72 accepted papers
Attention-based regression models are often trained by jointly optimizing Mean Squared Error (MSE) loss and Pearson correlation coefficient (PCC) loss, emphasizing the magnitude of errors and the order or shape of targets, respectively. A common but poorly understood phenomenon during training is th…
Drug target interaction (DTI) prediction is a cornerstone of computational drug discovery, enabling rational design, repurposing, and mechanistic insights. While deep learning has advanced DTI modeling, existing approaches primarily rely on SMILES–protein pairs and fail to exploit the rich multimoda…
Exploring how genetic sequences shape phenotypes is a fundamental challenge in biology and a key step toward scalable, hypothesis-driven experimentation. The task is complicated by the large modality gap between sequences and phenotypes, as well as the pleiotropic nature of gene–phenotype relationsh
Multimodal contrastive learning typically relies on pairwise similarities for alignment, but recent work has shown that Gramian volumes can capture higher-order correlations across modalities. However, Euclidean Gramian volumes suffer from volume collapse under L2 normalization, concentrating near u
Deep learning has significantly advanced numerous fields by training on extensive annotated datasets. However, this data-driven paradigm faces limitations such as limited adaptability and high annotation costs, particularly when precise adherence to detailed, domain-specific guidelines is required i
Unifying image clustering across different clustering scenarios remains challenging due to fundamental gaps among tasks. We introduce a Guideline-Driven Image Clustering Agent, the first universal framework that bridges these gaps through textual guidelines. To incorporate complex guidelines without
Exploring the functions of genes and gene products is crucial to a wide range of fields, including medical research, evolutionary biology, and environmental science. However, discovering new functions largely relies on expensive and exhaustive wet lab experiments. Existing methods of automatic funct…
Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we i…
"What I cannot create, I do not understand." Human wisdom reveals that creation is one of the highest forms of learning. For example, Diffusion Models have demonstrated remarkable semantic structural and memory capabilities in image generation, denoising, and restoration, which intuitively benefits…
Molecular property prediction aims to learn representations that map chemical structures to functional properties. While multimodal learning has emerged as a powerful paradigm to learn molecular representations, prior works have largely overlooked textual and taxonomic information of molecules for r…
Composed Image Retrieval (CIR) targets the retrieval of images conditioned on a reference image and a textual modification, but constructing labeled triplets (reference image, textual modification, target image) is inherently challenging. Existing Zero-Shot CIR (ZS-CIR) approaches often rely on well…
Artificial intelligence has significantly impacted medical applications, particularly with the advent of Medical Large Vision Language Models (Med-LVLMs), sparking optimism for the future of automated and personalized healthcare. However, the trustworthiness of Med-LVLMs remains unverified, posing s…
AI-aided drug discovery (AIDD) is gaining popularity due to its potential to make the search for new pharmaceuticals faster, less expensive, and more effective. Despite its extensive use in numerous fields (e.g., ADMET prediction, virtual screening), little research has been conducted on the out-of-…
The performance of deep learning models heavily relies on the quality of the training data. Inadequacies in the training data, such as corrupt input or noisy labels, can lead to the failure of model generalization. Recent studies propose repairing the model by identifying the training samples that c…
"Detecting and segmenting objects within whole slide images is essential in computational pathology workflow. Self-supervised learning (SSL) is appealing to such annotation-heavy tasks. Despite the extensive benchmarks in natural images for dense tasks, such studies are, unfortunately, absent in cur…
3D delineation of anatomical structures is a cardinal goal in medical imaging analysis. Prior to deep learning, statistical shape models (SSMs) that imposed anatomical constraints and produced high quality surfaces were a core technology. Today’s fully-convolutional networks (FCNs), while dominant,…
Valuation problems, such as feature interpretation, data valuation and model valuation for ensembles, become increasingly more important in many machine learning applications. Such problems are commonly solved by well-known game-theoretic criteria, such as Shapley value or Banzhaf value. In this wor…
Learning to reason about relations and dynamics over multiple interacting objects is a challenging topic in machine learning. The challenges mainly stem from that the interacting systems are exponentially-compositional, symmetrical, and commonly geometrically-constrained. Current methods, particular…
Transferability estimation has been an essential tool in selecting a pre-trained model and the layers in it for transfer learning, to transfer, so as to maximize the performance on a target task and prevent negative transfer. Existing estimation algorithms either require intensive training on target…
Retrosynthetic planning plays an important role in the field of organic chemistry, which could generate a synthetic route for the target product. The synthetic route is a series of reactions which are started from the available molecules. The most challenging problem in the generation of the synthet…
Graph Neural Networks (GNNs) have achieved remarkable performance on graph-based tasks. The key idea for GNNs is to obtain informative representation through aggregating information from local neighborhoods. However, it remains an open question whether the neighborhood information is adequately aggr…
Integration of heterogeneous and high-dimensional data (e.g., multiomics) is becoming increasingly important. Existing multimodal classification algorithms mainly focus on improving performance by exploiting the complementarity from different modalities. However, conventional approaches are basicall…
The large-scale whole-slide images (WSIs) facilitate the learning-based computational pathology methods. However, the gigapixel size of WSIs makes it hard to train a conventional model directly. Current approaches typically adopt multiple-instance learning (MIL) to tackle this problem. Among them, M…
Weakly-supervised whole-slide image (WSI) classification (WSWC) is a challenging task where a large number of unlabeled patches (instances) exist within each WSI (bag) while only a slide label is given. Despite recent progress for the multiple instance learning (MIL)-based WSI analysis, the major l…
The protein tertiary structure largely determines its interaction with other molecules. Despite its importance in various structure-related tasks, fully-supervised data are often time-consuming and costly to obtain. Existing pre-training models mostly focus on amino-acid sequences or multiple sequen…
Vision-language representation learning largely benefits from image-text alignment through contrastive losses (e.g., InfoNCE loss). The success of this alignment strategy is attributed to its capability in maximizing the mutual information (MI) between an image and its matched text. However, simply…
The immunohistochemistry (IHC) test of biopsy tissue is crucial to develop targeted treatment and evaluate prognosis for cancer patients. The IHC staining slide is usually digitized into the whole-slide image (WSI) with gigapixels for quantitative image analysis. To perform a whole image prediction…
Recent studies imply that deep neural networks are vulnerable to adversarial examples, i.e., inputs with a slight but intentional perturbation are incorrectly classified by the network. Such vulnerability makes it risky for some security-related applications (e.g., semantic segmentation in autonomou…
More recently, there has been a surge of interest in employing machine learning approaches to expedite the drug discovery process where virtual screening for hit discovery and ADMET prediction for lead optimization play essential roles. One of the main obstacles to the wide success of machine learni…
Given the input graph and its label/property, several key problems of graph learning, such as finding interpretable subgraphs, graph denoising and graph compression, can be attributed to the fundamental problem of recognizing a subgraph of the original one. This subgraph shall be as informative…
Graph Neural Networks (GNNs) draw their strength from explicitly modeling the topological information of structured data. However, existing GNNs suffer from limited capability in capturing the hierarchical graph representation which plays an important role in graph classification. In this paper, we…
Meta-learning has proven to be a powerful paradigm for transferring the knowledge from previous tasks to facilitate the learning of a novel task. Current dominant algorithms train a well-generalized model initialization which is adapted to each task via the support set. The crux lies in optimizing t…
In adversarial training (AT), the main focus has been the objective and optimizer while the model has been less studied, so that the models being used are still those classic ones in standard training (ST). Classic network architectures (NAs) are generally worse than searched NA in ST, which should…
The surrogate that predicts the performance of hyperparameters has been a key component for sequential model-based hyperparameter optimization. In practical applications, a trial of a hyper-parameter configuration may be so costly that a surrogate is expected to return an optimal configuration with…
Nucleus instance segmentation and classification in histopathological images is an essential prerequisite in pathology diagnosis/prognosis. However, nucleus annotations (e.g., segmentation and labeling) require domain experts, and annotating nuclei at pixel-level is time-consuming and labor-intensiv…
Graph Convolutional Networks (GCNs) are promising deep learning approaches in learning representations for graph-structured data. Despite the proliferation of such methods, it is well known that they are vulnerable to carefully crafted adversarial attacks on the graph structure. In this paper, we fi…
Recently, the teacher-student knowledge distillation framework has demonstrated its potential in training Graph Neural Networks (GNNs). However, due to the difficulty of training over-parameterized GNN models, one may not easily obtain a satisfactory teacher model for distillation. Furthermore, the…
Protein secondary structure prediction (PSSP) is an essential task in computational biology. To achieve the accurate PSSP, the general and vital feature engineering is to use multiple sequence alignment (MSA) for Position-Specific Scoring Matrix (PSSM) extraction. However, when only low-quality PSSM…
Many approaches have been proposed for time series forecasting, in light of its significance in wide applications including business demand prediction. However, the existing methods suffer from two key limitations. Firstly, most point prediction models only predict an exact value of each time step…
Neural architecture search (NAS) has become an important approach to automatically find effective architectures. To cover all possible good architectures, we need to search in an extremely large search space with billions of candidate architectures. More critically, given a large search space, we ma…
Within medical imaging, organ/pathology segmentation models trained on current publicly available and fully-annotated datasets usually do not well-represent the heterogeneous modalities, phases, pathologies, and clinical scenarios encountered in real environments. On the other hand, there are tremen…
Deep multimodal fusion by using multiple sources of data for classification or regression has exhibited a clear advantage over the unimodal counterpart on various applications. Yet, current methods including aggregation-based and alignment-based fusion are still inadequate in balancing the trade-off…
Graph Neural Networks (GNN) and Variational Autoencoders (VAEs) have been widely used in modeling and generating graphs with latent factors. However there is no clear explanation of what these latent factors are and why they perform well. In this work, we present Dirichlet Graph Variational Autoenco…
Over-fitting and over-smoothing are two main obstacles of developing deep Graph Convolutional Networks (GCNs) for node classification. In particular, over-fitting weakens the generalization ability on small dataset, while over-smoothing impedes model training by isolating output representations from…
Unsupervised domain adaptation enables to alleviate the need for pixel-wise annotation in the semantic segmentation. One of the most common strategies is to translate images from the source domain to the target domain and then align their marginal distributions in the feature space using adversarial…
Retrosynthesis is the process of recursively decomposing target molecules into available building blocks. It plays an important role in solving problems in organic synthesis planning. To automate or assist in the retrosynthesis analysis, various retrosynthesis prediction algorithms have been propose…
Recent advances in neural architecture search inspire many channel number search algorithms~(CNS) for convolutional neural networks. To improve searching efficiency, parameter sharing is widely applied, which reuses parameters among different channel configurations. Nevertheless, it is unclear how p…
How to obtain informative representations of molecules is a crucial prerequisite in AI-driven drug design and discovery. Recent researches abstract molecules as graphs and employ Graph Neural Networks (GNNs) for molecular representation learning. Nevertheless, two issues impede the usage of GNNs in…
Recently, Neural Architecture Search (NAS) has been successfully applied to multiple artificial intelligence areas and shows better performance compared with hand-designed networks. However, the existing NAS methods only target a specific task. Most of them usually do well in searching an architectu…
Deep networks have achieved impressive performance in various domains, but their applications are largely limited by the prohibitive computational overhead. In this paper, we propose a novel algorithm, namely collaborative channel pruning (CCP), to reduce the computational overhead with negligible p…
For constrained nonconvex minimization problems, we propose a meta stochastic projection-free optimization algorithm, named Normalized Frank Wolfe Updating, that can take any Gradient Estimator (GE) as input. For this algorithm, we prove its convergence rate, regardless of the choice of GE. Using a…
Dynamic Time Warping (DTW) is widely used as a similarity measure in various domains. Due to its invariance against warping in the time axis, DTW provides more meaningful discrepancy measurements between two signals than other dis- tance measures. In this paper, we propose a novel component in an ar…
In this paper, we present a sample distributed greedy pursuit method for non-convex sparse learning under cardinality constraint. Given the training samples uniformly randomly partitioned across multiple machines, the proposed method alternates between local inexact sparse minimization of a Newton-t…
The communication overhead has become a significant bottleneck in data-parallel network with the increasing of model size and data samples. In this work, we propose a new algorithm LPC-SVRG with quantized gradients and its acceleration ALPC-SVRG to effectively reduce the communication complexity wh…
Most state-of-the-art action localization systems process each action proposal individually, without explicitly exploiting their relations during learning. However, the relations between proposals actually play an important role in action localization, since a meaningful action always consists of mu…
In order to learn quickly with few samples, meta-learning utilizes prior knowledge learned from previous tasks. However, a critical challenge in meta-learning is task uncertainty and heterogeneity, which can not be handled via globally sharing knowledge among tasks. In this paper, based on gradient-…
Bayesian optimisation is a popular technique for hyperparameter learning but typically requires initial exploration even in cases where similar prior tasks have been solved. We propose to transfer information across tasks using learnt representations of training datasets used in those tasks. This re…
This paper studies Learning from Observations (LfO) for imitation learning with access to state-only demonstrations. In contrast to Learning from Demonstration (LfD) that involves both action and state supervisions, LfO is more practical in leveraging previously inapplicable resources (e.g., videos)…
Designing effective architectures is one of the key factors behind the success of deep neural networks. Existing deep architectures are either manually designed or automatically searched by some Neural Architecture Search (NAS) methods. However, even a well-searched architecture may still contain ma…
Unsupervised domain adaptation (UDA) transfers knowledge from a label-rich source domain to a fully-unlabeled target domain. To tackle this task, recent approaches resort to discriminative domain transfer in virtue of pseudo-labels to enforce the class-level distribution alignment across the source…
Fatorization machines (FM) are a popular model class to learn pairwise interactions by a low-rank approximation. Different from existing FM-based approaches which use a fixed rank for all features, this paper proposes a Rank-Aware FM (RaFM) model which adopts pairwise interactions from embeddings wi…
Graph Convolutional Networks (GCNs) have become a crucial tool on learning representations of graph vertices. The main challenge of adapting GCNs on large-scale graphs is the scalability issue that it incurs heavy cost both in computation and memory due to the uncontrollable neighborhood expansion a…
Generative adversarial networks (GANs) aim to generate realistic data from some prior distribution (e.g., Gaussian noises). However, such prior distribution is often independent of real data and thus may lose semantic information (e.g., geometric structure or content in images) of data. In practice,…
Channel pruning is one of the predominant approaches for deep model compression. Existing pruning methods either train from scratch with sparsity constraints on channels, or minimize the reconstruction error between the pre-trained feature maps and the compressed ones. Both strategies suffer from s…
Despite the recent success of end-to-end learned representations, hand-crafted optical flow features are still widely used in video analysis tasks. To fill this gap, we propose TVNet, a novel end-to-end trainable neural network, to learn optical-flow-like features from data. TVNet subsumes a specifi…
Large-scale distributed optimization is of great importance in various applications. For data-parallel based distributed learning, the inter-node gradient communication often becomes the performance bottleneck. In this paper, we propose the error compensated quantized stochastic gradient descent alg…
In transfer learning, what and how to transfer are two primary issues to be addressed, as different transfer learning algorithms applied between a source and a target domain result in different knowledge transferred and thereby the performance improvement in the target domain. Determining the optima…
Dense event captioning aims to detect and describe all events of interest contained in a video. Despite the advanced development in this area, existing methods tackle this task by making use of dense temporal annotations, which is dramatically source-consuming. This paper formulates a new problem: w…
The Convolutional Neural Network (CNN) based region proposal generation method (i.e. region proposal network), trained using bounding box annotations, is an essential component in modern fully supervised object detectors. However, Weakly Supervised Object Detection (WSOD) has not benefited from CNN-…
Linear Dynamical Systems (LDSs) are fundamental tools for modeling spatio-temporal data in various disciplines. Though rich in modeling, analyzing LDSs is not free of difficulty, mainly because LDSs do not comply with Euclidean geometry and hence conventional learning techniques can not be applied d…
Image-based precision medicine techniques can be used to better treat cancer patients. However, the gigapixel resolution of Whole Slide Histopathological Images (WSIs) makes traditional survival models computationally impossible. These models usually adopt manually labeled discriminative patches fro…
The definition of the similarity measure is an essential component in image registration. In this paper, we propose a novel similarity measure for registration of two or more images. The proposed method is motivated by that the optimally registered images can be deeply sparsified in the gradient dom…