Bo Wang

John Giorgi, Gary D. Bader, Bo Wang · utoronto

Motivated by the fact that many relations cross the sentence boundary, there has been increasing interest in document-level relation extraction (DocRE). DocRE requires integrating information within and across sentences, capturing complex interactions between mentions of entities. Most existing methods are pipeline-based, requiring entities as input. However, jointly learning to extract entities and relations can improve performance and be more efficient due to shared parameters and training steps. In this paper, we develop a sequence-to-sequence approach, seq2rel, that can learn the subtasks of DocRE (entity extraction, coreference resolution and relation extraction) end-to-end, replacing a pipeline of task-specific components. Using a simple strategy we call entity hinting, we compare our approach to existing pipeline-based methods on several popular biomedical datasets, in some cases exceeding their performance. We also report the first end-to-end results on these datasets for future comparison. Finally, we demonstrate that, under our model, an end-to-end approach outperforms a pipeline-based approach. Our code, data and trained models are available at {\url{https://github.com/johngiorgi/seq2rel}}. An online demo is available at {\url{https://share.streamlit.io/johngiorgi/seq2rel/main/demo.py}}.

Xiao Liu, Heyan Huang, Ge Shi et al. · microsoft-research

We consider event extraction in a generative manner with template-based conditional generation. Although there is a rising trend of casting the task of event extraction as a sequence generation problem with prompts, these generation-based methods have two significant challenges, including using suboptimal prompts and static event type information. In this paper, we propose a generative template-based event extraction method with dynamic prefix (GTEE-DynPref) by integrating context information with type-specific prefixes to learn a context-specific prefix for each context. Experimental results show that our model achieves competitive results with the state-of-the-art classification-based model OneIE on ACE 2005 and achieves the best performances on ERE. Additionally, our model is proven to be portable to new types of events effectively.

Jinfeng Zhou, Chujie Zheng, Bo Wang et al. · tsinghua

Empathetic conversation is psychologically supposed to be the result of conscious alignment and interaction between the cognition and affection of empathy. However, existing empathetic dialogue models usually consider only the affective aspect or treat cognition and affection in isolation, which limits the capability of empathetic response generation. In this work, we propose the CASE model for empathetic dialogue generation. It first builds upon a commonsense cognition graph and an emotional concept graph and then aligns the user's cognition and affection at both the coarse-grained and fine-grained levels. Through automatic and manual evaluation, we demonstrate that CASE outperforms state-of-the-art baselines of empathetic dialogues and can generate more empathetic and informative responses.

Bo Wang, Yifan Zhang, Jian Li et al.

The occlusion problem remains a crucial challenge in optical flow estimation (OFE). Despite the recent significant progress brought about by deep learning, most existing deep learning OFE methods still struggle to handle occlusions; in particular, those based on two frames cannot correctly handle occlusions because occluded regions have no visual correspondences. However, there is still hope in multi-frame settings, which can potentially mitigate the occlusion issue in OFE. Unfortunately, multi-frame OFE (MOFE) remains underexplored, and the limited studies on it are mainly specially designed for pyramid backbones or else obtain the aligned previous frame's features, such as correlation volume and optical flow, through time-consuming backward flow calculation or non-differentiable forward warping transformation. This study proposes an efficient MOFE framework named SplatFlow to address these shortcomings. SplatFlow introduces the differentiable splatting transformation to align the previous frame's motion feature and designs a Final-to-All embedding method to input the aligned motion feature into the current frame's estimation, thus remodeling the existing two-frame backbones. The proposed SplatFlow is efficient yet more accurate, as it can handle occlusions properly. Extensive experimental evaluations show that SplatFlow substantially outperforms all published methods on the KITTI2015 and Sintel benchmarks. Especially on the Sintel benchmark, SplatFlow achieves errors of 1.12 (clean pass) and 2.07 (final pass), with surprisingly significant 19.4% and 16.2% error reductions, respectively, from the previous best results submitted. The code for SplatFlow is available at https://github.com/wwsource/SplatFlow.

Lazar Atanackovic, Alexander Tong, Bo Wang et al. · mila, utoronto

One of the grand challenges of cell biology is inferring the gene regulatory network (GRN) which describes interactions between genes and their products that control gene expression and cellular function. We can treat this as a causal discovery problem but with two non-standard challenges: (1) regulatory networks are inherently cyclic so we should not model a GRN as a directed acyclic graph (DAG), and (2) observations have significant measurement noise, so for typical sample sizes there will always be a large equivalence class of graphs that are likely given the data, and we want methods that capture this uncertainty. Existing methods either focus on challenge (1), identifying cyclic structure from dynamics, or on challenge (2) learning complex Bayesian posteriors over DAGs, but not both. In this paper we leverage the fact that it is possible to estimate the "velocity" of gene expression with RNA velocity techniques to develop an approach that addresses both challenges. Because we have access to velocity information, we can treat the Bayesian structure learning problem as a problem of sparse identification of a dynamical system, capturing cyclic feedback loops through time. Since our objective is to model uncertainty over discrete structures, we leverage Generative Flow Networks (GFlowNets) to estimate the posterior distribution over the combinatorial space of possible sparse dependencies. Our results indicate that our method learns posteriors that better encapsulate the distributions of cyclic structures compared to counterpart state-of-the-art Bayesian structure learning approaches.

Jun Ma, Yuting He, Feifei Li et al.

Medical image segmentation is a critical component in clinical practice, facilitating accurate diagnosis, treatment planning, and disease monitoring. However, existing methods, often tailored to specific modalities or disease types, lack generalizability across the diverse spectrum of medical image segmentation tasks. Here we present MedSAM, a foundation model designed for bridging this gap by enabling universal medical image segmentation. The model is developed on a large-scale medical image dataset with 1,570,263 image-mask pairs, covering 10 imaging modalities and over 30 cancer types. We conduct a comprehensive evaluation on 86 internal validation tasks and 60 external validation tasks, demonstrating better accuracy and robustness than modality-wise specialist models. By delivering accurate and efficient segmentation across a wide spectrum of tasks, MedSAM holds significant potential to expedite the evolution of diagnostic tools and the personalization of treatment plans.

John Giorgi, Luca Soldaini, Bo Wang et al. · allen-ai, utoronto

Multi-document summarization (MDS) assumes a set of topic-related documents are provided as input. In practice, this document set is not always available; it would need to be retrieved given an information need, i.e. a question or topic statement, a setting we dub "open-domain" MDS. We study this more challenging setting by formalizing the task and bootstrapping it using existing datasets, retrievers and summarizers. Via extensive automatic and human evaluation, we determine: (1) state-of-the-art summarizers suffer large reductions in performance when applied to open-domain MDS, (2) additional training in the open-domain setting can reduce this sensitivity to imperfect retrieval, and (3) summarizers are insensitive to the retrieval of duplicate documents and the order of retrieved documents, but highly sensitive to other errors, like the retrieval of irrelevant documents. Based on our results, we provide practical guidelines to enable future work on open-domain MDS, e.g. how to choose the number of retrieved documents to summarize. Our results suggest that new retrieval and summarization methods and annotated resources for training and evaluation are necessary for further progress in the open-domain setting.

De Cheng, Gerong Wang, Bo Wang et al.

Zero-shot learning (ZSL) aims to learn models that can recognize unseen image semantics based on the training of data with seen semantics. Recent studies either leverage the global image features or mine discriminative local patch features to associate the extracted visual features to the semantic attributes. However, due to the lack of the necessary top-down guidance and semantic alignment for ensuring the model attending to the real attribute-correlation regions, these methods still encounter a significant semantic gap between the visual modality and the attribute modality, which makes their prediction on unseen semantics unreliable. To solve this problem, this paper establishes a novel transformer encoder-decoder model, called hybrid routing transformer (HRT). In HRT encoder, we embed an active attention, which is constructed by both the bottom-up and the top-down dynamic routing pathways to generate the attribute-aligned visual feature. While in HRT decoder, we use static routing to calculate the correlation among the attribute-aligned visual features, the corresponding attribute semantics, and the class attribute vectors to generate the final class label predictions. This design makes the presented transformer model a hybrid of 1) top-down and bottom-up attention pathways and 2) dynamic and static routing pathways. Comprehensive experiments on three widely-used benchmark datasets, namely CUB, SUN, and AWA2, are conducted. The obtained experimental results demonstrate the effectiveness of the proposed method.

Iman Munire Bilal, Bo Wang, Adam Tsakalidis et al.

We introduce the task of microblog opinion summarisation (MOS) and share a dataset of 3100 gold-standard opinion summaries to facilitate research in this domain. The dataset contains summaries of tweets spanning a 2-year period and covers more topics than any other public Twitter summarisation dataset. Summaries are abstractive in nature and have been created by journalists skilled in summarising news articles following a template separating factual information (main story) from author opinions. Our method differs from previous work on generating gold-standard summaries from social media, which usually involves selecting representative posts and thus favours extractive summarisation models. To showcase the dataset's utility and challenges, we benchmark a range of abstractive and extractive state-of-the-art summarisation models and achieve good performance, with the former outperforming the latter. We also show that fine-tuning is necessary to improve performance and investigate the benefits of using different sample sizes.

Weijie Xu, Jinjin Zhao, Francis Iannacci et al. · amazon-science

Generative modeling has been used frequently in synthetic data generation. Fairness and privacy are two big concerns for synthetic data. Although Recent GAN [\cite{goodfellow2014generative}] based methods show good results in preserving privacy, the generated data may be more biased. At the same time, these methods require high computation resources. In this work, we design a fast, fair, flexible and private data generation method. We show the effectiveness of our method theoretically and empirically. We show that models trained on data generated by the proposed method can perform well (in inference stage) on real application scenarios.

Bo Wang, Zhao Zhang, Mingbo Zhao et al.

Mainstream image caption models are usually two-stage captioners, i.e., calculating object features by pre-trained detector, and feeding them into a language model to generate text descriptions. However, such an operation will cause a task-based information gap to decrease the performance, since the object features in detection task are suboptimal representation and cannot provide all necessary information for subsequent text generation. Besides, object features are usually represented by the last layer features that lose the local details of input images. In this paper, we propose a novel One-Stage Image Captioner (OSIC) with dynamic multi-sight learning, which directly transforms input image into descriptive sentences in one stage. As a result, the task-based information gap can be greatly reduced. To obtain rich features, we use the Swin Transformer to calculate multi-level features, and then feed them into a novel dynamic multi-sight embedding module to exploit both global structure and local texture of input images. To enhance the global modeling of encoder for caption, we propose a new dual-dimensional refining module to non-locally model the interaction of the embedded features. Finally, OSIC can obtain rich and useful information to improve the image caption task. Extensive comparisons on benchmark MS-COCO dataset verified the superior performance of our method.

Bo Wang, Tao Wu, Minfeng Zhu et al.

Interactive image synthesis from user-guided input is a challenging task when users wish to control the scene structure of a generated image with ease.Although remarkable progress has been made on layout-based image synthesis approaches, in order to get realistic fake image in interactive scene, existing methods require high-precision inputs, which probably need adjustment several times and are unfriendly to novice users. When placement of bounding boxes is subject to perturbation, layout-based models suffer from "missing regions" in the constructed semantic layouts and hence undesirable artifacts in the generated images. In this work, we propose Panoptic Layout Generative Adversarial Networks (PLGAN) to address this challenge. The PLGAN employs panoptic theory which distinguishes object categories between "stuff" with amorphous boundaries and "things" with well-defined shapes, such that stuff and instance layouts are constructed through separate branches and later fused into panoptic layouts. In particular, the stuff layouts can take amorphous shapes and fill up the missing regions left out by the instance layouts. We experimentally compare our PLGAN with state-of-the-art layout-based models on the COCO-Stuff, Visual Genome, and Landscape datasets. The advantages of PLGAN are not only visually demonstrated but quantitatively verified in terms of inception score, Fréchet inception distance, classification accuracy score, and coverage.

Zizheng Huang, Haoxing Chen, Ziqi Wen et al.

Contrastive learning (CL) continuously achieves significant breakthroughs across multiple domains. However, the most common InfoNCE-based methods suffer from some dilemmas, such as \textit{uniformity-tolerance dilemma} (UTD) and \textit{gradient reduction}, both of which are related to a $\mathcal{P}_{ij}$ term. It has been identified that UTD can lead to unexpected performance degradation. We argue that the fixity of temperature is to blame for UTD. To tackle this challenge, we enrich the CL loss family by presenting a Model-Aware Contrastive Learning (MACL) strategy, whose temperature is adaptive to the magnitude of alignment that reflects the basic confidence of the instance discrimination task, then enables CL loss to adjust the penalty strength for hard negatives adaptively. Regarding another dilemma, the gradient reduction issue, we derive the limits of an involved gradient scaling factor, which allows us to explain from a unified perspective why some recent approaches are effective with fewer negative samples, and summarily present a gradient reweighting to escape this dilemma. Extensive remarkable empirical results in vision, sentence, and graph modality validate our approach's general improvement for representation learning and downstream tasks.

Guoqing Ma, Haoyang Huang, Kun Yan et al.

We present Step-Video-T2V, a state-of-the-art text-to-video pre-trained model with 30B parameters and the ability to generate videos up to 204 frames in length. A deep compression Variational Autoencoder, Video-VAE, is designed for video generation tasks, achieving 16x16 spatial and 8x temporal compression ratios, while maintaining exceptional video reconstruction quality. User prompts are encoded using two bilingual text encoders to handle both English and Chinese. A DiT with 3D full attention is trained using Flow Matching and is employed to denoise input noise into latent frames. A video-based DPO approach, Video-DPO, is applied to reduce artifacts and improve the visual quality of the generated videos. We also detail our training strategies and share key observations and insights. Step-Video-T2V's performance is evaluated on a novel video generation benchmark, Step-Video-T2V-Eval, demonstrating its state-of-the-art text-to-video quality when compared with both open-source and commercial engines. Additionally, we discuss the limitations of current diffusion-based model paradigm and outline future directions for video foundation models. We make both Step-Video-T2V and Step-Video-T2V-Eval available at https://github.com/stepfun-ai/Step-Video-T2V. The online version can be accessed from https://yuewen.cn/videos as well. Our goal is to accelerate the innovation of video foundation models and empower video content creators.

Fan Li, Bo Wang, Pin Wang et al.

The challenge of imbalanced learning lies not only in class imbalance problem, but also in the class overlapping problem which is complex. However, most of the existing algorithms mainly focus on the former. The limitation prevents the existing methods from breaking through. To address this limitation, this paper proposes an ensemble learning algorithm based on dual clustering and stage-wise hybrid sampling (DCSHS). The DCSHS has three parts. Firstly, we design a projection clustering combination framework (PCC) guided by Davies-Bouldin clustering effectiveness index (DBI), which is used to obtain high-quality clusters and combine them to obtain a set of cross-complete subsets (CCS) with balanced class and low overlapping. Secondly, according to the characteristics of subset classes, a stage-wise hybrid sampling algorithm is designed to realize the de-overlapping and balancing of subsets. Finally, a projective clustering transfer mapping mechanism (CTM) is constructed for all processed subsets by means of transfer learning, thereby reducing class overlapping and explore structure information of samples. The major advantage of our algorithm is that it can exploit the intersectionality of the CCS to realize the soft elimination of overlapping majority samples, and learn as much information of overlapping samples as possible, thereby enhancing the class overlapping while class balancing. In the experimental section, more than 30 public datasets and over ten representative algorithms are chosen for verification. The experimental results show that the DCSHS is significantly best in terms of various evaluation criteria.

Jingfeng Yao, Xinggang Wang, Yuehao Song et al.

The diagnosis and treatment of chest diseases play a crucial role in maintaining human health. X-ray examination has become the most common clinical examination means due to its efficiency and cost-effectiveness. Artificial intelligence analysis methods for chest X-ray images are limited by insufficient annotation data and varying levels of annotation, resulting in weak generalization ability and difficulty in clinical dissemination. Here we present EVA-X, an innovative foundational model based on X-ray images with broad applicability to various chest disease detection tasks. EVA-X is the first X-ray image based self-supervised learning method capable of capturing both semantic and geometric information from unlabeled images for universal X-ray image representation. Through extensive experimentation, EVA-X has demonstrated exceptional performance in chest disease analysis and localization, becoming the first model capable of spanning over 20 different chest diseases and achieving leading results in over 11 different detection tasks in the medical field. Additionally, EVA-X significantly reduces the burden of data annotation in the medical AI field, showcasing strong potential in the domain of few-shot learning. The emergence of EVA-X will greatly propel the development and application of foundational medical models, bringing about revolutionary changes in future medical research and clinical practice. Our codes and models are available at: https://github.com/hustvl/EVA-X.

Bo Wang, Yihong Wang, Xiubao Sui et al.

Guided image filter is a well-known local filter in image processing. However, the presence of halo artifacts is a common issue associated with this type of filter. This paper proposes an algorithm that utilizes gradient information to accurately identify the edges of an image. Furthermore, the algorithm uses weighted information to distinguish flat areas from edge areas, resulting in sharper edges and reduced blur in flat areas. This approach mitigates the excessive blurring near edges that often leads to halo artifacts. Experimental results demonstrate that the proposed algorithm significantly suppresses halo artifacts at the edges, making it highly effective for both image denoising and detail enhancement.

Chuang Yu, Jinmiao Zhao, Yunpeng Liu et al.

While large-scale visual foundation models (VFMs) exhibit strong generalization across diverse visual domains, their potential for single-frame infrared small target (SIRST) detection remains largely unexplored. To fill this gap, we systematically introduce the frozen representations from VFMs into the SIRST task for the first time and propose a Foundation-Driven Efficient Paradigm (FDEP), which can seamlessly adapt to existing encoder-decoder-based methods and significantly improve accuracy without additional inference overhead. Specifically, a Semantic Alignment Modulation Fusion (SAMF) module is designed to achieve dynamic alignment and deep fusion of the global semantic priors from VFMs with task-specific features. Meanwhile, to avoid the inference time burden introduced by VFMs, we propose a Collaborative Optimization-based Implicit Self-Distillation (CO-ISD) strategy, which enables implicit semantic transfer between the main and lightweight branches through parameter sharing and synchronized backpropagation. In addition, to unify the fragmented evaluation system, we construct a Holistic SIRST Evaluation (HSE) metric that performs multi-threshold integral evaluation at both pixel-level confidence and target-level robustness, providing a stable and comprehensive basis for fair model comparison. Extensive experiments demonstrate that the SIRST detection networks equipped with our FDEP framework achieve state-of-the-art (SOTA) performance on multiple public datasets. Our code is available at https://github.com/YuChuang1205/FDEP-Framework

Yunfeng Li, Bo Wang, Ye Li

The main problem in RGB-T tracking is the correct and optimal merging of the cross-modal features of visible and thermal images. Some previous methods either do not fully exploit the potential of RGB and TIR information for channel and spatial feature fusion or lack a direct interaction between the template and the search area, which limits the model's ability to fully utilize the original semantic information of both modalities. To address these limitations, we investigate how to achieve a direct fusion of cross-modal channels and spatial features in RGB-T tracking and propose CSTNet. It uses the Vision Transformer (ViT) as the backbone and adds a Joint Spatial and Channel Fusion Module (JSCFM) and Spatial Fusion Module (SFM) integrated between the transformer blocks to facilitate cross-modal feature interaction. The JSCFM module achieves joint modeling of channel and multi-level spatial features. The SFM module includes a cross-attention-like architecture for cross modeling and joint learning of RGB and TIR features. Comprehensive experiments show that CSTNet achieves state-of-the-art performance. To enhance practicality, we retrain the model without JSCFM and SFM modules and use CSNet as the pretraining weight, and propose CSTNet-small, which achieves 50% speedup with an average decrease of 1-2% in SR and PR performance. CSTNet and CSTNet-small achieve real-time speeds of 21 fps and 33 fps on the Nvidia Jetson Xavier, meeting actual deployment requirements. Code is available at https://github.com/LiYunfengLYF/CSTNet.

Mengting Chen, Yuxin Fang, Xinggang Wang et al.

Few-shot learning is a challenging task that aims at training a classifier for unseen classes with only a few training examples. The main difficulty of few-shot learning lies in the lack of intra-class diversity within insufficient training samples. To alleviate this problem, we propose a novel generative framework, Diversity Transfer Network (DTN), that learns to transfer latent diversities from known categories and composite them with support features to generate diverse samples for novel categories in feature space. The learning problem of the sample generation (i.e., diversity transfer) is solved via minimizing an effective meta-classification loss in a single-stage network, instead of the generative loss in previous works. Besides, an organized auxiliary task co-training over known categories is proposed to stabilize the meta-training process of DTN. We perform extensive experiments and ablation studies on three datasets, i.e., \emph{mini}ImageNet, CIFAR100 and CUB. The results show that DTN, with single-stage training and faster convergence speed, obtains the state-of-the-art results among the feature generation based few-shot learning methods. Code and supplementary material are available at: \texttt{https://github.com/Yuxin-CV/DTN}

Zhishuai Zhang, Wei Shen, Siyuan Qiao et al.

Recent anchor-based deep face detectors have achieved promising performance, but they are still struggling to detect hard faces, such as small, blurred and partially occluded faces. A reason is that they treat all images and faces equally, without putting more effort on hard ones; however, many training images only contain easy faces, which are less helpful to achieve better performance on hard images. In this paper, we propose that the robustness of a face detector against hard faces can be improved by learning small faces on hard images. Our intuitions are (1) hard images are the images which contain at least one hard face, thus they facilitate training robust face detectors; (2) most hard faces are small faces and other types of hard faces can be easily converted to small faces by shrinking. We build an anchor-based deep face detector, which only output a single feature map with small anchors, to specifically learn small faces and train it by a novel hard image mining strategy. Extensive experiments have been conducted on WIDER FACE, FDDB, Pascal Faces, and AFW datasets to show the effectiveness of our method. Our method achieves APs of 95.7, 94.9 and 89.7 on easy, medium and hard WIDER FACE val dataset respectively, which surpass the previous state-of-the-arts, especially on the hard subset. Code and model are available at https://github.com/bairdzhang/smallhardface.

Josep Crego, Jungi Kim, Guillaume Klein et al.

Since the first online demonstration of Neural Machine Translation (NMT) by LISA, NMT development has recently moved from laboratory to production systems as demonstrated by several entities announcing roll-out of NMT engines to replace their existing technologies. NMT systems have a large number of training configurations and the training process of such systems is usually very long, often a few weeks, so role of experimentation is critical and important to share. In this work, we present our approach to production-ready systems simultaneously with release of online demonstrators covering a large variety of languages (12 languages, for 32 language pairs). We explore different practical choices: an efficient and evolutive open-source framework; data preparation; network architecture; additional implemented features; tuning for production; etc. We discuss about evaluation methodology, present our first findings and we finally outline further work. Our ultimate goal is to share our expertise to build competitive production systems for "generic" translation. We aim at contributing to set up a collaborative framework to speed-up adoption of the technology, foster further research efforts and enable the delivery and adoption to/by industry of use-case specific engines integrated in real production workflows. Mastering of the technology would allow us to build translation engines suited for particular needs, outperforming current simplest/uniform systems.

Jiang Yuan, Ji Ma, Bo Wang et al.

Implicit degradation modeling-based blind super-resolution (SR) has attracted more increasing attention in the community due to its excellent generalization to complex degradation scenarios and wide application range. How to extract more discriminative degradation representations and fully adapt them to specific image features is the key to this task. In this paper, we propose a new Content-decoupled Contrastive Learning-based blind image super-resolution (CdCL) framework following the typical blind SR pipeline. This framework introduces negative-free contrastive learning technique for the first time to model the implicit degradation representation, in which a new cyclic shift sampling strategy is designed to ensure decoupling between content features and degradation features from the data perspective, thereby improving the purity and discriminability of the learned implicit degradation space. In addition, we propose a detail-aware implicit degradation adapting module that can better adapt degradation representations to specific LR features by enhancing the basic adaptation unit's perception of image details, significantly reducing the overall SR model complexity. Extensive experiments on synthetic and real data show that our method achieves highly competitive quantitative and qualitative results in various degradation settings while obviously reducing parameters and computational costs, validating the feasibility of designing practical and lightweight blind SR tools.

Shihao Ma, Andy G. X. Zeng, Benjamin Haibe-Kains et al.

High-throughput omics profiling advancements have greatly enhanced cancer patient stratification. However, incomplete data in multi-omics integration presents a significant challenge, as traditional methods like sample exclusion or imputation often compromise biological diversity and dependencies. Furthermore, the critical task of accurately classifying new patients with partial omics data into existing subtypes is commonly overlooked. To address these issues, we introduce IntegrAO (Integrate Any Omics), an unsupervised framework for integrating incomplete multi-omics data and classifying new samples. IntegrAO first combines partially overlapping patient graphs from diverse omics sources and utilizes graph neural networks to produce unified patient embeddings. Our systematic evaluation across five cancer cohorts involving six omics modalities demonstrates IntegrAO's robustness to missing data and its accuracy in classifying new samples with partial profiles. An acute myeloid leukemia case study further validates its capability to uncover biological and clinical heterogeneity in incomplete datasets. IntegrAO's ability to handle heterogeneous and incomplete data makes it an essential tool for precision oncology, offering a holistic approach to patient characterization.

Adamo Young, Fei Wang, David S Wishart et al.

Compound identification from tandem mass spectrometry (MS/MS) data is a critical step in the analysis of complex mixtures. Typical solutions for the MS/MS spectrum to compound (MS2C) problem involve comparing the unknown spectrum against a library of known spectrum-molecule pairs, an approach that is limited by incomplete library coverage. Compound to MS/MS spectrum (C2MS) models can improve retrieval rates by augmenting real libraries with predicted MS/MS spectra. Unfortunately, many existing C2MS models suffer from problems with mass accuracy, generalization, or interpretability. We develop a new probabilistic method for C2MS prediction, FraGNNet, that can efficiently and accurately simulate MS/MS spectra with high mass accuracy. Our approach formulates the C2MS problem as learning a distribution over molecule fragments. FraGNNet achieves state-of-the-art performance in terms of prediction error and surpasses existing C2MS models as a tool for retrieval-based MS2C.

Qinqian Lei, Bo Wang, Robby T. Tan

Detecting human-object interactions (HOI) in a few-shot setting remains a challenge. Existing meta-learning methods struggle to extract representative features for classification due to the limited data, while existing few-shot HOI models rely on HOI text labels for classification. Moreover, some query images may display visual similarity to those outside their class, such as similar backgrounds between different HOI classes. This makes learning more challenging, especially with limited samples. Bongard-HOI (Jiang et al. 2022) epitomizes this HOI few-shot problem, making it the benchmark we focus on in this paper. In our proposed method, we introduce novel label-uncertain query augmentation techniques to enhance the diversity of the query inputs, aiming to distinguish the positive HOI class from the negative ones. As these augmented inputs may or may not have the same class label as the original inputs, their class label is unknown. Those belonging to a different class become hard samples due to their visual similarity to the original ones. Additionally, we introduce a novel pseudo-label generation technique that enables a mean teacher model to learn from the augmented label-uncertain inputs. We propose to augment the negative support set for the student model to enrich the semantic information, fostering diversity that challenges and enhances the student's learning. Experimental results demonstrate that our method sets a new state-of-the-art (SOTA) performance by achieving 68.74% accuracy on the Bongard-HOI benchmark, a significant improvement over the existing SOTA of 66.59%. In our evaluation on HICO-FS, a more general few-shot recognition dataset, our method achieves 73.27% accuracy, outperforming the previous SOTA of 71.20% in the 5-way 5-shot task.

Augustin Toma, Ronald Xie, Steven Palayew et al.

Medical errors in clinical text pose significant risks to patient safety. The MEDIQA-CORR 2024 shared task focuses on detecting and correcting these errors across three subtasks: identifying the presence of an error, extracting the erroneous sentence, and generating a corrected sentence. In this paper, we present our approach that achieved top performance in all three subtasks. For the MS dataset, which contains subtle errors, we developed a retrieval-based system leveraging external medical question-answering datasets. For the UW dataset, reflecting more realistic clinical notes, we created a pipeline of modules to detect, localize, and correct errors. Both approaches utilized the DSPy framework for optimizing prompts and few-shot examples in large language model (LLM) based programs. Our results demonstrate the effectiveness of LLM based programs for medical error correction. However, our approach has limitations in addressing the full diversity of potential errors in medical documentation. We discuss the implications of our work and highlight future research directions to advance the robustness and applicability of medical error detection and correction systems.

Ze Yu Zhao, Zheng Zhu, Guilin Li et al.

In this work, we introduce an innovative autoregressive model leveraging Generative Pretrained Transformer (GPT) architectures, tailored for fraud detection in payment systems. Our approach innovatively confronts token explosion and reconstructs behavioral sequences, providing a nuanced understanding of transactional behavior through temporal and contextual analysis. Utilizing unsupervised pretraining, our model excels in feature representation without the need for labeled data. Additionally, we integrate a differential convolutional approach to enhance anomaly detection, bolstering the security and efficacy of one of the largest online payment merchants in China. The scalability and adaptability of our model promise broad applicability in various transactional contexts.

Junzhuo Li, Bo Wang, Xiuze Zhou et al.

Mixture-of-Experts (MoE) models offer immense capacity via sparsely gated expert subnetworks, yet adapting them to multiple domains without catastrophic forgetting remains an open challenge. Existing approaches either incur prohibitive computation, suffer cross-domain interference, or require separate runs per domain. We propose DES-MoE, a dynamic expert specialization framework for multi-domain adaptation of Mixture-of-Experts models. DES-MoE addresses catastrophic forgetting through three innovations: (1) an adaptive router balancing pre-trained knowledge retention and task-specific updates via distillation, (2) real-time expert-domain correlation mapping to isolate domain-specific gradients, and (3) a three-phase adaptive fine-tuning schedule that progressively freezes non-specialized parameters. Evaluated on six domains (math, code, law, etc.), DES-MoE matches single-domain ESFT performance while training one unified model, reduces forgetting by 89% compared to full fine-tuning as domains scale from 2 to 6, and achieves 68% faster convergence than conventional methods. Our work establishes dynamic expert isolation as a scalable paradigm for multi-task MoE adaptation.

Juexiao Zhou, Zhongyi Han, Mankun Xin et al.

Global population aging presents increasing challenges to healthcare systems, with coronary artery disease (CAD) responsible for approximately 17.8 million deaths annually, making it a leading cause of global mortality. As CAD is largely preventable, early detection and proactive management are essential. In this work, we introduce DigitalShadow, an advanced early warning system for CAD, powered by a fine-tuned facial foundation model. The system is pre-trained on 21 million facial images and subsequently fine-tuned into LiveCAD, a specialized CAD risk assessment model trained on 7,004 facial images from 1,751 subjects across four hospitals in China. DigitalShadow functions passively and contactlessly, extracting facial features from live video streams without requiring active user engagement. Integrated with a personalized database, it generates natural language risk reports and individualized health recommendations. With privacy as a core design principle, DigitalShadow supports local deployment to ensure secure handling of user data.

Bo Wang, Lei Wang, Junyang Chen et al.

Deep learning-based medical image segmentation technology aims at automatic recognizing and annotating objects on the medical image. Non-local attention and feature learning by multi-scale methods are widely used to model network, which drives progress in medical image segmentation. However, those attention mechanism methods have weakly non-local receptive fields' strengthened connection for small objects in medical images. Then, the features of important small objects in abstract or coarse feature maps may be deserted, which leads to unsatisfactory performance. Moreover, the existing multi-scale methods only simply focus on different sizes of view, whose sparse multi-scale features collected are not abundant enough for small objects segmentation. In this work, a multi-dimensional attention segmentation model with cascade multi-scale convolution is proposed to predict accurate segmentation for small objects in medical images. As the weight function, multi-dimensional attention modules provide coefficient modification for significant/informative small objects features. Furthermore, The cascade multi-scale convolution modules in each skip-connection path are exploited to capture multi-scale features in different semantic depth. The proposed method is evaluated on three datasets: KiTS19, Pancreas CT of Decathlon-10, and MICCAI 2018 LiTS Challenge, demonstrating better segmentation performances than the state-of-the-art baselines.

Wei Xie, Bo Wang, Cheng Li et al.

While biomanufacturing plays a significant role in supporting the economy and ensuring public health, it faces critical challenges, including complexity, high variability, lengthy lead time, and very limited process data, especially for personalized new cell and gene biotherapeutics. Driven by these challenges, we propose an interpretable semantic bioprocess probabilistic knowledge graph and develop a game theory based risk and sensitivity analyses for production process to facilitate quality-by-design and stability control. Specifically, by exploring the causal relationships and interactions of critical process parameters and quality attributes (CPPs/CQAs), we create a Bayesian network based probabilistic knowledge graph characterizing the complex causal interdependencies of all factors. Then, we introduce a Shapley value based sensitivity analysis, which can correctly quantify the variation contribution from each input factor on the outputs (i.e., productivity, product quality). Since the bioprocess model coefficients are learned from limited process observations, we derive the Bayesian posterior distribution to quantify model uncertainty and further develop the Shapley value based sensitivity analysis to evaluate the impact of estimation uncertainty from each set of model coefficients. Therefore, the proposed bioprocess risk and sensitivity analyses can identify the bottlenecks, guide the reliable process specifications and the most "informative" data collection, and improve production stability.

Wei Shen, Yilu Guo, Yan Wang et al.

Age estimation from facial images is typically cast as a label distribution learning or regression problem, since aging is a gradual progress. Its main challenge is the facial feature space w.r.t. ages is inhomogeneous, due to the large variation in facial appearance across different persons of the same age and the non-stationary property of aging. In this paper, we propose two Deep Differentiable Random Forests methods, Deep Label Distribution Learning Forest (DLDLF) and Deep Regression Forest (DRF), for age estimation. Both of them connect split nodes to the top layer of convolutional neural networks (CNNs) and deal with inhomogeneous data by jointly learning input-dependent data partitions at the split nodes and age distributions at the leaf nodes. This joint learning follows an alternating strategy: (1) Fixing the leaf nodes and optimizing the split nodes and the CNN parameters by Back-propagation; (2) Fixing the split nodes and optimizing the leaf nodes by Variational Bounding. Two Deterministic Annealing processes are introduced into the learning of the split and leaf nodes, respectively, to avoid poor local optima and obtain better estimates of tree parameters free of initial values. Experimental results show that DLDLF and DRF achieve state-of-the-art performance on three age estimation datasets.

Xingchao Peng, Qinxun Bai, Xide Xia et al.

Conventional unsupervised domain adaptation (UDA) assumes that training data are sampled from a single domain. This neglects the more practical scenario where training data are collected from multiple sources, requiring multi-source domain adaptation. We make three major contributions towards addressing this problem. First, we collect and annotate by far the largest UDA dataset, called DomainNet, which contains six domains and about 0.6 million images distributed among 345 categories, addressing the gap in data availability for multi-source UDA research. Second, we propose a new deep learning approach, Moment Matching for Multi-Source Domain Adaptation M3SDA, which aims to transfer knowledge learned from multiple labeled source domains to an unlabeled target domain by dynamically aligning moments of their feature distributions. Third, we provide new theoretical insights specifically for moment matching approaches in both single and multiple source domain adaptation. Extensive experiments are conducted to demonstrate the power of our new dataset in benchmarking state-of-the-art multi-source domain adaptation methods, as well as the advantage of our proposed model. Dataset and Code are available at \url{http://ai.bu.edu/M3SDA/}.

Haichao Shi, Peng Li, Bo Wang et al.

Recently it has shown that the policy-gradient methods for reinforcement learning have been utilized to train deep end-to-end systems on natural language processing tasks. What's more, with the complexity of understanding image content and diverse ways of describing image content in natural language, image captioning has been a challenging problem to deal with. To the best of our knowledge, most state-of-the-art methods follow a pattern of sequential model, such as recurrent neural networks (RNN). However, in this paper, we propose a novel architecture for image captioning with deep reinforcement learning to optimize image captioning tasks. We utilize two networks called "policy network" and "value network" to collaboratively generate the captions of images. The experiments are conducted on Microsoft COCO dataset, and the experimental results have verified the effectiveness of the proposed method.

Marinka Zitnik, Francis Nguyen, Bo Wang et al.

New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include a myriad of properties describing genome, epigenome, transcriptome, microbiome, phenotype, and lifestyle. No single data type, however, can capture the complexity of all the factors relevant to understanding a phenomenon such as a disease. Integrative methods that combine data from multiple technologies have thus emerged as critical statistical and computational approaches. The key challenge in developing such approaches is the identification of effective models to provide a comprehensive and relevant systems view. An ideal method can answer a biological or medical question, identifying important features and predicting outcomes, by harnessing heterogeneous data across several dimensions of biological variation. In this Review, we describe the principles of data integration and discuss current methods and available implementations. We provide examples of successful data integration in biology and medicine. Finally, we discuss current challenges in biomedical integrative methods and our perspective on the future development of the field.

Wei Shen, Yilu Guo, Yan Wang et al.

Age estimation from facial images is typically cast as a nonlinear regression problem. The main challenge of this problem is the facial feature space w.r.t. ages is heterogeneous, due to the large variation in facial appearance across different persons of the same age and the non-stationary property of aging patterns. In this paper, we propose Deep Regression Forests (DRFs), an end-to-end model, for age estimation. DRFs connect the split nodes to a fully connected layer of a convolutional neural network (CNN) and deal with heterogeneous data by jointly learning input-dependant data partitions at the split nodes and data abstractions at the leaf nodes. This joint learning follows an alternating strategy: First, by fixing the leaf nodes, the split nodes as well as the CNN parameters are optimized by Back-propagation; Then, by fixing the split nodes, the leaf nodes are optimized by iterating a step-size free and fast-converging update rule derived from Variational Bounding. We verify the proposed DRFs on three standard age estimation benchmarks and achieve state-of-the-art results on all of them.

Siyuan Qiao, Zhishuai Zhang, Wei Shen et al.

Depth is one of the keys that make neural networks succeed in the task of large-scale image recognition. The state-of-the-art network architectures usually increase the depths by cascading convolutional layers or building blocks. In this paper, we present an alternative method to increase the depth. Our method is by introducing computation orderings to the channels within convolutional layers or blocks, based on which we gradually compute the outputs in a channel-wise manner. The added orderings not only increase the depths and the learning capacities of the networks without any additional computation costs, but also eliminate the overlap singularities so that the networks are able to converge faster and perform better. Experiments show that the networks based on our method achieve the state-of-the-art performances on CIFAR and ImageNet datasets.

Arkaitz Zubiaga, Alex Voss, Rob Procter et al.

In contrast to much previous work that has focused on location classification of tweets restricted to a specific country, here we undertake the task in a broader context by classifying global tweets at the country level, which is so far unexplored in a real-time scenario. We analyse the extent to which a tweet's country of origin can be determined by making use of eight tweet-inherent features for classification. Furthermore, we use two datasets, collected a year apart from each other, to analyse the extent to which a model trained from historical tweets can still be leveraged for classification of new tweets. With classification experiments on all 217 countries in our datasets, as well as on the top 25 countries, we offer some insights into the best use of tweet-inherent features for an accurate country-level classification of tweets. We find that the use of a single feature, such as the use of tweet content alone -- the most widely used feature in previous work -- leaves much to be desired. Choosing an appropriate combination of both tweet content and metadata can actually lead to substantial improvements of between 20\% and 50\%. We observe that tweet content, the user's self-reported location and the user's real name, all of which are inherent in a tweet and available in a real-time scenario, are particularly useful to determine the country of origin. We also experiment on the applicability of a model trained on historical tweets to classify new tweets, finding that the choice of a particular combination of features whose utility does not fade over time can actually lead to comparable performance, avoiding the need to retrain. However, the difficulty of achieving accurate classification increases slightly for countries with multiple commonalities, especially for English and Spanish speaking countries.

Bo Wang, Anna Goldenberg

Analysis of high dimensional noisy data is of essence across a variety of research fields. Feature selection techniques are designed to find the relevant feature subset that can facilitate classification or pattern detection. Traditional (supervised) feature selection methods utilize label information to guide the identification of relevant feature subsets. In this paper, however, we consider the unsupervised feature selection problem. Without the label information, it is particularly difficult to identify a small set of relevant features due to the noisy nature of real-world data which corrupts the intrinsic structure of the data. Our Gradient-based Laplacian Feature Selection (GLFS) selects important features by minimizing the variance of the Laplacian regularized least squares regression model. With $\ell_1$ relaxation, GLFS can find a sparse subset of features that is relevant to the Laplacian manifolds. Extensive experiments on simulated, three real-world object recognition and two computational biology datasets, have illustrated the power and superior performance of our approach over multiple state-of-the-art unsupervised feature selection methods. Additionally, we show that GLFS selects a sparser set of more relevant features in a supervised setting outperforming the popular elastic net methodology.