Shanghua Gao

CV
h-index59
25papers
1,375citations
Novelty51%
AI Score62

25 Papers

CVMar 25, 2023Code
MDTv2: Masked Diffusion Transformer is a Strong Image Synthesizer

Shanghua Gao, Pan Zhou, Ming-Ming Cheng et al.

Despite its success in image synthesis, we observe that diffusion probabilistic models (DPMs) often lack contextual reasoning ability to learn the relations among object parts in an image, leading to a slow learning process. To solve this issue, we propose a Masked Diffusion Transformer (MDT) that introduces a mask latent modeling scheme to explicitly enhance the DPMs' ability to contextual relation learning among object semantic parts in an image. During training, MDT operates in the latent space to mask certain tokens. Then, an asymmetric diffusion transformer is designed to predict masked tokens from unmasked ones while maintaining the diffusion generation process. Our MDT can reconstruct the full information of an image from its incomplete contextual input, thus enabling it to learn the associated relations among image tokens. We further improve MDT with a more efficient macro network structure and training strategy, named MDTv2. Experimental results show that MDTv2 achieves superior image synthesis performance, e.g., a new SOTA FID score of 1.58 on the ImageNet dataset, and has more than 10x faster learning speed than the previous SOTA DiT. The source code is released at https://github.com/sail-sg/MDT.

CVAug 7, 2024Code
MoExtend: Tuning New Experts for Modality and Task Extension

Shanshan Zhong, Shanghua Gao, Zhongzhan Huang et al.

Large language models (LLMs) excel in various tasks but are primarily trained on text data, limiting their application scope. Expanding LLM capabilities to include vision-language understanding is vital, yet training them on multimodal data from scratch is challenging and costly. Existing instruction tuning methods, e.g., LLAVA, often connects a pretrained CLIP vision encoder and LLMs via fully fine-tuning LLMs to bridge the modality gap. However, full fine-tuning is plagued by catastrophic forgetting, i.e., forgetting previous knowledge, and high training costs particularly in the era of increasing tasks and modalities. To solve this issue, we introduce MoExtend, an effective framework designed to streamline the modality adaptation and extension of Mixture-of-Experts (MoE) models. MoExtend seamlessly integrates new experts into pre-trained MoE models, endowing them with novel knowledge without the need to tune pretrained models such as MoE and vision encoders. This approach enables rapid adaptation and extension to new modal data or tasks, effectively addressing the challenge of accommodating new modalities within LLMs. Furthermore, MoExtend avoids tuning pretrained models, thus mitigating the risk of catastrophic forgetting. Experimental results demonstrate the efficacy and efficiency of MoExtend in enhancing the multimodal capabilities of LLMs, contributing to advancements in multimodal AI research. Code: https://github.com/zhongshsh/MoExtend.

LGJul 9, 2024Code
Composable Interventions for Language Models

Arinbjorn Kolbeinsson, Kyle O'Brien, Tianjin Huang et al.

Test-time interventions for language models can enhance factual accuracy, mitigate harmful outputs, and improve model efficiency without costly retraining. But despite a flood of new methods, different types of interventions are largely developing independently. In practice, multiple interventions must be applied sequentially to the same model, yet we lack standardized ways to study how interventions interact. We fill this gap by introducing composable interventions, a framework to study the effects of using multiple interventions on the same language models, featuring new metrics and a unified codebase. Using our framework, we conduct extensive experiments and compose popular methods from three emerging intervention categories -- Knowledge Editing, Model Compression, and Machine Unlearning. Our results from 310 different compositions uncover meaningful interactions: compression hinders editing and unlearning, composing interventions hinges on their order of application, and popular general-purpose metrics are inadequate for assessing composability. Taken together, our findings showcase clear gaps in composability, suggesting a need for new multi-objective interventions. All of our code is public: https://github.com/hartvigsen-group/composable-interventions.

CVJun 10, 2022Code
SERE: Exploring Feature Self-relation for Self-supervised Transformer

Zhong-Yu Li, Shanghua Gao, Ming-Ming Cheng

Learning representations with self-supervision for convolutional networks (CNN) has been validated to be effective for vision tasks. As an alternative to CNN, vision transformers (ViT) have strong representation ability with spatial self-attention and channel-level feedforward networks. Recent works reveal that self-supervised learning helps unleash the great potential of ViT. Still, most works follow self-supervised strategies designed for CNN, e.g., instance-level discrimination of samples, but they ignore the properties of ViT. We observe that relational modeling on spatial and channel dimensions distinguishes ViT from other networks. To enforce this property, we explore the feature SElf-RElation (SERE) for training self-supervised ViT. Specifically, instead of conducting self-supervised learning solely on feature embeddings from multiple views, we utilize the feature self-relations, i.e., spatial/channel self-relations, for self-supervised learning. Self-relation based learning further enhances the relation modeling ability of ViT, resulting in stronger representations that stably improve performance on multiple downstream tasks. Our source code is publicly available at: https://github.com/MCG-NKU/SERE.

CVJun 14, 2022
RF-Next: Efficient Receptive Field Search for Convolutional Neural Networks

Shanghua Gao, Zhong-Yu Li, Qi Han et al.

Temporal/spatial receptive fields of models play an important role in sequential/spatial tasks. Large receptive fields facilitate long-term relations, while small receptive fields help to capture the local details. Existing methods construct models with hand-designed receptive fields in layers. Can we effectively search for receptive field combinations to replace hand-designed patterns? To answer this question, we propose to find better receptive field combinations through a global-to-local search scheme. Our search scheme exploits both global search to find the coarse combinations and local search to get the refined receptive field combinations further. The global search finds possible coarse combinations other than human-designed patterns. On top of the global search, we propose an expectation-guided iterative local search scheme to refine combinations effectively. Our RF-Next models, plugging receptive field search to various models, boost the performance on many tasks, e.g., temporal action segmentation, object detection, instance segmentation, and speech synthesis. The source code is publicly available on http://mmcheng.net/rfnext.

CVNov 12, 2023
ChatAnything: Facetime Chat with LLM-Enhanced Personas

Yilin Zhao, Xinbin Yuan, Shanghua Gao et al.

In this technical report, we target generating anthropomorphized personas for LLM-based characters in an online manner, including visual appearance, personality and tones, with only text descriptions. To achieve this, we first leverage the in-context learning capability of LLMs for personality generation by carefully designing a set of system prompts. We then propose two novel concepts: the mixture of voices (MoV) and the mixture of diffusers (MoD) for diverse voice and appearance generation. For MoV, we utilize the text-to-speech (TTS) algorithms with a variety of pre-defined tones and select the most matching one based on the user-provided text description automatically. For MoD, we combine the recent popular text-to-image generation techniques and talking head algorithms to streamline the process of generating talking objects. We termed the whole framework as ChatAnything. With it, users could be able to animate anything with any personas that are anthropomorphic using just a few text inputs. However, we have observed that the anthropomorphic objects produced by current generative models are often undetectable by pre-trained face landmark detectors, leading to failure of the face motion generation, even if these faces possess human-like appearances because those images are nearly seen during the training (e.g., OOD samples). To address this issue, we incorporate pixel-level guidance to infuse human face landmarks during the image generation phase. To benchmark these metrics, we have built an evaluation dataset. Based on it, we verify that the detection rate of the face landmark is significantly increased from 57.0% to 92.5% thus allowing automatic face animation based on generated speech content. The code and more results can be found at https://chatanything.github.io/.

AIMay 27
AutoScientists: Self-Organizing Agent Teams for Long-Running Scientific Experimentation

Shanghua Gao, Ada Fang, Marinka Zitnik

Scientific research proceeds through iterative cycles of hypothesis generation, experiment design, execution, and revision. AI agents can automate parts of this process, but existing approaches typically follow a single research trajectory or coordinate through a central planner with fixed objectives. As a result, they struggle to sustain parallel exploration, adapt as experimental evidence changes, or preserve knowledge of failed directions over long-running experiments. We introduce AutoScientists, a decentralized team of AI agents for long-running computational scientific experimentation. Agents interpret a shared experimental state, self-organize into teams around promising hypotheses, critique proposals before using experimental compute, and share successes and failures to reduce redundant exploration. Under matched experimental budgets, AutoScientists improves over prior AI agents across biomedical machine learning, language-model training optimization, and protein fitness prediction. On BioML-Bench, spanning biomedical imaging, protein engineering, single-cell omics, and drug discovery, AutoScientists achieves a mean leaderboard percentile of 74.4% across 24 tasks, improving over the strongest AI agent by +8.33%. On GPT training optimization, AutoScientists reaches a target validation bits-per-byte 1.9x faster than Autoresearch and continues discovering improvements from a starting champion where the single-agent approach finds none (7 vs. 0 accepted improvements). On ProteinGym fitness prediction, AutoScientists discovers a method for ACE2-Spike binding that improves over the current state-of-the-art model by +12.5% in Spearman correlation. Applied without modification across all 217 ProteinGym assays, the same method improves over the prior state of the art by +6.5% (Spearman correlation).

CVOct 20, 2022
Towards Sustainable Self-supervised Learning

Shanghua Gao, Pan Zhou, Ming-Ming Cheng et al.

Although increasingly training-expensive, most self-supervised learning (SSL) models have repeatedly been trained from scratch but not fully utilized, since only a few SOTAs are employed for downstream tasks. In this work, we explore a sustainable SSL framework with two major challenges: i) learning a stronger new SSL model based on the existing pretrained SSL model, also called as "base" model, in a cost-friendly manner, ii) allowing the training of the new model to be compatible with various base models. We propose a Target-Enhanced Conditional (TEC) scheme which introduces two components to the existing mask-reconstruction based SSL. Firstly, we propose patch-relation enhanced targets which enhances the target given by base model and encourages the new model to learn semantic-relation knowledge from the base model by using incomplete inputs. This hardening and target-enhancing help the new model surpass the base model, since they enforce additional patch relation modeling to handle incomplete input. Secondly, we introduce a conditional adapter that adaptively adjusts new model prediction to align with the target of different base models. Extensive experimental results show that our TEC scheme can accelerate the learning speed, and also improve SOTA SSL base models, e.g., MAE and iBOT, taking an explorative step towards sustainable SSL.

LGFeb 29, 2024Code
UniTS: A Unified Multi-Task Time Series Model

Shanghua Gao, Teddy Koker, Owen Queen et al.

Although pre-trained transformers and reprogrammed text-based LLMs have shown strong performance on time series tasks, the best-performing architectures vary widely across tasks, with most models narrowly focused on specific areas, such as time series forecasting. Unifying predictive and generative time series tasks within a single model remains challenging. We introduce UniTS, a unified multi-task time series model that utilizes task tokenization to integrate predictive and generative tasks into a single framework. UniTS employs a modified transformer block to capture universal time series representations, enabling transferability from a heterogeneous, multi-domain pre-training dataset-characterized by diverse dynamic patterns, sampling rates, and temporal scales-to a wide range of downstream datasets with varied task specifications and data domains. Tested on 38 datasets across human activity sensors, healthcare, engineering, and finance, UniTS achieves superior performance compared to 12 forecasting models, 20 classification models, 18 anomaly detection models, and 16 imputation models, including adapted text-based LLMs. UniTS also demonstrates strong few-shot and prompt capabilities when applied to new domains and tasks. In single-task settings, UniTS outperforms competitive task-specialized time series models. Code and datasets are available at https://github.com/mims-harvard/UniTS.

CVJul 2, 2025Code
Representation Entanglement for Generation: Training Diffusion Transformers Is Much Easier Than You Think

Ge Wu, Shen Zhang, Ruijing Shi et al.

REPA and its variants effectively mitigate training challenges in diffusion models by incorporating external visual representations from pretrained models, through alignment between the noisy hidden projections of denoising networks and foundational clean image representations. We argue that the external alignment, which is absent during the entire denoising inference process, falls short of fully harnessing the potential of discriminative representations. In this work, we propose a straightforward method called Representation Entanglement for Generation (REG), which entangles low-level image latents with a single high-level class token from pretrained foundation models for denoising. REG acquires the capability to produce coherent image-class pairs directly from pure noise, substantially improving both generation quality and training efficiency. This is accomplished with negligible additional inference overhead, requiring only one single additional token for denoising (<0.5\% increase in FLOPs and latency). The inference process concurrently reconstructs both image latents and their corresponding global semantics, where the acquired semantic knowledge actively guides and enhances the image generation process. On ImageNet 256$\times$256, SiT-XL/2 + REG demonstrates remarkable convergence acceleration, achieving $\textbf{63}\times$ and $\textbf{23}\times$ faster training than SiT-XL/2 and SiT-XL/2 + REPA, respectively. More impressively, SiT-L/2 + REG trained for merely 400K iterations outperforms SiT-XL/2 + REPA trained for 4M iterations ($\textbf{10}\times$ longer). Code is available at: https://github.com/Martinser/REG.

AISep 27, 2025Code
Democratizing AI scientists using ToolUniverse

Shanghua Gao, Richard Zhu, Pengwei Sui et al.

AI scientists are emerging computational systems that serve as collaborative partners in discovery. These systems remain difficult to build because they are bespoke, tied to rigid workflows, and lack shared environments that unify tools, data, and analyses into a common ecosystem. In genomics, unified ecosystems have transformed research by enabling interoperability, reuse, and community-driven development; AI scientists require comparable infrastructure. We present ToolUniverse, an ecosystem for building AI scientists from any language or reasoning model across open- and closed-weight models. ToolUniverse standardizes how AI scientists identify and call tools by providing more than 600 machine learning models, datasets, APIs, and scientific packages for data analysis, knowledge retrieval, and experimental design. It automatically refines tool interfaces for correct use by AI scientists, generates new tools from natural language descriptions, iteratively optimizes tool specifications, and composes tools into agentic workflows. In a case study of hypercholesterolemia, ToolUniverse was used to create an AI scientist to identify a potent analog of a drug with favorable predicted properties. The open-source ToolUniverse is available at https://aiscientist.tools.

CLMar 6
Qworld: Question-Specific Evaluation Criteria for LLMs

Shanghua Gao, Yuchang Su, Pengwei Sui et al.

Evaluating large language models (LLMs) on open-ended questions is difficult because response quality depends on the question's context. Binary scores and static rubrics fail to capture these context-dependent requirements. Existing methods define criteria at the dataset level or generate them in a single pass, which limits their ability to explore the evaluation space implied by each question. We introduce One-Question-One-World (Qworld), a method that generates question-specific evaluation criteria using a recursive expansion tree. Given a question, Qworld decomposes it into scenarios, perspectives, and fine-grained binary criteria through structured hierarchical and horizontal expansion. The resulting criteria specify what a high-quality answer must address for that question. On HealthBench, Qworld covers 89% of expert-authored criteria and generates 79% novel criteria validated by human experts. Experts rate Qworld criteria higher in insight and granularity than those produced by prior methods. When applied to 11 frontier LLMs on HealthBench and Humanity's Last Exam, Qworld reveals capability differences in dimensions such as long-term impact, equity, error handling, and interdisciplinary reasoning that coarse rubrics do not distinguish. By formulating criteria generation as structured coverage of question-implied evaluation axes, Qworld enables evaluation that adapts to each question rather than relying on fixed task-level criteria.

AIApr 3, 2024
Empowering Biomedical Discovery with AI Agents

Shanghua Gao, Ada Fang, Yepeng Huang et al.

We envision "AI scientists" as systems capable of skeptical learning and reasoning that empower biomedical research through collaborative agents that integrate AI models and biomedical tools with experimental platforms. Rather than taking humans out of the discovery process, biomedical AI agents combine human creativity and expertise with AI's ability to analyze large datasets, navigate hypothesis spaces, and execute repetitive tasks. AI agents are poised to be proficient in various tasks, planning discovery workflows and performing self-assessment to identify and mitigate gaps in their knowledge. These agents use large language models and generative models to feature structured memory for continual learning and use machine learning tools to incorporate scientific knowledge, biological principles, and theories. AI agents can impact areas ranging from virtual cell simulation, programmable control of phenotypes, and the design of cellular circuits to developing new therapies.

AIDec 5, 2023
Let's Think Outside the Box: Exploring Leap-of-Thought in Large Language Models with Creative Humor Generation

Shanshan Zhong, Zhongzhan Huang, Shanghua Gao et al.

Chain-of-Thought (CoT) guides large language models (LLMs) to reason step-by-step, and can motivate their logical reasoning ability. While effective for logical tasks, CoT is not conducive to creative problem-solving which often requires out-of-box thoughts and is crucial for innovation advancements. In this paper, we explore the Leap-of-Thought (LoT) abilities within LLMs -- a non-sequential, creative paradigm involving strong associations and knowledge leaps. To this end, we study LLMs on the popular Oogiri game which needs participants to have good creativity and strong associative thinking for responding unexpectedly and humorously to the given image, text, or both, and thus is suitable for LoT study. Then to investigate LLMs' LoT ability in the Oogiri game, we first build a multimodal and multilingual Oogiri-GO dataset which contains over 130,000 samples from the Oogiri game, and observe the insufficient LoT ability or failures of most existing LLMs on the Oogiri game. Accordingly, we introduce a creative Leap-of-Thought (CLoT) paradigm to improve LLM's LoT ability. CLoT first formulates the Oogiri-GO dataset into LoT-oriented instruction tuning data to train pretrained LLM for achieving certain LoT humor generation and discrimination abilities. Then CLoT designs an explorative self-refinement that encourages the LLM to generate more creative LoT data via exploring parallels between seemingly unrelated concepts and selects high-quality data to train itself for self-refinement. CLoT not only excels in humor generation in the Oogiri game but also boosts creative abilities in various tasks like cloud guessing game and divergent association task. These findings advance our understanding and offer a pathway to improve LLMs' creative capacities for innovative applications across domains. The dataset, code, and models will be released online. https://zhongshsh.github.io/CLoT/.

AIMar 14, 2025
TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools

Shanghua Gao, Richard Zhu, Zhenglun Kong et al.

Precision therapeutics require multimodal adaptive models that generate personalized treatment recommendations. We introduce TxAgent, an AI agent that leverages multi-step reasoning and real-time biomedical knowledge retrieval across a toolbox of 211 tools to analyze drug interactions, contraindications, and patient-specific treatment strategies. TxAgent evaluates how drugs interact at molecular, pharmacokinetic, and clinical levels, identifies contraindications based on patient comorbidities and concurrent medications, and tailors treatment strategies to individual patient characteristics. It retrieves and synthesizes evidence from multiple biomedical sources, assesses interactions between drugs and patient conditions, and refines treatment recommendations through iterative reasoning. It selects tools based on task objectives and executes structured function calls to solve therapeutic tasks that require clinical reasoning and cross-source validation. The ToolUniverse consolidates 211 tools from trusted sources, including all US FDA-approved drugs since 1939 and validated clinical insights from Open Targets. TxAgent outperforms leading LLMs, tool-use models, and reasoning agents across five new benchmarks: DrugPC, BrandPC, GenericPC, TreatmentPC, and DescriptionPC, covering 3,168 drug reasoning tasks and 456 personalized treatment scenarios. It achieves 92.1% accuracy in open-ended drug reasoning tasks, surpassing GPT-4o and outperforming DeepSeek-R1 (671B) in structured multi-step reasoning. TxAgent generalizes across drug name variants and descriptions. By integrating multi-step inference, real-time knowledge grounding, and tool-assisted decision-making, TxAgent ensures that treatment recommendations align with established clinical guidelines and real-world evidence, reducing the risk of adverse events and improving therapeutic decision-making.

AIJan 25, 2025
A Causality-aware Paradigm for Evaluating Creativity of Multimodal Large Language Models

Zhongzhan Huang, Shanshan Zhong, Pan Zhou et al.

Recently, numerous benchmarks have been developed to evaluate the logical reasoning abilities of large language models (LLMs). However, assessing the equally important creative capabilities of LLMs is challenging due to the subjective, diverse, and data-scarce nature of creativity, especially in multimodal scenarios. In this paper, we consider the comprehensive pipeline for evaluating the creativity of multimodal LLMs, with a focus on suitable evaluation platforms and methodologies. First, we find the Oogiri game, a creativity-driven task requiring humor, associative thinking, and the ability to produce unexpected responses to text, images, or both. This game aligns well with the input-output structure of modern multimodal LLMs and benefits from a rich repository of high-quality, human-annotated creative responses, making it an ideal platform for studying LLM creativity. Next, beyond using the Oogiri game for standard evaluations like ranking and selection, we propose LoTbench, an interactive, causality-aware evaluation framework, to further address some intrinsic risks in standard evaluations, such as information leakage and limited interpretability. The proposed LoTbench not only quantifies LLM creativity more effectively but also visualizes the underlying creative thought processes. Our results show that while most LLMs exhibit constrained creativity, the performance gap between LLMs and humans is not insurmountable. Furthermore, we observe a strong correlation between results from the multimodal cognition benchmark MMMU and LoTbench, but only a weak connection with traditional creativity metrics. This suggests that LoTbench better aligns with human cognitive theories, highlighting cognition as a critical foundation in the early stages of creativity and enabling the bridging of diverse concepts. https://lotbench.github.io

CLFeb 6, 2025
Multimodal Medical Code Tokenizer

Xiaorui Su, Shvat Messica, Yepeng Huang et al.

Foundation models trained on patient electronic health records (EHRs) require tokenizing medical data into sequences of discrete vocabulary items. Existing tokenizers treat medical codes from EHRs as isolated textual tokens. However, each medical code is defined by its textual description, its position in ontological hierarchies, and its relationships to other codes, such as disease co-occurrences and drug-treatment associations. Medical vocabularies contain more than 600,000 codes with critical information for clinical reasoning. We introduce MedTok, a multimodal medical code tokenizer that uses the text descriptions and relational context of codes. MedTok processes text using a language model encoder and encodes the relational structure with a graph encoder. It then quantizes both modalities into a unified token space, preserving modality-specific and cross-modality information. We integrate MedTok into five EHR models and evaluate it on operational and clinical tasks across in-patient and out-patient datasets, including outcome prediction, diagnosis classification, drug recommendation, and risk stratification. Swapping standard EHR tokenizers with MedTok improves AUPRC across all EHR models, by 4.10% on MIMIC-III, 4.78% on MIMIC-IV, and 11.32% on EHRShot, with the largest gains in drug recommendation. Beyond EHR modeling, we demonstrate using MedTok tokenizer with medical QA systems. Our results demonstrate the potential of MedTok as a unified tokenizer for medical codes, improving tokenization for medical foundation models.

GNFeb 10
STRAND: Sequence-Conditioned Transport for Single-Cell Perturbations

Boyang Fu, George Dasoulas, Sameer Gabbita et al.

Predicting how genetic perturbations change cellular state is a core problem for building controllable models of gene regulation. Perturbations targeting the same gene can produce different transcriptional responses depending on their genomic locus, including different transcription start sites and regulatory elements. Gene-level perturbation models collapse these distinct interventions into the same representation. We introduce STRAND, a generative model that predicts single-cell transcriptional responses by conditioning on regulatory DNA sequence. STRAND represents a perturbation by encoding the sequence at its genomic locus and uses this representation to parameterize a conditional transport process from control to perturbed cell states. Representing perturbations by sequence, rather than by a fixed set of gene identifiers, supports zero-shot inference at loci not seen during training and expands inference-time genomic coverage from ~1.5% for gene-level single-cell foundation models to ~95% of the genome. We evaluate STRAND on CRISPR perturbation datasets in K562, Jurkat, and RPE1 cells. STRAND improves discrimination scores by up to 33% in low-sample regimes, achieves the best average rank on unseen gene perturbation benchmarks, and improves transfer to novel cell lines by up to 0.14 in Pearson correlation. Ablations isolate the gains to sequence conditioning and transport, and case studies show that STRAND resolves functionally alternative transcription start sites missed by gene-level models.

LGMar 4
When Sensors Fail: Temporal Sequence Models for Robust PPO under Sensor Drift

Kevin Vogt-Lowell, Theodoros Tsiligkaridis, Rodney Lafuente-Mercado et al.

Real-world reinforcement learning systems must operate under distributional drift in their observation streams, yet most policy architectures implicitly assume fully observed and noise-free states. We study robustness of Proximal Policy Optimization (PPO) under temporally persistent sensor failures that induce partial observability and representation shift. To respond to this drift, we augment PPO with temporal sequence models, including Transformers and State Space Models (SSMs), to enable policies to infer missing information from history and maintain performance. Under a stochastic sensor failure process, we prove a high-probability bound on infinite-horizon reward degradation that quantifies how robustness depends on policy smoothness and failure persistence. Empirically, on MuJoCo continuous-control benchmarks with severe sensor dropout, we show Transformer-based sequence policies substantially outperform MLP, RNN, and SSM baselines in robustness, maintaining high returns even when large fractions of sensors are unavailable. These results demonstrate that temporal sequence reasoning provides a principled and practical mechanism for reliable operation under observation drift caused by sensor unreliability.

HCSep 23, 2025
YAC: Bridging Natural Language and Interactive Visual Exploration with Generative AI for Biomedical Data Discovery

Devin Lange, Shanghua Gao, Pengwei Sui et al.

Incorporating natural language input has the potential to improve the capabilities of biomedical data discovery interfaces. However, user interface elements and visualizations are still powerful tools for interacting with data, even in the new world of generative AI. In our prototype system, YAC, Yet Another Chatbot, we bridge the gap between natural language and interactive visualizations by generating structured declarative output with a multi-agent system and interpreting that output to render linked interactive visualizations and apply data filters. Furthermore, we include widgets, which allow users to adjust the values of that structured output through user interface elements. We reflect on the capabilities and design of this system with an analysis of its technical dimensions and illustrate the capabilities through four usage scenarios.

HCSep 19, 2025
A Generative AI System for Biomedical Data Discovery with Grammar-Based Visualizations

Devin Lange, Shanghua Gao, Pengwei Sui et al.

We explore the potential for combining generative AI with grammar-based visualizations for biomedical data discovery. In our prototype, we use a multi-agent system to generate visualization specifications and apply filters. These visualizations are linked together, resulting in an interactive dashboard that is progressively constructed. Our system leverages the strengths of natural language while maintaining the utility of traditional user interfaces. Furthermore, we utilize generated interactive widgets enabling user adjustment. Finally, we demonstrate the potential utility of this system for biomedical data discovery with a case study.

CVDec 10, 2023
A Decoupled Spatio-Temporal Framework for Skeleton-based Action Segmentation

Yunheng Li, Zhongyu Li, Shanghua Gao et al.

Effectively modeling discriminative spatio-temporal information is essential for segmenting activities in long action sequences. However, we observe that existing methods are limited in weak spatio-temporal modeling capability due to two forms of decoupled modeling: (i) cascaded interaction couples spatial and temporal modeling, which over-smooths motion modeling over the long sequence, and (ii) joint-shared temporal modeling adopts shared weights to model each joint, ignoring the distinct motion patterns of different joints. We propose a Decoupled Spatio-Temporal Framework (DeST) to address the above issues. Firstly, we decouple the cascaded spatio-temporal interaction to avoid stacking multiple spatio-temporal blocks, while achieving sufficient spatio-temporal interaction. Specifically, DeST performs once unified spatial modeling and divides the spatial features into different groups of subfeatures, which then adaptively interact with temporal features from different layers. Since the different sub-features contain distinct spatial semantics, the model could learn the optimal interaction pattern at each layer. Meanwhile, inspired by the fact that different joints move at different speeds, we propose joint-decoupled temporal modeling, which employs independent trainable weights to capture distinctive temporal features of each joint. On four large-scale benchmarks of different scenes, DeST significantly outperforms current state-of-the-art methods with less computational complexity.

CVJun 6, 2021
Large-scale Unsupervised Semantic Segmentation

Shanghua Gao, Zhong-Yu Li, Ming-Hsuan Yang et al.

Empowered by large datasets, e.g., ImageNet, unsupervised learning on large-scale data has enabled significant advances for classification tasks. However, whether the large-scale unsupervised semantic segmentation can be achieved remains unknown. There are two major challenges: i) we need a large-scale benchmark for assessing algorithms; ii) we need to develop methods to simultaneously learn category and shape representation in an unsupervised manner. In this work, we propose a new problem of large-scale unsupervised semantic segmentation (LUSS) with a newly created benchmark dataset to help the research progress. Building on the ImageNet dataset, we propose the ImageNet-S dataset with 1.2 million training images and 50k high-quality semantic segmentation annotations for evaluation. Our benchmark has a high data diversity and a clear task objective. We also present a simple yet effective method that works surprisingly well for LUSS. In addition, we benchmark related un/weakly/fully supervised methods accordingly, identifying the challenges and possible directions of LUSS. The benchmark and source code is publicly available at https://github.com/LUSSeg.

CVMay 19, 2018
Optimizing the F-measure for Threshold-free Salient Object Detection

Kai Zhao, Shanghua Gao, Wenguan Wang et al.

Current CNN-based solutions to salient object detection (SOD) mainly rely on the optimization of cross-entropy loss (CELoss). Then the quality of detected saliency maps is often evaluated in terms of F-measure. In this paper, we investigate an interesting issue: can we consistently use the F-measure formulation in both training and evaluation for SOD? By reformulating the standard F-measure we propose the relaxed F-measure which is differentiable w.r.t the posterior and can be easily appended to the back of CNNs as the loss function. Compared to the conventional cross-entropy loss of which the gradients decrease dramatically in the saturated area, our loss function, named FLoss, holds considerable gradients even when the activation approaches the target. Consequently, the FLoss can continuously force the network to produce polarized activations. Comprehensive benchmarks on several popular datasets show that FLoss outperforms the state-of-the-art with a considerable margin. More specifically, due to the polarized predictions, our method is able to obtain high-quality saliency maps without carefully tuning the optimal threshold, showing significant advantages in real-world applications.

CVJan 5, 2018
Hi-Fi: Hierarchical Feature Integration for Skeleton Detection

Kai Zhao, Wei Shen, Shanghua Gao et al.

In natural images, the scales (thickness) of object skeletons may dramatically vary among objects and object parts, making object skeleton detection a challenging problem. We present a new convolutional neural network (CNN) architecture by introducing a novel hierarchical feature integration mechanism, named Hi-Fi, to address the skeleton detection problem. The proposed CNN-based approach has a powerful multi-scale feature integration ability that intrinsically captures high-level semantics from deeper layers as well as low-level details from shallower layers. % By hierarchically integrating different CNN feature levels with bidirectional guidance, our approach (1) enables mutual refinement across features of different levels, and (2) possesses the strong ability to capture both rich object context and high-resolution details. Experimental results show that our method significantly outperforms the state-of-the-art methods in terms of effectively fusing features from very different scales, as evidenced by a considerable performance improvement on several benchmarks.