论文检索

Deep Learning · Large Language Models

Kaiyun Yang, Ruilin Yang, Zhimin Yao, Jikai Wang, Wei Ge

Vision-language models can perform new tasks without parameter updates through in-context learning (ICL), whose core mechanism is utilizing the support set for task induction. In standard ICL setting, once the task is induced, its decision boundary, i.e., the criterion, remains fixed. However, in real-world applications, many tasks exhibit a stable high-level intent, while their decision criteria shift according to specific requirements. Thus we introduce a new test setting, denoted as Criterion-Conditional In-Context Learning (CC-ICL), where models must infer the latent criterion from context under a fixed task semantics. To evaluate this capability, we propose two complementary metrics, Criterion-Sensitivity and Criterion-Invariance, capturing model's robustness and adaptability under criterion shifts. We further construct CC-Bench, a multi-domain benchmark that supports evaluation under the CC-ICL setting through hierarchical annotation, enabling legitimate ground-truth variation under fixed tasks. Experiments on CC-Bench reveal that most models exhibit a ''rigid boundary'' bias, struggling to align their decisions with the latent criterion. We also find that even a simple multi-criteria training strategy can significantly reduce this bias, improving Criterion-Sensitivity and enabling 7B-scale models to surpass proprietary models without degrading general multimodal performance.

Applications · Health / Medicine

Silas Ruhrberg Estevez, Nicolas Huynh, Tennison Liu, Roderik Kortlever, Gerard Evan, David Bentley, Mihaela van der Schaar

Inferring dynamics from population snapshots is a fundamental challenge in machine learning and biology. In scRNA-sequencing (scRNA-seq), destructive measurements preclude direct tracking of individual cells across time, making trajectory inference underdetermined. Optimal Transport (OT) provides a principled framework for snapshot alignment, but a long-standing modeling question is which cost functions yield biologically meaningful couplings. Standard OT approaches rely on gene-expression distances, implicitly treating cells as independent points and neglecting structured cell-cell communication mediated by ligand--receptor signaling. We introduce $\texttt{CellBRIDGE}$ ($\textit{Cell-Based Regularized Interaction-Driven Gene Expression}$), which augments feature-based OT with a directed, typed interaction cost derived from ligand-receptor activity. By explicitly modeling cell--cell communication, $\texttt{CellBRIDGE}$ improves cross-snapshot couplings and downstream trajectory estimates across synthetic and real scRNA-seq datasets relative to feature-only baselines. Notably, $\texttt{CellBRIDGE}$ enables mechanistically interpretable in silico perturbations: on lung cancer data, silencing specific ligand-receptor pairs induces trajectory shifts that recapitulate expected effects of targeted pathway inhibition.

Applications · Health / Medicine

YuCheng Yuan, Ji Yuanfeng, Zhongxiao Li, Ruijiang Li

Spatial proteomics enables single-cell-resolution characterization of protein expression within tissue architecture, playing a critical role in understanding tumor microenvironments and guiding precision medicine. However, current analysis workflows remain fragmented, requiring expert manual orchestration of heterogeneous tools and limiting research scalability and reproducibility. We present **SP-Mind**, the first autonomous AI agent designed to unify the spatial proteomics analysis pipeline, from raw multiplexed tissue imaging to downstream phenotype discovery. Equipped with expert-curated biological analysis skills and specialized computational tools, SP-Mind converts natural-language queries into end-to-end analytical workflows without task-specific fine-tuning. To rigorously evaluate its capabilities, we introduce **SP-Bench**, a comprehensive benchmark spanning diverse tissue types and imaging technologies (fluorescence-based and mass spectrometry imaging), comprising 102 tasks across 18 distinct categories. Through extensive evaluation on SP-Bench and established downstream tasks, SP-Mind achieves **state-of-the-art** performance compared to existing open-source biomedical agent baselines. Code and benchmark will be publicly available upon acceptance.

Applications · Health / Medicine

Weiren Zhao, DONG Yi, Cheng Chen

Unifying multimodal understanding and generation is a compelling frontier that is beginning to emerge in the medical field. However, the limited existing unified medical models typically treat understanding and generation as disjoint objectives, lacking a meaningful functional synergy. In this work, we identify and address a critical question in unified medical modeling: what form of “understanding” truly benefits generation. We present SynerMedGen, a unified framework built on the proposed principle of generation-aligned understanding, which synergizes understanding objectives with generation tasks via task alignment. SynerMedGen introduces three generation-aligned understanding tasks and a two-stage training strategy that transfers generation-beneficial representations learned during understanding training to medical image synthesis. Remarkably, even with understanding training alone, our SynerMedGen achieves strong zero-shot performance across 22 medical image synthesis tasks and demonstrates robust generalization to unseen datasets. When combined with generation training, SynerMedGen consistently outperforms state-of-the-art specialized medical image synthesis models as well as recent unified medical models. We also release a large-scale dataset named SynerMed consisting of 1M paired synthesis samples and 2M generation-derived understanding instances to support further research on understanding-generation synergy.

Applications · Health / Medicine

Susu Hu, Stefanie Speidel

Inferring spatial transcriptomics (ST) from histology enables scalable histogenomic profiling, yet current methods are largely restricted to single-tissue models. This fragmentation fails to leverage biological principles shared across cancer types and hinders application to data-scarce scenarios. While pan-cancer training offers a solution, the resulting heterogeneity challenges monolithic architectures. To bridge this gap, we introduce **MoLF** (*Mixture-of-Latent-Flow*), a generative model for pan-cancer histogenomic prediction. MoLF leverages a conditional Flow Matching objective to map noise to the gene latent manifold, parameterized by a Mixture-of-Experts (MoE) velocity field. By dynamically routing inputs to specialized sub-networks, this architecture effectively decouples the optimization of diverse tissue patterns. Our experiments demonstrate that MoLF establishes a new state-of-the-art, consistently outperforming both specialized and foundation model baselines on pan-cancer benchmarks. Furthermore, MoLF exhibits zero-shot generalization to cross-species data, suggesting it captures fundamental, conserved histo-molecular mechanisms.

Applications · Health / Medicine

Chi-Min Chan, Ehsan Hajiramezanali, Xiner Li, Edward De Brouwer, Carl Edwards, Wei Xue, Sirui Han, Yike Guo, Gabriele Scalia

In scientific reasoning tasks, the veracity of the reasoning process is as critical as the final outcome. While Process Reward Models (PRMs) offer a solution to the coarse-grained supervision problems inherent in Outcome Reward Models (ORMs), their deployment is hindered by the prohibitive cost of obtaining expert-verified step-wise labels. This paper addresses the challenge of training reliable PRMs using abundant but noisy "weak" supervision. We argue that existing Weak-to-Strong Generalization (W2SG) theories lack prescriptive guidelines for selecting high-quality training signals from noisy data. To bridge this gap, we introduce the Dual-Consensus Weak-to-Strong (DC-W2S) framework. By intersecting Self-Consensus (SC) metrics among weak supervisors with Neighborhood-Consensus (NC) metrics in the embedding space, we stratify supervision signals into distinct reliability regimes. We then employ a curriculum of instance-level balanced sampling and label-level reliability-aware masking to guide the training process. We demonstrate that DC-W2S enables the training of robust PRMs for complex reasoning without exhaustive expert annotation, proving that strategic data curation is more effective than indiscriminate training on large-scale noisy datasets.

Zitong Li, Jinzhuo Wu, Fukang Zhao, Xinyue Wang, Jun Chen-CUG, Zhuo Cheng, Dapeng Luo

Recent Open-vocabulary Object Detection (OVD) approaches adapt CLIP through region-level distillation to improve semantic alignment for novel categories. However, the distilled regional features are often used for both classification and localization, enhancing semantic consistency at the expense of spatial fidelity. To resolve this, we propose Object-level Semantic and Spatial Distillation (OSSD), a two-stage framework that explicitly decouples semantic and spatial feature learning. OSSD first distills object-level semantics from CLIP’s global [CLS] embeddings to enhance region discrimination, and then injects fine-grained spatial and structural priors via spatial distillation from a detector trained only on COCO base categories. Furthermore, we propose a Location Quality Estimation Head (LQEH) that predicts class-agnostic localization quality, complementing objectness confidence to improve the novel-object perception. Extensive experiments show that our method achieves 49.2 AP50 on the OV-COCO benchmark. exceeding the best previous result by 3.6\%, On the OV-LVIS benchmark, our method reaches 40.5 mAP on novel categories, outperforming previous state-of-the-art methods.

Applications · Health / Medicine

Cheng Wang, Jinpu Cai, Chongxiao Mao, Yuxuan Wang, Xinzhu Jiang, Yunhao Qiao, Luqi Yang, Luting Zhou, Qiuyu Lian, Hongyi Xin

Geometry-preserving dimension reduction is critical for single-cell transcriptomics, where low-dimensional distances should reflect biological divergence between cell types along the transcriptomic manifold. Due to inadequate metrics, the global structure is not sufficiently preserved in the low-dimensional manifold in standard dimension reduction regimes. We model RNA counts as Multinomial samples, leveraging their hierarchical closure property: gene-level counts refine functional gene-group counts via nested Multinomial distributions. Extending Chentsov's Theorem, we show that the Fisher-Rao metric on coarse (gene-group) and fine (gene) statistical manifolds is isometric. Following this isometry property, we propose InfoGlobe, an information-preserving statistical manifold learning framework that projects cells from high-dimensional hyperspheres (full transcriptome) to low-dimensional hyperspheres (functional groups) while preserving information geometry. Embeddings on the low-dimensional sphere explicitly represent Multinomial distributions by functional gene groups. Benchmarks demonstrate superior preservation of local-and-global cell-type geodesic distances, automatic and robust gene-group discovery, nuanced cell subtype resolution without manual feature engineering and natural batch effect mitigation without explicit alignments.

Applications · Health / Medicine

Haoran liu, Xiaoli Lin, Jing Hu, Yu Zou, Xiaolong Zhang

Polypharmacology provides a powerful strategy for treating complex diseases, but identifying molecules that simultaneously satisfy coupled constraints across multiple biological targets remains difficult. Existing methods typically model protein pockets in isolation and struggle to jointly account for multiple heterogeneous binding sites when designing a single shared ligand. To address these limitations, we propose a pocket-structure-centric generative framework for polypharmacology. This framework introduces a novel protein topological representation that selectively masks ligand-irrelevant residues while explicitly modeling backbone folding geometry and inter-residue spatial proximity within binding pockets. In addition, structural representations are jointly fused with amino acid and nucleotide sequences to capture their complementary information across targets. Experiments on COVID-19, schizophrenia, and tumor targets show that this framework generates valid candidates with significantly improved binding affinities compared to state-of-the-art methods.

Applications · Health / Medicine

Yuchen Hua, Xingang Peng, Jianzhu Ma, Muhan Zhang

Generative modeling of three-dimensional (3D) molecules is a fundamental yet challenging problem in drug discovery and materials science. Existing approaches typically represent molecules as 3D graphs and co-generate discrete atom types with continuous atomic coordinates, leading to intrinsic learning difficulties such as heterogeneous modality entanglement and geometry–chemistry coherence constraints. We propose VecMol, a novel representation that models 3D molecules as continuous vector fields over Euclidean space, where vectors point toward nearby atoms and implicitly encode molecular structure. The vector field is parameterized by a neural field and generated using a latent diffusion model, avoiding explicit graph generation and decoupling structure learning from discrete atom instantiation. Experiments on the QM9 and GEOM-Drugs benchmarks demonstrate that VecMol achieves competitive generation quality, suggesting vector-field-based representations as a promising new direction for 3D molecular generation.

Applications · Health / Medicine

Zitao Chen, Jiatong Ji, Yinjun Jia, Wei-Ying Ma, Yanyan Lan

Recent advances in 3D molecular modeling have achieved high-fidelity structural synthesis, yet these models often lack an explicit and manipulable representation space. To address this, MolFLAE introduced a fixed-dimensional, E(3)-equivariant latent space, providing a novel framework for molecular editing independent of atom counts. However, because its latent space was primarily optimized for geometric reconstruction, it remains semantically shallow and inadequate for comprehensive representation learning. In this work, we propose **MolAlign3D**, which evolves this architecture into a unified semantic-generative engine. By anchoring MolFLAE’s manipulable latents with embeddings from a pre-trained molecular encoder, we yield a manifold that is both semantically dense and geometrically precise. Experiments show that MolAlign3D achieves high-fidelity molecular reconstruction and attains comparable performance on molecular property prediction benchmarks. Notably, the integration of rich semantic priors significantly enhances zero-shot molecular manipulation, including atom-number editing and latent-space interpolation, outperforming prior fixed-dimensional equivariant latent baseline.

Applications · Health / Medicine

Zekai Chen, Xunkai Li, Sirui Zhang, Henan Sun, Jia Li, Qiangqiang Dai, Hongchao Qin, Zhenjun Li, Bing Zhou, Rong-Hua Li 等

De novo ligand design is a fundamental task that seeks to generate protein or molecule candidates that can effectively dock with protein receptors and achieve strong binding affinity entirely from scratch. It holds paramount significance for a wide spectrum of biomedical applications. However, most existing studies are constrained by the \textbf{Pseudo De Novo}, \textbf{Limited Docking Modeling}, and \textbf{Inflexible Ligand Type}. To address these issues, we propose MagicDock, a forward-looking framework grounded in the progressive pipeline and differentiable surface modeling. (1) We adopt a well-designed gradient inversion framework. To begin with, general docking knowledge of receptors and ligands is incorporated into the backbone model. Subsequently, the docking knowledge is instantiated as reverse gradient flows by binding prediction, which iteratively guide the de novo generation of ligands. (2) We emphasize differentiable surface modeling in the \textit{generation process}, leveraging learnable 3D point-cloud representations to precisely capture docking details, thereby ensuring that the generated ligands preserve docking validity through interpretable spatial fingerprints. (3) We introduce customized designs for different ligand types and integrate them into a unified gradient inversion framework with flexible triggers, thereby ensuring broad applicability. Moreover, we provide sufficient theoretical guarantees for MagicDock. Extensive experiments across 9 scenarios demonstrate that MagicDock achieves average improvements of 7.0\% and 7.4\% over SOTA baselines specialized for protein or molecule ligand design, respectively.

Social Aspects · Accountability, Transparency, and Interpretability

Sourav Banerjee, Saikat Saha

This position paper argues that AI leaderboards are structurally ill-suited to serving the Global South because they lack independent governance, conflict-of-interest policies, and mechanisms for metric evolution. The barrier is not missing data; high-quality regional benchmarks already exist: IndicSUPERB, MILU, and LAHAJA for India; IrokoBench for Africa; AlGhafa for Arabic. The barrier is institutional design. Global leaderboards do not include these benchmarks, and no governance mechanism compels them to do so. Commercial pressure corrects leaderboard failures when paying customers in the Global North are affected. The Global South lacks equivalent leverage. Without governance, failures affecting Hindi, Swahili, or Arabic speakers persist indefinitely as documented but unaddressed gaps. Using India as a case study (1.4 billion people, 22 scheduled languages, high-quality benchmarks, but no trusted aggregation), we report findings from a consultation with 58 AI practitioners showing consistent preference for formal governance and disclosure-based conflict management. The solution is not more data but better institutions: regional leaderboards with independent governance from the start.

Applications · Computer Vision

Rongjiang Zhu, Wei Kang, Zeqi Liu, Chen junyu, Shuo Yang, Xinxiao Wu

Traditional 3D visual grounding typically assumes that natural language expressions unambiguously refer to target objects in a 3D scene. However, in practical applications, human instructions are often ambiguous or insufficient, which may lead existing models to associate the query with multiple possible objects, resulting in incorrect results. In this paper, we propose a new task, 3D visual grounding with referential ambiguity, which allows for referential ambiguity in language descriptions, making it more broadly applicable to real-world scenarios. To tackle this task, we propose an interactive grounding framework that performs multi-round question-answer interactions, in which the model actively generates clarifying questions and receives human-provided answers to acquire additional object attributes, spatial relationships, and other contextual information, thereby resolving referential ambiguity and achieving accurate grounding. To support the learning of interactive grounding, we construct a large-scale dataset named AmbiRefer3D, which contains 47,085 samples with 141,255 annotations of question-answer dialogues that capture interactive disambiguation processes, covering 7,316 indoor 3D scenes. Furthermore, we establish multi-round evaluation metrics to measure both disambiguation efficiency and grounding accuracy.

General Machine Learning · Representation Learning

Yilin Chen, Tianyu Lu, Cizhang Zhao, Hannah Wayment-Steele, Po-Ssu Huang

Building physically grounded protein representations is central to computational biology, yet most existing approaches rely on sequence-pretrained language models or backbone-only graphs that overlook side-chain geometry and chemical detail. We present SLAE, a unified all-atom framework for learning protein representations from each residue’s local atomic neighborhood using only atom types and interatomic geometries. To encourage expressive feature extraction, we introduce a novel multi-task autoencoder objective that combines coordinate reconstruction, sequence recovery, and energy regression. SLAE reconstructs allatom structures with high fidelity from latent residue environments and achieves state-of-the-art performance across diverse downstream tasks via transfer learning. SLAE’s latent space is chemically informative and environmentally sensitive, enabling quantitative assessment of structural qualities and smooth interpolation between conformations at all-atom resolution.

Applications · Computer Vision

Chenming Zhu, Peizhou Cao, Jingli Lin, Wenbo Hu, Yunlong Ran, Tai Wang, Jiangmiao Pang, Xihui Liu

Human spatial understanding arises from jointly perceiving geometry and semantics, enabling consistent object identification and localization across viewpoints and time. Current video segmentation models depend on explicit object appearance memory banks for instance tracking, yet they remain vulnerable to large viewpoint changes and long-term occlusions. Leveraging the spatial consistency afforded by modern feed-forward 3D reconstruction models, we propose the Geometry Grounded Tracking Anything Model (G$^2$TAM), a unified framework for promptable instance tracking in 3D using only unordered RGB images or videos. G$^2$TAM employs spatially aligned geometric representations as implicit memory, ensuring stable instance identity and localization across frames and views. At its core is a cross-modal spatial encoder that integrates visual and textual prompts into a shared geometric space, enabling end-to-end spatial reconstruction and instance-consistent mask prediction. To support training and evaluation, we construct InsTrack, a large-scale dataset with a dedicated validation split for benchmarking. Extensive experiments show that G$^2$TAM delivers strong cross-view consistency, promptable instance spatial tracking, video object segmentation, and spatial reconstruction, establishing a foundation for interactive, geometry-grounded spatial reasoning.

Applications · Computer Vision

YiCheng Xiao, Yu Chen, Hao-Xuan Ma, Jiale Hong, Caorui Li, Lingxiang Wu, Haiyun Guo, Jinqiao Wang

While CLIP has achieved strong performance across vision–language tasks, fine-grained image–text alignment remains challenging. Recent efforts improve textual granularity by leveraging long, detailed descriptions and replacing CLIP’s text encoder with LLM, but often overlook the visual-side bottleneck: achieving finer alignment requires region- and pixel-level visual grounding, not just finer text. To address this issue, we propose PixCLIP, a framework that jointly enhances both sides by accommodating visual prompt regions and long-form text within a unified training objective. Firstly, to support training at this granularity, we develop an automated annotation pipeline that produces long-form descriptions with pixel-level localization, and use it to construct LongGRIT, a high-quality dataset with nearly 1.5M samples. Furthermore, we introduce a three-branch pixel–text alignment framework that aligns image regions with corresponding textual descriptions across multiple granularities. Experiments show that PixCLIP achieves state-of-the-art performance on pixel- and region-level alignment tasks while preserving strong results on standard global image–text retrieval benchmarks, even with arbitrarily shaped region prompts and long compositional texts.

Applications · Computer Vision

Shiyan Tong, Jinxia Zhang, Zhiyuan Wang, Hao Tian, YingYing Wang, Kanjian Zhang, Haikun Wei

Recent advances in zero-shot referring image segmentation (RIS), driven by foundation models such as SAM and CLIP, have improved cross-modal alignment between visual regions and natural language expressions. Nevertheless, selecting the correct segmentation proposal remains challenging, as existing methods typically rely on independent proposal scoring and lack contextual reasoning among visually similar candidates. To address this limitation, we propose RefChess, a training-free framework that reformulates proposal selection as a decision-making problem under contextual perturbations rather than a single-step ranking task. RefChess models each proposal as a candidate chess move and applies Monte-Carlo Tree Search to evaluate its robustness by simulating interactions with competing regions, guided by a stability-aware reward that integrates language decomposition, vision–language similarity, object-centric cues, and spatial guidance signals. Experimental results on standard RIS benchmarks indicate that this decision-centric formulation leads to consistent improvements in robustness and referring segmentation performance. Code is available at \url{anonymous URL}.

Deep Learning · Large Language Models

Sangeun Park, Minhae Kwon

A central goal of large language model (LLM) research is to build agentic systems that can plan, act, and adapt through sustained interaction with dynamic environments. While recent LLM-based agents exhibit impressive contextual reasoning, their long-horizon decision-making remains fragile, often suffering from $\textit{objective drift}$, where goals and plans drift over extended interactions. We introduce $\texttt{Multi}^2$, a hierarchical multi-agent decision-making framework that explicitly decomposes agent behavior into complementary roles. A high-level agent ($\texttt{System 1}$) focuses on context-aware sub-goal generation using supervised fine-tuning (SFT), while a low-level agent ($\texttt{System 2}$) executes atomic actions through offline-to-online reinforcement learning (RL) in interactive environments. This separation enables stable long-horizon control, mitigates objective drift, and allows efficient adaptation. Across diverse interactive environments, $\texttt{Multi}^2$ consistently outperforms strong agentic baselines, demonstrating improved robustness and coordination in multi-turn interaction. Beyond performance, we introduce and release three hierarchical benchmark datasets, filling a long-standing gap in training and evaluating hierarchical decision-making for LLM-based agents.

Applications · Time Series

Mengzhou Gao, Kaiwei Wang, Pengfei Jiao

Neural Flows efficiently model irregular multivariate time series by directly learning ODE solution trajectories with neural networks, bypassing step-by-step numerical solvers. Despite their efficiency, many existing approaches treat variables independently, leaving inter-variable interactions underexplored. Moreover, their one-step mapping makes interaction modeling inherently challenging, as it removes the iterative refinement of interactions during learning. To address this challenge, we propose one-step Graph-Structured Neural Flows (GSNF), which introduce two auxiliary-trajectory self-supervision strategies to strengthen interaction learning: (i) interaction-aware trajectory generation via re-initialization, which induces trajectory divergence to expose graph-induced interactions, with a theoretically derived lower bound on divergence; and (ii) reverse-time trajectory generation, which enforces forward–backward consistency to regularize graph learning, enabled by flow invertibility. Experiments on five real-world datasets show that GSNF achieves state-of-the-art classification performance with highly competitive training time and memory usage.