_Summ).

Write Summary Step-by-Step: A Pilot Study of Stepwise Summarization

Nowadays, neural text generation has made tremendous progress in abstractive summarization tasks. However, most of the existing summarization models take in the whole document all at once, which sometimes cannot meet the needs in practice. Practically, social text streams such as news events and tweets keep growing from time to time, and can only be fed to the summarization system step by step. Hence, in this paper, we propose the task of Stepwise Summarization, which aims to generate a new appended summary each time a new document is proposed. The appended summary should not only summarize the newly added content but also be coherent with the previous summary, to form an up-to-date complete summary. To tackle this challenge, we design an adversarial learning model, named Stepwise Summary Generator (SSG). First, SSG selectively processes the new document under the guidance of the previous summary, obtaining polished document representation. Next, SSG generates the summary considering both the previous summary and the document. Finally, a convolutional-based discriminator is employed to determine whether the newly generated summary is coherent with the previous summary. For the experiment, we extend the traditional two-step update summarization setting to a multi-step stepwise setting, and re-propose a large-scale stepwise summarization dataset based on a public story generation dataset. Extensive experiments on this dataset show that SSG achieves state-of-the-art performance in terms of both automatic metrics and human evaluations. Ablation studies demonstrate the effectiveness of each module in our framework. We also discuss the benefits and limitations of recent large language models on this task.