61 accepted papers
Recent vision-language models (VLMs) achieve remarkable reasoning through reinforcement learning (RL), which provides a feasible solution for realizing continuous self-evolving large vision-language models (LVLMs) in the era of experience. However, RL for VLMs requires abundant high-quality multimod
Distributed Image Compression (DIC) is crucial for multi-view transmission, especially when operating at extremely low bitrates (< 0.1 bpp). Its core challenge is effectively utilizing side information to achieve high-quality reconstruction under strict bitrate budgets. However, existing DIC approac
Estimating single-cell responses across various perturbations facilitates the identification of key genes and enhances drug screening, significantly boosting experimental efficiency. However, single-cell sequencing is a destructive process, making it impossible to capture the same cell's phenotype b…
While Visual Multi-Agent Systems (VMAS) promise to enhance comprehensive abilities through inter-agent collaboration, empirical evidence reveals a counter-intuitive "scaling wall": increasing agent turns often degrades performance while exponentially inflating token costs. We attribute this failure …
Unified Multimodal Models (UMMs) are redefining the landscape of artificial intelligence by coupling perception and generation across language, vision, and structured reasoning. Yet, despite their growing sophistication, a critical gap persists in evaluation: existing benchmarks largely measure disc
Mathematical geometric reasoning is essential for scientific discovery and educational development, requiring precise logic and rigorous formal verification. While recent advances in Multimodal Large Language Models (MLLMs) have improved reasoning tasks, existing models typically struggle with forma
Solving complex geometric problems inherently requires \textit{interleaved reasoning}: a tight alternation between constructing diagrams and performing logical deductions. Although recent Multimodal Large Language Models (MLLMs) have demonstrated strong capabilities in visual generation and plotting…
Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, riski…
Multimodal Large Language Models often suffer from object hallucinations, where generated outputs are inconsistent with the visual evidence. This issue is typically attributed to the over-reliance on language priors, which can override the visual context. Recent training-free decoding strategies add…
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce RiboSphere, a framework that learns discrete geometric representations of RNA by c…
Designing 3D ligands that bind to a given protein pocket with high affinity is a fundamental task in Structure-Based Drug Design (SBDD). However, the lack of synthesizability of 3D ligands has been hindering progress toward experimental validation; moreover, computationally evaluating synthesizabili…
Video generation has advanced rapidly, but current models remain limited to short clips, far from the length and complexity of real-world narratives. Long video generation is thus both important and challenging. Existing approaches either attempt to extend the modeling length of video diffusion mode…
The AlphaFold Protein Structure Database (AFDB) offers unparalleled structural coverage at near-experimental accuracy, positioning it as a valuable resource for data-driven protein design. However, its direct use in training deep models that are sensitive to fine-grained atomic geometry—such as inve…
Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. However, a lack of systematic understanding persists due to the diverse settings, complex implementation, difficult reprodu…
Score Distillation Sampling (SDS) has been successfully extended to text-driven 3D scene editing with 2D pretrained diffusion models. However, SDS-based editing methods suffer from lengthy optimization processes with slow inference and low quality. We attribute the issue of lengthy optimization to t…
Motif-scaffolding is a fundamental component of protein design, which aims to construct the scaffold structure that stabilizes motifs conferring desired functions. Recent advances in generative models are promising for designing scaffolds, with two main approaches: training-based and sampling-based…
Is there a foreign language describing protein sequences and structures simultaneously? Protein structures, represented by continuous 3D points, have long posed a challenge due to the contrasting modeling paradigms of discrete sequences. We introduce FoldTokenizer to represent protein sequence-struc…
We introduce the task of text-to-diagram generation, which focuses on creating structured visual representations directly from textual descriptions. Existing approaches in text-to-image and text-to-code generation lack the logical organization and flexibility needed to produce accurate, editable dia…
Post-translational modifications (PTMs) profoundly expand the complexity and functionality of the proteome, regulating protein attributes and interactions that are crucial for biological processes. Accurately predicting PTM sites and their specific types is therefore essential for elucidating protei…
Masked Image Modeling (MIM) with Vector Quantization (VQ) has achieved great success in both self-supervised pre-training and image generation. However, most existing methods struggle to address the trade-off in the shared latent space for generation quality vs. representation learning and efficienc…
Designing protein sequences that fold into a target 3D structure—known as protein inverse folding—is a fundamental challenge in protein engineering. While recent deep learning methods have achieved impressive performance by recovering native sequences, they often overlook the one-to-many nature of t…
Proteomics is the large-scale study of proteins. Tandem mass spectrometry, as the only high-throughput technique for protein sequence identification, plays a pivotal role in proteomics research. One of the long-standing challenges in this field is peptide identification, which entails determining th…
Antibodies are Y-shaped proteins that protect the host by binding to specific antigens, and their binding is mainly determined by the Complementary Determining Regions (CDRs) in the antibody. Despite the great progress made in CDR design, existing computational methods still encounter several challe…
Hand-drawn sketches are a natural and efficient medium for capturing and conveying ideas. Despite significant advancements in controllable natural image generation, translating freehand sketches into structured, machine-readable diagrams remains a labor-intensive and predominantly manual task. The p
The development of therapeutic antibodies heavily relies on accurate predictions of how antigens will interact with antibodies. Existing computational methods in antibody design often overlook crucial conformational changes that antigens undergo during the binding process, significantly impacting th…
Can we model Non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The Non-Euclidean property have posed a long term challenge in graph modeling. Despite recent graph neural networks and graph transformers efforts encoding graphs as Euclidean vec…
Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Despite the development of several deep learning methods for predicting amino acid sequences (peptides) responsible for generating the obser…
Antibodies are crucial proteins produced by the immune system in response to foreign substances or antigens. The specificity of an antibody is determined by its complementarity-determining regions (CDRs), which are located in the variable domains of the antibody chains and form the antigen-binding s…
The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field, current methods suffer from poor generalization and high complexit…
Recent years have witnessed the great success of graph pre-training for graph representation learning. With hundreds of graph pre-training tasks proposed, integrating knowledge acquired from multiple pre-training tasks has become a popular research topic. In this paper, we identify two important col…
Protein representation learning is critical in various tasks in biology, such as drug design and protein structure or function prediction, which has primarily benefited from protein language models and graph neural networks. These models can capture intrinsic patterns from protein sequences and stru…
Molecular relational learning (MRL) is crucial for understanding the interaction behaviors between molecular pairs, a critical aspect of drug discovery and development. However, the large feasible model space of MRL poses significant challenges to benchmarking, and existing MRL frameworks face limit…
The pre-training architectures of large language models encompass various types including autoencoding models autoregressive models and encoder-decoder models. We posit that any modality can potentially benefit from a large language model as long as it undergoes vector quantization to become discret…
Recent studies have shown competitive performance in protein inverse folding, while most of them disregard the importance of predictive confidence, fail to cover the vast protein space, and do not incorporate common protein knowledge. Given the great success of pretrained models on diverse protein-r…
Learning effective representations is imperative for comprehending proteins and deciphering their biological functions. Recent strides in language models and graph neural networks have empowered protein models to harness primary or tertiary structure information for representation learning. Neverthe…
The scarcity of annotated data has sparked significant interest in unsupervised pre-training methods that leverage medical reports as auxiliary signals for medical visual representation learning. However existing research overlooks the multi-granularity nature of medical visual representation and la…
By contextualizing the kernel as global as possible, Modern ConvNets have shown great potential in computer vision tasks. However, recent progress on \textit{multi-order game-theoretic interaction} within deep neural networks (DNNs) reveals the representation bottleneck of modern ConvNets, where the…
We present NN4SysBench, a benchmark suite for neural network verification that is composed of applications from the domain of computer systems. We call these neural networks for computer systems or NN4Sys. NN4Sys is booming: there are many proposals for using neural networks in computer systems—for…
Compound-Protein Interaction (CPI) prediction aims to predict the pattern and strength of compound-protein interactions for rational drug discovery. Existing deep learning-based methods utilize only the single modality of protein sequences or structures and lack the co-modeling of the joint distribu…
Protein representation learning is indispensable for various downstream applications of artificial intelligence for bio-medicine research, such as drug design and function prediction. However, achieving effective representation learning for proteins poses challenges due to the diversity of data moda…
While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have th…
Accurate prediction of protein-ligand binding structures, a task known as molecular docking is crucial for drug design but remains challenging. While deep learning has shown promise, existing methods often depend on holo-protein structures (docked, and not accessible in realistic tasks) or neglect p…
Semi-supervised learning (SSL) has witnessed great progress with various improvements in the self-training framework with pseudo labeling. The main challenge is how to distinguish high-quality pseudo labels against the confirmation bias. However, existing pseudo-label selection strategies are limite…
Molecule inverse folding has been a long-standing challenge in chemistry and biology, with the potential to revolutionize drug discovery and material science. Despite specified models have been proposed for different small- or macro-molecules, few have attempted to unify the learning process, result…
Similar to natural language models, pre-trained genome language models are proposed to capture the underlying intricacies within genomes with unsupervised sequence modeling. They have become essential tools for researchers and practitioners in biology. However, the hand-crafted tokenization policies…
Spatiotemporal predictive learning is a paradigm that empowers models to learn spatial and temporal patterns by predicting future frames from past frames in an unsupervised manner. This method typically uses recurrent units to capture long-term dependencies, but these units often come with high comp…
Sign language recognition (SLR) is a weakly supervised task that annotates sign videos as textual glosses. Recent studies show that insufficient training caused by the lack of large-scale available sign datasets becomes the main bottleneck for SLR. Most SLR works thereby adopt pretrained visual modu…
Representing graph data in a low-dimensional space for subsequent tasks is the purpose of attributed graph embedding. Most existing neural network approaches learn latent representations by minimizing reconstruction errors. Rare work considers the data distribution and the topological structure of l…
The linear sequence of amino acids determines protein structure and function. Protein design, known as the inverse of protein structure prediction, aims to obtain a novel protein sequence that will fold into the defined structure. Recent works on computational protein design have studied designing s…
Mixup is an efficient data augmentation approach that improves the generalization of neural networks by smoothing the decision boundary with mixed data. Recently, dynamic mixup methods have improved previous \textit{static} policies effectively (e.g., linear interpolation) by maximizing target-relat…
Recent years have witnessed the prosperity of pre-training graph neural networks (GNNs) for molecules. Typically, atom types as node attributes are randomly masked, and GNNs are then trained to predict masked types as in AttrMask \citep{hu2020strategies}, following the Masked Language Modeling (MLM)…
Spatio-temporal predictive learning is a learning paradigm that enables models to learn spatial and temporal patterns by predicting future frames from given past frames in an unsupervised manner. Despite remarkable progress in recent years, a lack of systematic understanding persists due to the dive…
In an era of countless content offerings, recommender systems alleviate information overload by providing users with personalized content suggestions. Due to the scarcity of explicit user feedback, modern recommender systems typically optimize for the same fixed combination of implicit feedback sign…
How can we design protein sequences folding into the desired structures effectively and efficiently? AI methods for structure-based protein design have attracted increasing attention in recent years; however, few methods can simultaneously improve the accuracy and efficiency due to the lack of expre…
Protein inverse folding has attracted increasing attention in recent years. However, we observe that current methods are usually limited to the CATH dataset and the recovery metric. The lack of a unified framework for ensembling and comparing different methods hinders the comprehensive investigation…
Spatiotemporal predictive learning aims to generate future frames by learning from historical frames. In this paper, we investigate existing methods and present a general framework of spatiotemporal predictive learning, in which the spatial encoder and decoder capture intra-frame features and the mi…
Molecular Property Prediction (MPP) is a crucial task in the AI-driven Drug Discovery (AIDD) pipeline, which has recently gained considerable attention thanks to advancements in deep learning. However, recent research has revealed that deep models struggle to beat traditional non-deep ones on MPP. I…
Dropout has emerged as one of the most frequently used techniques for training deep neural networks (DNNs). Although effective, the sampled sub-model by random dropout during training is inconsistent with the full model (without dropout) during inference. To mitigate this undesirable gap, we propose…
Recent advances in contrastive learning have enlightened diverse applications across various semi-supervised fields. Jointly training supervised learning and unsupervised learning with a shared feature encoder becomes a common scheme. Though it benefits from taking advantage of both feature-dependen…
Datasets with noisy labels present challenges for training Deep Neural Networks (DNNs) with high generalization ability. An direct idea is to correct the noisy labels for robust learning. However, existing label correction methods can not handle with heavy noise or datasets with samples of many cate…
From CNN, RNN, to ViT, we have witnessed remarkable advancements in video prediction, incorporating auxiliary inputs, elaborate neural architectures, and sophisticated training strategies. We admire these progresses but are confused about the necessity: is there a simple method that can perform comp…