[
{
"id": "/contact/",
"title": "Contact",
"url": "/contact/",
"section": "Contact",
"venue": "",
"date": "",
"content": "Contact Email yuzhou.chang@osumc.edu chang.1754@osu.edu ychang13@bidmc.harvard.edu Office 2255 Kenny RdColumbus, OH 43210, USA š Curriculum Vitae Download my full CV in PDF format. š Download CV (PDF)"
},
{
"id": "/games/",
"title": "Mini Game",
"url": "/games/",
"section": "Mini Game",
"venue": "",
"date": "",
"content": "Snake Game of Life Snake Score 0 Best 0 Speed Chill Slow Normal Fast Insane Mode Normal Maybe Dead Never Dead Restart Pause About Snake From Blockade (1976) to Nokia phones (1997). Minimal rules, maximum addiction ā every meal narrows the safe paths through your own tail. Conway's Game of Life Pattern Gosper's Glider Gun Glider Lightweight Spaceship Pulsar Acorn (methuselah) Random soup Clear board Rule Conway B3/S23 HighLife B36/S23 Seeds B2/S Day & Night Replicator Maze 34 Life Speed Slow Normal Fast Blazing Pause Step Restart gen 0 Ā· live 0 About Game of Life John Conway, 1970. Two rules ā survive on 2ā3 neighbours, born on 3 (B3/S23) ā yield a Turing-complete universe. Gosper's Glider Gun (1970) was the first known pattern that grows without bound. Click cells while paused to edit. Edges wrap."
},
{
"id": "/news/",
"title": "News",
"url": "/news/",
"section": "News",
"venue": "",
"date": "",
"content": "Latest News 2026-04-30 ā New Comment in Nature Biotechnology: Tracing the rise of biomedical foundation models . Chang Y, Cheng H, Modi M, Wang G, Xu D, Ma Q. Nature Biotechnology, 2026. A survey of biological foundation models with an outlook for future developments. 2026-03-31 ā New paper in Cell Reports Medicine: Epstein-Barr virus orchestrates spatial reorganization and immunomodulation in the classic Hodgkin lymphoma tumor microenvironment. Yeo YY, Qiu H, Bai Y, Zhu B, Chang Y, ā¦ Jiang S. Cell Reports Medicine, 2026. 2026-03-24 ā New paper in Cancer Discovery: Same-Slide Spatial Multi-Omics Integration with IN-DEPTH Reveals Tumor Virus-Linked Spatial Reorganization of the Tumor Microenvironment. Yiu SPT, Chang Y, Yeo YY, Qiu H, ā¦ Ma Q, Jiang S. Cancer Discovery, 2026. 2024 ā Started postdoctoral research at OSU & Harvard Medical School (BIDMC). 2023 ā Successfully defended Ph.D. dissertation at The Ohio State University. For the full publication list, see my Google Scholar profile."
},
{
"id": "/publications/",
"title": "Publications",
"url": "/publications/",
"section": "Publications",
"venue": "",
"date": "",
"content": "You can also find my articles on my Google Scholar profile. Journal Articles Tracing the rise of biomedical foundation models Published in Nature Biotechnology, 2026 Recommended citation: Yuzhou Chang, Hao Cheng, Mirage Modi, Guangyu Wang, Dong Xu, Qin Ma. (2026). \"Tracing the rise of biomedical foundation models\" Nature Biotechnology.Download Paper Abstract 4163: A general-purpose AI foundation model for spatial proteomics Published in Cancer Research, 2026 Abstract Standard spatial proteomics (SP) pipelines for biomarker discovery have traditionally relied on cell segmentation followed by single-marker thresholding or rule-based mechanisms to assign cell phenotypes. However, this often suffers from a laborious process of manual annotations and neglects cell states chaā¦ Recommended citation: Andrew H. Song, Anurag Vaidya, Mohammed Shaban, Yuzhou Chang, Huaying Qiu, Yao Yu Yeo, Guillaume Jaume, W. L. K. Wu, et al.. (2026). \"Abstract 4163: A general-purpose AI foundation model for spatial proteomics\" Cancer Research.Download Paper Epstein-Barr virus orchestrates spatial reorganization and immunomodulation in the classic Hodgkin lymphoma tumor microenvironment Published in Cell Reports Medicine, 2026 Classic Hodgkin lymphoma (cHL) is composed of rare malignant Hodgkin and Reed-Sternberg (HRS) cells within a T-cell-rich tumor microenvironment (TME). Epstein-Barr virus (EBV) is present in ā¼25% of cases, but its contribution to pathogenesis and immunomodulation remains unclear ..."
},
{
"id": "/research/",
"title": "Research",
"url": "/research/",
"section": "Research",
"venue": "",
"date": "",
"content": "Research Interests Graph Signal Processing Leveraging graph-based methods for spatial transcriptomics analysis, developing novel algorithms for understanding cellular networks. Foundation Models Developing and applying multiplexed foundation models for few-shot and zero-shot learning in biological contexts. Spatial Omics Creating computational tools to study cell-cell communication and tissue architecture using cutting-edge spatial technologies. Immuno-Oncology Utilizing spatial transcriptomics for insights into tumor-immune interactions and therapeutic target identification. Gene Regulatory Networks Advancing methodologies to decode gene regulation and understand complex biological systems. AI for Science Developing agentic workflows to accelerate hypothesis generation, experiment design, and analysis across biomedical research. Topic Map A live view of recurring themes across my publications. Click any term to see the papers that mention it. Loading topic mapā¦ Term Ć"
},
{
"id": "/sitemap/",
"title": "Sitemap",
"url": "/sitemap/",
"section": "Sitemap",
"venue": "",
"date": "",
"content": "## Yuzhou Chang Postdoctoral researcher in computational biology at The Ohio State University and Beth Israel Deaconess Medical Center, Harvard Medical School. Working on spatial omics, graph signal processing, foundation models, and immuno-oncology. ## Contact Email yuzhou.chang@osumc.edu chang.1754@osu.edu ychang13@bidmc.harvard.edu Office 2255 Kenny RdColumbus, OH 43210, USA Profiles ORCID 0000-0003-4893-1886 Google Scholar GitHub @BMEngineeR ## Site Research News Publications Software Contact Blog CV (PDF) XML sitemap (for crawlers)"
},
{
"id": "/sketchpad/",
"title": "Sketchpad",
"url": "/sketchpad/",
"section": "Sketchpad",
"venue": "",
"date": "",
"content": "A quick whiteboard powered by Excalidraw. Sketches stay in your browser; export as PNG/SVG to keep them. Tip: if the board looks cramped, use the popup arrow at the top-right of the iframe (or visit excalidraw.com directly) for full-screen."
},
{
"id": "/software/",
"title": "Software",
"url": "/software/",
"section": "Software",
"venue": "",
"date": "",
"content": "## Open-Source Software SpaGFT A graph Fourier transform framework for spatial omics ā characterizing tissue modules and spatially variable genes. github.com/OSU-BMBL/SpaGFT RESEPT Deep-learning framework for tissue architecture identification from spatial transcriptomics. github.com/OSU-BMBL/RESEPT BioGSP (R) Graph signal processing toolkit for biological data analysis, R implementation. github.com/BMEngineeR/BioGSP KRONOS Foundation model framework for spatial proteomics. Collaboration with Mahmood Lab. github.com/mahmoodlab/KRONOS pycodex Python toolkit for CODEX multiplexed imaging analysis. Built and maintained by Wenrui Wu ā sharing here as a highly useful resource. github.com/BMEngineeR/pycodex For all open-source projects, please visit my GitHub profile."
},
{
"id": "/year-archive/",
"title": "Blog posts",
"url": "/year-archive/",
"section": "Blog",
"venue": "",
"date": "",
"content": "{% include base_path %} {% capture written_year %}'None'{% endcapture %} {% for post in site.posts %} {% capture year %}{{ post.date | date: '%Y' }}{% endcapture %} {% if year != written_year %} {{ year }} {% capture written_year %}{{ year }}{% endcapture %} {% endif %} {% include archive-single.html %} {% endfor %}"
},
{
"id": "/posts/2026/03/in-depth-sgcc/",
"title": "Same-Slide Spatial Multi-Omics Integration with IN-DEPTH Reveals Tumor Virus-Linked Spatial Reorganization of the Tumor Microenvironment",
"url": "/posts/2026/03/in-depth-sgcc/",
"section": "Blog",
"venue": "",
"date": "2026-03-26",
"content": "Originally posted on LinkedIn ā March 26, 2026. Why same-slide multi-omics? Tumors are not just a collection of cell types ā they are a spatial composition. Knowing which cells are present in a tumor microenvironment is only the first question. The harder one is: how are those cells arranged? Which cell states appear together, which remain separated, and which spatial arrangements are linked to immune function or therapy response? To answer this we need both what each cell is doing (transcriptomics) and which functional protein states it sits in (proteomics) ā and we need them on the same physical slide, so the spatial coordinates line up exactly. Thatās the motivation behind IN-DEPTH (IN-situ DEtailed Phenotyping To High-resolution transcriptomics): a streamlined workflow that uses single-cell spatial-proteomic imaging to guide spatial-transcriptomic capture on the same tissue section, without the RNA signal loss that plagues sequential staining workflows. Reading multi-scale spatial relationships with SGCC Even with paired protein and RNA on a single slide, integrating the two modalities is non-trivial. Off-the-shelf correlation scores collapse rich multi-scale spatial information into a single number, throwing away the structure that makes a tumor microenvironment interesting in the first place. We borrowed ideas from graph signal processing ā specifically the spectral decomposition of signals defined on a tissue graph ā and built Spectral Graph Cross-Correlation (SGCC)..."
},
{
"id": "/publication/2018-08-02-senp3-maintains-the-stability-and-function-of-regulatory-t-c",
"title": "SENP3 maintains the stability and function of regulatory T cells via BACH2 deSUMOylation",
"url": "/publication/2018-08-02-senp3-maintains-the-stability-and-function-of-regulatory-t-c",
"section": "Publications",
"venue": "Nature Communications",
"date": "2018-08-02",
"content": "Abstract Regulatory T (Treg) cells are essential for maintaining immune homeostasis and tolerance, but the mechanisms regulating the stability and function of Treg cells have not been fully elucidated. Here we show SUMO-specific protease 3 (SENP3) is a pivotal regulator of Treg cells that functions by controlling thā¦"
},
{
"id": "/publication/2020-03-26-integrative-methods-and-practical-challenges-for-single-cell",
"title": "Integrative Methods and Practical Challenges for Single-Cell Multi-omics",
"url": "/publication/2020-03-26-integrative-methods-and-practical-challenges-for-single-cell",
"section": "Publications",
"venue": "Trends in biotechnology",
"date": "2020-03-26",
"content": ""
},
{
"id": "/publication/2020-05-18-iris3-integrated-cell-type-specific-regulon-inference-server",
"title": "IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq",
"url": "/publication/2020-05-18-iris3-integrated-cell-type-specific-regulon-inference-server",
"section": "Publications",
"venue": "PMC",
"date": "2020-05-18",
"content": "A group of genes controlled as a unit, usually by the same repressor or activator gene, is known as a regulon. The ability to identify active regulons within a specific cell type, i.e., cell-type-specific regulons (CTSR), provides an extraordinary opportunity to pinpoint crucial regulators and target genes responsibā¦"
},
{
"id": "/publication/2020-08-03-scgnn-a-novel-graph-neural-network-framework-for-single-cell",
"title": "scGNN: a novel graph neural network framework for single-cell RNA-Seq analyses",
"url": "/publication/2020-08-03-scgnn-a-novel-graph-neural-network-framework-for-single-cell",
"section": "Publications",
"venue": "bioRxiv (Cold Spring Harbor Laboratory)",
"date": "2020-08-03",
"content": "ABSTRACT Single-cell RNA-sequencing (scRNA-Seq) is widely used to reveal the heterogeneity and dynamics of tissues, organisms, and complex diseases, but its analyses still suffer from multiple grand challenges, including the sequencing sparsity and complex differential patterns in gene expression. We introduce the sā¦"
},
{
"id": "/publication/2021-02-15-iris-fgm-an-integrative-single-cell-rna-seq-interpretation-s",
"title": "IRIS-FGM: an integrative single-cell RNA-Seq interpretation system for functional gene module analysis",
"url": "/publication/2021-02-15-iris-fgm-an-integrative-single-cell-rna-seq-interpretation-s",
"section": "Publications",
"venue": "Bioinformatics",
"date": "2021-02-15",
"content": "SUMMARY: Single-cell RNA-Seq (scRNA-Seq) data is useful in discovering cell heterogeneity and signature genes in specific cell populations in cancer and other complex diseases. Specifically, the investigation of condition-specific functional gene modules (FGM) can help to understand interactive gene networks and comā¦"
},
{
"id": "/publication/2021-03-25-scgnn-is-a-novel-graph-neural-network-framework-for-single-c",
"title": "scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses",
"url": "/publication/2021-03-25-scgnn-is-a-novel-graph-neural-network-framework-for-single-c",
"section": "Publications",
"venue": "Nature Communications",
"date": "2021-03-25",
"content": "Single-cell RNA-sequencing (scRNA-Seq) is widely used to reveal the heterogeneity and dynamics of tissues, organisms, and complex diseases, but its analyses still suffer from multiple grand challenges, including the sequencing sparsity and complex differential patterns in gene expression. We introduce the scGNN (sinā¦"
},
{
"id": "/publication/2021-06-24-a-bayesian-multivariate-mixture-model-for-spatial-transcript",
"title": "A Bayesian Multivariate Mixture Model for Spatial Transcriptomics Data",
"url": "/publication/2021-06-24-a-bayesian-multivariate-mixture-model-for-spatial-transcript",
"section": "Publications",
"venue": "bioRxiv (Cold Spring Harbor Laboratory)",
"date": "2021-06-24",
"content": "Abstract High throughput spatial transcriptomics (HST) is a rapidly emerging class of experimental technologies that allow for profiling gene expression in tissue samples at or near single-cell resolution while retaining the spatial location of each sequencing unit within the tissue sample. Through analyzing HST datā¦"
},
{
"id": "/publication/2021-07-08-spatially-resolved-transcriptomics-reveals-unique-gene-signa",
"title": "Spatially resolved transcriptomics reveals unique gene signatures associated with human temporal cortical architecture and Alzheimerās pathology",
"url": "/publication/2021-07-08-spatially-resolved-transcriptomics-reveals-unique-gene-signa",
"section": "Publications",
"venue": "bioRxiv (Cold Spring Harbor Laboratory)",
"date": "2021-07-08",
"content": "Abstract Alzheimerās disease (AD) is pathologically characterized by amyloid beta (AĪ²) plaques, neurofibrillary tangles (tau aggregates), and alterations in microglia, astrocytes and oligodendrocytes. The mesial temporal lobe is a vulnerable brain region in early AD; however, little is known about the transcriptome-ā¦"
},
{
"id": "/publication/2021-09-10-spatially-resolved-transcriptomics-reveals-gene-signatures-u",
"title": "Spatially resolved transcriptomics reveals gene signatures underlying the vulnerability of human middle temporal gyrus in Alzheimer's disease",
"url": "/publication/2021-09-10-spatially-resolved-transcriptomics-reveals-gene-signatures-u",
"section": "Publications",
"venue": "Research Square",
"date": "2021-09-10",
"content": ""
},
{
"id": "/publication/2021-11-03-deepmaps-single-cell-biological-network-inference-using-hete",
"title": "DeepMAPS: Single-cell biological network inference using heterogeneous graph transformer",
"url": "/publication/2021-11-03-deepmaps-single-cell-biological-network-inference-using-hete",
"section": "Publications",
"venue": "bioRxiv (Cold Spring Harbor Laboratory)",
"date": "2021-11-03",
"content": "Abstract We present DeepMAPS (Deep learning-based Multi-omics Analysis Platform for Single-cell data) for biological network inference from single-cell multi-omics (scMulti-omics). DeepMAPS includes both cells and genes in a heterogeneous graph to simultaneously infer cell-cell, cell-gene, and gene-gene relations. Tā¦"
},
{
"id": "/publication/2021-12-01-spatial-transcriptomics-of-human-middle-temporal-gyrus-revea",
"title": "Spatial transcriptomics of human middle temporal gyrus reveals layerāspecific gene expression in early Alzheimerās disease",
"url": "/publication/2021-12-01-spatial-transcriptomics-of-human-middle-temporal-gyrus-revea",
"section": "Publications",
"venue": "Alzheimer s & Dementia",
"date": "2021-12-01",
"content": "Background In many neurodegenerative diseases including Alzheimerās disease (AD), specific subpopulations of cells and brain regions are more sensitive to dysfunction and degeneration than others. For example, excitatory neurons in the layer 2/3 of middle temporal gyrus (MTG) is particularly vulnerable to degeneratiā¦"
},
{
"id": "/publication/2022-01-01-define-and-visualize-pathological-architectures-of-human-tis",
"title": "Define and visualize pathological architectures of human tissues from spatially resolved transcriptomics using deep learning",
"url": "/publication/2022-01-01-define-and-visualize-pathological-architectures-of-human-tis",
"section": "Publications",
"venue": "Computational and Structural Biotechnology Journal",
"date": "2022-01-01",
"content": "Spatially resolved transcriptomics provides a new way to define spatial contexts and understand the pathogenesis of complex human diseases. Although some computational frameworks can characterize spatial context via various clustering methods, the detailed spatial architectures and functional zonation often cannot bā¦"
},
{
"id": "/publication/2022-01-10-treatment-with-soluble-cd24-attenuates-covid-19-associated-s",
"title": "Treatment with soluble CD24 attenuates COVID-19-associated systemic immunopathology",
"url": "/publication/2022-01-10-treatment-with-soluble-cd24-attenuates-covid-19-associated-s",
"section": "Publications",
"venue": "Journal of Hematology & Oncology",
"date": "2022-01-10",
"content": "Abstract Background Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19) through direct lysis of infected lung epithelial cells, which releases damage-associated molecular patterns and induces a pro-inflammatory cytokine milieu causing systemic inflammation. Anti-viā¦"
},
{
"id": "/publication/2022-03-02-maple-a-hybrid-framework-for-multi-sample-spatial-transcript",
"title": "MAPLE: A Hybrid Framework for Multi-Sample Spatial Transcriptomics Data",
"url": "/publication/2022-03-02-maple-a-hybrid-framework-for-multi-sample-spatial-transcript",
"section": "Publications",
"venue": "bioRxiv (Cold Spring Harbor Laboratory)",
"date": "2022-03-02",
"content": "High throughput spatial transcriptomics (HST) technologies provide unprecedented opportunity to identify spatially resolved cell sub-populations in tissue samples. However, existing methods preclude joint analysis of multiple HST samples, do not allow for differential abundance analysis (DAA), and ignore uncertaintyā¦"
},
{
"id": "/publication/2022-04-07-wolframin-is-a-novel-regulator-of-tau-pathology-and-neurodeg",
"title": "Wolframin is a novel regulator of tau pathology and neurodegeneration",
"url": "/publication/2022-04-07-wolframin-is-a-novel-regulator-of-tau-pathology-and-neurodeg",
"section": "Publications",
"venue": "Acta Neuropathologica",
"date": "2022-04-07",
"content": ""
},
{
"id": "/publication/2022-04-14-androgen-conspires-with-the-cd8-sup-sup-t-cell-exhaustion-pr",
"title": "Androgen conspires with the CD8 + T cell exhaustion program and contributes to sex bias in cancer",
"url": "/publication/2022-04-14-androgen-conspires-with-the-cd8-sup-sup-t-cell-exhaustion-pr",
"section": "Publications",
"venue": "Science Immunology",
"date": "2022-04-14",
"content": "Sex bias exists in the development and progression of nonreproductive organ cancers, but the underlying mechanisms are enigmatic. Studies so far have focused largely on sexual dimorphisms in cancer biology and socioeconomic factors. Here, we establish a role for CD8 + T cellādependent antitumor immunity in mediatingā¦"
},
{
"id": "/publication/2022-06-27-a-shared-disease-associated-oligodendrocyte-signature-among",
"title": "A shared disease-associated oligodendrocyte signature among multiple CNS pathologies",
"url": "/publication/2022-06-27-a-shared-disease-associated-oligodendrocyte-signature-among",
"section": "Publications",
"venue": "Nature Neuroscience",
"date": "2022-06-27",
"content": ""
},
{
"id": "/publication/2022-07-04-sex-biased-adaptive-immune-regulation-in-cancer-development",
"title": "Sex-biased adaptive immune regulation in cancer development and therapy",
"url": "/publication/2022-07-04-sex-biased-adaptive-immune-regulation-in-cancer-development",
"section": "Publications",
"venue": "iScience",
"date": "2022-07-04",
"content": "T cell dysfunction or exhaustion in the tumor microenvironment and summarize ongoing clinical efforts to determine the impact of androgen blockade on cancer immunotherapy. Finally, we outline a framework for future research in cancer biology and immuno-oncology, underscoring the importance of a holistic research appā¦"
},
{
"id": "/publication/2022-07-27-a-bayesian-multivariate-mixture-model-for-high-throughput-sp",
"title": "A Bayesian Multivariate Mixture Model for High Throughput Spatial Transcriptomics",
"url": "/publication/2022-07-27-a-bayesian-multivariate-mixture-model-for-high-throughput-sp",
"section": "Publications",
"venue": "Biometrics",
"date": "2022-07-27",
"content": "High throughput spatial transcriptomics (HST) is a rapidly emerging class of experimental technologies that allow for profiling gene expression in tissue samples at or near single-cell resolution while retaining the spatial location of each sequencing unit within the tissue sample. Through analyzing HST data, we seeā¦"
},
{
"id": "/publication/2022-09-01-selective-targeting-of-garp-ltgf-axis-in-the-tumor-microenvi",
"title": "Selective targeting of GARP-LTGFĪ² axis in the tumor microenvironment augments PD-1 blockade via enhancing CD8+ T cell antitumor immunity",
"url": "/publication/2022-09-01-selective-targeting-of-garp-ltgf-axis-in-the-tumor-microenvi",
"section": "Publications",
"venue": "Journal for ImmunoTherapy of Cancer",
"date": "2022-09-01",
"content": "Background Immune checkpoint blockade (ICB) has revolutionized cancer immunotherapy. However, most patients with cancer fail to respond clinically. One potential reason is the accumulation of immunosuppressive transforming growth factor Ī² (TGFĪ²) in the tumor microenvironment (TME). TGFĪ² drives cancer immune evasionā¦"
},
{
"id": "/publication/2022-11-01-1064-exercise-induced-hormone-irisin-inhibits-integrin-v-tgf",
"title": "1064ā
Exercise induced hormone irisin inhibits Integrin Ī±v-TGF-Ī² axis in tumor microenvironment to improve CD8+ T cell mediated tumor control",
"url": "/publication/2022-11-01-1064-exercise-induced-hormone-irisin-inhibits-integrin-v-tgf",
"section": "Publications",
"venue": "Regular and Young Investigator Award Abstracts",
"date": "2022-11-01",
"content": "Background It has been reported multiple times that exercise can prevent cancer development, help anti-tumor therapies, and lower relapse rate after successful cancer treatment. However, an underlying molecular mechanism for these beneficial effects remained elusive. Recent studies revealed that cytotoxic iā¦"
},
{
"id": "/publication/2022-11-01-839-selective-targeting-of-garp-ltgf-axis-in-the-tumor-micro",
"title": "839ā
Selective targeting of GARP-LTGFĆ Axis in the tumor microenvironment augments PD-1 blockade via enhancing CD8+ T cell anti-tumor immunity",
"url": "/publication/2022-11-01-839-selective-targeting-of-garp-ltgf-axis-in-the-tumor-micro",
"section": "Publications",
"venue": "Regular and Young Investigator Award Abstracts",
"date": "2022-11-01",
"content": "Background Immune checkpoint blockade (ICB) targeting programed cell death protein 1 (PD-1) and its ligand has revolutionized cancer immunotherapy. Unfortunately, while some cancer patients experience robust and lasting remission following treatment, most fail to respond clinically. Accumulation of transforā¦"
},
{
"id": "/publication/2022-12-13-spatial-omics-representation-and-functional-tissue-module-in",
"title": "Spatial omics representation and functional tissue module inference using graph Fourier transform",
"url": "/publication/2022-12-13-spatial-omics-representation-and-functional-tissue-module-in",
"section": "Publications",
"venue": "bioRxiv (Cold Spring Harbor Laboratory)",
"date": "2022-12-13",
"content": "Abstract Tissue module (TM) is a spatially organized tissue region and executes specialized biological functions, recurring and varying at different tissue sites. However, the computational identification of TMs poses challenges due to their convoluted biological functions, poorly-defined molecular features, and varā¦"
},
{
"id": "/publication/2022-12-21-spatially-resolved-transcriptomics-reveals-genes-associated",
"title": "Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimerās disease",
"url": "/publication/2022-12-21-spatially-resolved-transcriptomics-reveals-genes-associated",
"section": "Publications",
"venue": "Acta Neuropathologica Communications",
"date": "2022-12-21",
"content": "Human middle temporal gyrus (MTG) is a vulnerable brain region in early Alzheimerās disease (AD), but little is known about the molecular mechanisms underlying this regional vulnerability. Here we utilize the 10 Ć Visium platform to define the spatial transcriptomic profile in both AD and control (CT) MTG. We identiā¦"
},
{
"id": "/publication/2022-12-27-ribonucleotide-reductase-m2-rrm2-regulation-function-and-tar",
"title": "Ribonucleotide reductase M2 (RRM2): Regulation, function and targeting strategy in human cancer",
"url": "/publication/2022-12-27-ribonucleotide-reductase-m2-rrm2-regulation-function-and-tar",
"section": "Publications",
"venue": "Genes & Diseases",
"date": "2022-12-27",
"content": "Ribonucleotide reductase M2 (RRM2) is a small subunit in ribonucleotide reductases, which participate in nucleotide metabolism and catalyze the conversion of nucleotides to deoxynucleotides, maintaining the dNTP pools for DNA biosynthesis, repair, and replication. RRM2 performs a critical role in the malignant bioloā¦"
},
{
"id": "/publication/2023-01-03-recent-advances-of-bioactive-proteins-polypeptides-in-the-tr",
"title": "Recent advances of bioactive proteins/polypeptides in the treatment of breast cancer",
"url": "/publication/2023-01-03-recent-advances-of-bioactive-proteins-polypeptides-in-the-tr",
"section": "Publications",
"venue": "Food Science and Biotechnology",
"date": "2023-01-03",
"content": ""
},
{
"id": "/publication/2023-02-21-single-cell-biological-network-inference-using-a-heterogeneo",
"title": "Single-cell biological network inference using a heterogeneous graph transformer",
"url": "/publication/2023-02-21-single-cell-biological-network-inference-using-a-heterogeneo",
"section": "Publications",
"venue": "Nature Communications",
"date": "2023-02-21",
"content": "Single-cell multi-omics (scMulti-omics) allows the quantification of multiple modalities simultaneously to capture the intricacy of complex molecular mechanisms and cellular heterogeneity. Existing tools cannot effectively infer the active biological networks in diverse cell types and the response of these networksā¦"
},
{
"id": "/publication/2023-03-24-dimension-agnostic-and-granularity-based-spatially-variable",
"title": "Dimension-agnostic and granularity-based spatially variable gene identification",
"url": "/publication/2023-03-24-dimension-agnostic-and-granularity-based-spatially-variable",
"section": "Publications",
"venue": "bioRxiv (Cold Spring Harbor Laboratory)",
"date": "2023-03-24",
"content": "Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression with corresponding spatial coordinates in two or three dimensions and can be used to infer SVGs effectively. However, currentā¦"
},
{
"id": "/publication/2023-08-24-single-cell-profiling-of-murine-bladder-cancer-identifies-se",
"title": "Single-cell profiling of murine bladder cancer identifies sex-specific transcriptional signatures with prognostic relevance",
"url": "/publication/2023-08-24-single-cell-profiling-of-murine-bladder-cancer-identifies-se",
"section": "Publications",
"venue": "iScience",
"date": "2023-08-24",
"content": "Bladder cancer (BLCA) is more common in men but more aggressive in women. Sex-based differences in cancer biology are commonly studied using a murine model with BLCA generated by N-butyl-N-(4-hydroxybutyl)-nitrosamine (BBN). While tumors in the BBN model have been profiled, these profiles provide limited informationā¦"
},
{
"id": "/publication/2023-11-03-trem2-mediates-mhcii-associated-cd4-t-cell-response-against",
"title": "TREM2 mediates MHCII-associated CD4+ T-cell response against gliomas",
"url": "/publication/2023-11-03-trem2-mediates-mhcii-associated-cd4-t-cell-response-against",
"section": "Publications",
"venue": "Neuro-Oncology",
"date": "2023-11-03",
"content": "BACKGROUND: Myeloid cells comprise up to 50% of the total tumor mass in glioblastoma (GBM) and have been implicated in promoting tumor progression and immunosuppression. Modulating the response of myeloid cells to the tumor has emerged as a promising new approach for cancer treatment. In this regard, we focus on theā¦"
},
{
"id": "/publication/2023-11-14-dimension-agnostic-and-granularity-based-spatially-variable",
"title": "Dimension-agnostic and granularity-based spatially variable gene identification using BSP",
"url": "/publication/2023-11-14-dimension-agnostic-and-granularity-based-spatially-variable",
"section": "Publications",
"venue": "Nature Communications",
"date": "2023-11-14",
"content": "Identifying spatially variable genes (SVGs) is critical in linking molecular cell functions with tissue phenotypes. Spatially resolved transcriptomics captures cellular-level gene expression with corresponding spatial coordinates in two or three dimensions and can be used to infer SVGs effectively. However, currentā¦"
},
{
"id": "/publication/2024-03-07-epstein-barr-virus-orchestrates-spatial-reorganization-and-i",
"title": "Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment",
"url": "/publication/2024-03-07-epstein-barr-virus-orchestrates-spatial-reorganization-and-i",
"section": "Publications",
"venue": "bioRxiv (Cold Spring Harbor Laboratory)",
"date": "2024-03-07",
"content": "Classic Hodgkin Lymphoma (cHL) is a tumor composed of rare malignant Hodgkin and Reed-Sternberg (HRS) cells nested within a T-cell rich inflammatory immune infiltrate. cHL is associated with Epstein-Barr Virus (EBV) in 25% of cases. The specific contributions of EBV to the pathogenesis of cHL remain largely unknown,ā¦"
},
{
"id": "/publication/2024-04-17-a-contrastive-learning-approach-to-integrate-spatial-transcr",
"title": "A contrastive learning approach to integrate spatial transcriptomics and histological images",
"url": "/publication/2024-04-17-a-contrastive-learning-approach-to-integrate-spatial-transcr",
"section": "Publications",
"venue": "Computational and Structural Biotechnology Journal",
"date": "2024-04-17",
"content": "The rapid growth of spatially resolved transcriptomics technology provides new perspectives on spatial tissue architecture. Deep learning has been widely applied to derive useful representations for spatial transcriptome analysis. However, effectively integrating spatial multi-modal data remains challenging. Here, wā¦"
},
{
"id": "/publication/2024-05-23-spatial-and-functional-targeting-of-intratumoral-tregs-rever",
"title": "Spatial and functional targeting of intratumoral Tregs reverses CD8+ T cell exhaustion and promotes cancer immunotherapy",
"url": "/publication/2024-05-23-spatial-and-functional-targeting-of-intratumoral-tregs-rever",
"section": "Publications",
"venue": "Journal of Clinical Investigation",
"date": "2024-05-23",
"content": "Intratumoral Tregs are key mediators of cancer immunotherapy resistance, including anti-programmed cell death (ligand) 1 [anti-PD-(L)1] immune checkpoint blockade (ICB). The mechanisms driving Treg infiltration into the tumor microenvironment (TME) and the consequence on CD8+ T cell exhaustion remain elusive. Here,ā¦"
},
{
"id": "/publication/2024-07-12-analysis-of-community-connectivity-in-spatial-transcriptomic",
"title": "Analysis of community connectivity in spatial transcriptomics data",
"url": "/publication/2024-07-12-analysis-of-community-connectivity-in-spatial-transcriptomic",
"section": "Publications",
"venue": "Frontiers in Applied Mathematics and Statistics",
"date": "2024-07-12",
"content": "Introduction: The advent of high throughput spatial transcriptomics (HST) has allowed for unprecedented characterization of spatially distinct cell communities within a tissue sample. While a wide range of computational tools exist for detecting cell communities in HST data, none allow for the characterization of coā¦"
},
{
"id": "/publication/2024-08-29-graph-fourier-transform-for-spatial-omics-representation-and",
"title": "Graph Fourier transform for spatial omics representation and analyses of complex organs",
"url": "/publication/2024-08-29-graph-fourier-transform-for-spatial-omics-representation-and",
"section": "Publications",
"venue": "Nature Communications",
"date": "2024-08-29",
"content": "Spatial omics technologies decipher functional components of complex organs at cellular and subcellular resolutions. We introduce Spatial Graph Fourier Transform (SpaGFT) and apply graph signal processing to a wide range of spatial omics profiling platforms to generate their interpretable representations. This repreā¦"
},
{
"id": "/publication/2024-11-05-cytokine-linked-remodeling-of-the-immune-microenvironment-is",
"title": "Cytokine-Linked Remodeling of the Immune Microenvironment Is a Hallmark of Transformation in Follicular Lymphoma",
"url": "/publication/2024-11-05-cytokine-linked-remodeling-of-the-immune-microenvironment-is",
"section": "Publications",
"venue": "Blood",
"date": "2024-11-05",
"content": "Histologic transformation of follicular lymphoma (FL) to an aggressive lymphoma (transformed FL [tFL]) is a common disease complication associated with poor clinical outcomes. However, understanding of the mechanisms that drive FL transformation and the associated lymph node (LN) tumor microenvironment (TME) reorganā¦"
},
{
"id": "/publication/2024-12-01-specific-expression-of-apoe-in-astrocytes-reduces-a-accumula",
"title": "Specific expression of APOE in astrocytes reduces AĪ² accumulation and plaqueārelated pathology in a mouse model of amyloidosis",
"url": "/publication/2024-12-01-specific-expression-of-apoe-in-astrocytes-reduces-a-accumula",
"section": "Publications",
"venue": "Alzheimer s & Dementia",
"date": "2024-12-01",
"content": "BACKGROUND: Accumulation of the amyloid-Ī² (AĪ²) peptide into amyloid plaque is one of the key pathological markers of Alzheimerās disease (AD). Apolipoprotein E (APOE) is known to modify AD risk and has been reported to influence AĪ² accumulation in the brain in an isoform-dependent manner. ApoE can be produced by varā¦"
},
{
"id": "/publication/2024-12-22-same-slide-spatial-multi-omics-integration-reveals-tumor-vir",
"title": "Same-Slide Spatial Multi-Omics Integration Reveals Tumor Virus-Linked Spatial Reorganization of the Tumor Microenvironment",
"url": "/publication/2024-12-22-same-slide-spatial-multi-omics-integration-reveals-tumor-vir",
"section": "Publications",
"venue": "bioRxiv (Cold Spring Harbor Laboratory)",
"date": "2024-12-22",
"content": "The advent of spatial transcriptomics and spatial proteomics have enabled profound insights into tissue organization to provide systems-level understanding of diseases. Both technologies currently remain largely independent, and emerging same slide spatial multi-omics approaches are generally limited in plex, spatiaā¦"
},
{
"id": "/publication/2025-04-25-harnessing-the-power-of-single-cell-large-language-models-wi",
"title": "Harnessing the Power of Single Cell Large Language Models with Parameter Efficient Fine-Tuning using scPEFT",
"url": "/publication/2025-04-25-harnessing-the-power-of-single-cell-large-language-models-wi",
"section": "Publications",
"venue": "Research Square",
"date": "2025-04-25",
"content": ""
},
{
"id": "/publication/2025-05-13-sex-differences-in-bladder-cancer-understanding-biological-a",
"title": "Sex differences in bladder cancer: understanding biological and clinical implications",
"url": "/publication/2025-05-13-sex-differences-in-bladder-cancer-understanding-biological-a",
"section": "Publications",
"venue": "Biology of Sex Differences",
"date": "2025-05-13",
"content": "Bladder cancer (BC) remains a significant global health concern, with substantial sex and racial disparities in incidence, progression, and outcomes. BC is the sixth most common cancer among males and the seventeenth most common among females worldwide. Over 90% of BC cases are urothelial carcinoma (UC) with high deā¦"
},
{
"id": "/publication/2025-06-03-a-foundation-model-for-spatial-proteomics",
"title": "A Foundation Model for Spatial Proteomics",
"url": "/publication/2025-06-03-a-foundation-model-for-spatial-proteomics",
"section": "Publications",
"venue": "ArXiv.org",
"date": "2025-06-03",
"content": "Foundation models have begun to transform image analysis by acting as pretrained generalist backbones that can be adapted to many tasks even when post-training data are limited, yet their impact on spatial proteomics, imaging that maps proteins at single-cell resolution, remains limited. Here, we introduce KRONOS, aā¦"
},
{
"id": "/publication/2025-08-20-targeting-tgf-docking-receptor-glycoprotein-a-repetitions-pr",
"title": "Targeting TGFĪ² docking receptor glycoprotein A repetitions predominant (GARP) via novel chimeric antigen receptor (CAR)-T cell platform to treat glioblastoma",
"url": "/publication/2025-08-20-targeting-tgf-docking-receptor-glycoprotein-a-repetitions-pr",
"section": "Publications",
"venue": "Neuro-Oncology",
"date": "2025-08-20",
"content": "BACKGROUND: Glycoprotein A-repetitions predominant (GARP) is a cell surface non-signaling receptor for docking and activating latent transforming growth factor beta (LTGFĪ²) expressed by regulatory T cells, platelets, and tumor cells. In lung and breast cancers, its expression correlates with advanced stage and poorā¦"
},
{
"id": "/publication/2025-09-13-multi-scaled-transcriptomics-of-chronically-inflamed-nasal-e",
"title": "Multi-scaled transcriptomics of chronically inflamed nasal epithelium reveals immune-epithelial dynamics and tissue remodeling in nasal polyp formation",
"url": "/publication/2025-09-13-multi-scaled-transcriptomics-of-chronically-inflamed-nasal-e",
"section": "Publications",
"venue": "Immunity",
"date": "2025-09-13",
"content": "T cell dysregulation, and mast cell enrichment. We identified key immune-epithelial interactions in tissue remodeling, particularly involving basal progenitor and tuft cells. A distinct basal cell trajectory was implicated in nasal polyp formation. Orthogonal validation with spatial transcriptomics from >100 individā¦"
},
{
"id": "/publication/2026-02-24-single-cell-and-spatial-methods-for-multimodal-functional-gl",
"title": "Single-Cell and Spatial Methods for Multimodal Functional Glycan Profiling in Tissues",
"url": "/publication/2026-02-24-single-cell-and-spatial-methods-for-multimodal-functional-gl",
"section": "Publications",
"venue": "bioRxiv (Cold Spring Harbor Laboratory)",
"date": "2026-02-24",
"content": "Glycans regulate multiple physiological processes, including immune recognition and cancer progression. In disease, altered glycan landscapes are interpreted by human lectins. Functional glycan-lectin interactions are difficult to profile because glycans are not genome-encoded and their changes are poorly captured bā¦"
},
{
"id": "/publication/2026-03-24-molecular-characterization-of-humanized-apoe-mouse-models-re",
"title": "Molecular characterization of humanized APOE mouse models reveals source and genotype dependent differences",
"url": "/publication/2026-03-24-molecular-characterization-of-humanized-apoe-mouse-models-re",
"section": "Publications",
"venue": "Molecular Neurodegeneration",
"date": "2026-03-24",
"content": "Humanized APOE targeted-replacement (TR) mice are essential tools for studying apoE isoform effects in Alzheimerās disease (AD) and other apoE-related disorders. Despite their widespread use, existing APOE mouse models, generated with different gene targeting strategies, have not been directly compared in terms of aā¦"
},
{
"id": "/publication/2026-03-24-same-slide-spatial-multi-omics-integration-with-in-depth-rev",
"title": "Same-Slide Spatial Multi-Omics Integration with IN-DEPTH Reveals Tumor Virus-Linked Spatial Reorganization of the Tumor Microenvironment",
"url": "/publication/2026-03-24-same-slide-spatial-multi-omics-integration-with-in-depth-rev",
"section": "Publications",
"venue": "Cancer Discovery",
"date": "2026-03-24",
"content": "Spatial transcriptomics and proteomics have enabled profound insights into tissue organization, yet these technologies remain largely disparate, and emerging same-slide multi-omics approaches are limited in plex, spatial resolution, signal retention, and integrative analytics. We introduce IN-situ DEtailed Phenotypiā¦"
},
{
"id": "/publication/2026-03-31-epstein-barr-virus-orchestrates-spatial-reorganization-and-i",
"title": "Epstein-Barr virus orchestrates spatial reorganization and immunomodulation in the classic Hodgkin lymphoma tumor microenvironment",
"url": "/publication/2026-03-31-epstein-barr-virus-orchestrates-spatial-reorganization-and-i",
"section": "Publications",
"venue": "Cell Reports Medicine",
"date": "2026-03-31",
"content": "Classic Hodgkin lymphoma (cHL) is composed of rare malignant Hodgkin and Reed-Sternberg (HRS) cells within a T-cell-rich tumor microenvironment (TME). Epstein-Barr virus (EBV) is present in ā¼25% of cases, but its contribution to pathogenesis and immunomodulation remains unclear due to technical barriers. Using complā¦"
},
{
"id": "/publication/2026-04-03-abstract-4163-a-general-purpose-ai-foundation-model-for-spat",
"title": "Abstract 4163: A general-purpose AI foundation model for spatial proteomics",
"url": "/publication/2026-04-03-abstract-4163-a-general-purpose-ai-foundation-model-for-spat",
"section": "Publications",
"venue": "Cancer Research",
"date": "2026-04-03",
"content": "Abstract Standard spatial proteomics (SP) pipelines for biomarker discovery have traditionally relied on cell segmentation followed by single-marker thresholding or rule-based mechanisms to assign cell phenotypes. However, this often suffers from a laborious process of manual annotations and neglects cell states chaā¦"
},
{
"id": "/publication/2026-04-30-tracing-the-rise-of-biomedical-foundation-models",
"title": "Tracing the rise of biomedical foundation models",
"url": "/publication/2026-04-30-tracing-the-rise-of-biomedical-foundation-models",
"section": "Publications",
"venue": "Nature Biotechnology",
"date": "2026-04-30",
"content": ""
}
,
{
"id": "paper-2605.12197",
"title": "A Unified Graph Language Model for Multi-Domain Multi-Task Graph Alignment Instruction Tuning",
"url": "/paper-tracking/archive/#paper-2605.12197-2026-05-18",
"section": "Paper Tracking Ā· Graph Ć LLM",
"venue": "2026-05-18",
"date": "2026-05-12",
"content": "Existing graph language models lack unified alignment of multi-domain, multi-task GNN representations with LLM token spaces. \"UniGraphLM: Unified Graph Language Model\" with graph-text pair pretraining and curriculum alignment tuning for multi-domain, multi-task graph representation alignment with LLMs. Wenwu Zhu arxiv 2605.12197"
},
{
"id": "paper-2605.13540",
"title": "Decoupled and Divergence-Conditioned Prompt for Multi-domain Dynamic Graph Foundation Models",
"url": "/paper-tracking/archive/#paper-2605.13540-2026-05-18",
"section": "Paper Tracking Ā· Graph Ć LLM",
"venue": "2026-05-18",
"date": "2026-05-13",
"content": "Multi-domain dynamic graphs have incompatible temporal semantics and divergent patterns, causing negative transfer in unified pre-training and adaptation. DyGFM: Dynamic Graph Foundation Model with semantic-temporal decoupled pre-training, divergence-aware expert routing, and divergence-conditioned prompt generation. Philip S. Yu arxiv 2605.13540"
},
{
"id": "paper-2605.14809",
"title": "GFMate: Empowering Graph Foundation Models with Test-time Prompt Tuning",
"url": "/paper-tracking/archive/#paper-2605.14809-2026-05-18",
"section": "Paper Tracking Ā· Graph Ć LLM",
"venue": "2026-05-18",
"date": "2026-05-14",
"content": "Existing graph foundation model prompts entangle source domain information and pre-training strategies, limiting generalization to unseen target domains and neglecting unlabelled test data. GFMate: pre-training-agnostic test-time graph prompt tuning using centroid and layer prompts with complementary learning objective Zi Huang arxiv 2605.14809"
},
{
"id": "paper-2605.10876",
"title": "AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents",
"url": "/paper-tracking/archive/#paper-2605.10876-2026-05-18",
"section": "Paper Tracking Ā· Spatial Single-Cell Study",
"venue": "2026-05-18",
"date": "2026-05-11",
"content": "No standard benchmark exists for predicting phenotypic outcomes of cellular perturbations across diverse assays in drug discovery. approach: LLM and agentic systems evaluated on gene ranking prediction from free-text screen descriptions using adjusted nDCG metric Gabriele Scalia arxiv 2605.10876"
},
{
"id": "paper-2605.14104",
"title": "DUET: Dual-Paradigm Adaptive Expert Triage with Single-cell Inductive Prior for Spatial Transcriptomics Prediction",
"url": "/paper-tracking/archive/#paper-2605.14104-2026-05-18",
"section": "Paper Tracking Ā· Spatial Single-Cell Study",
"venue": "2026-05-18",
"date": "2026-05-13",
"content": "Existing methods for inferring spatial gene expression from histology images oversimplify morphology-to-expression mapping and underutilize large-scale single-cell data as biological constraints. DUET: dual-paradigm framework synergizing parametric regression and memory-based retrieval with cellular inductive priors and adaptive expert triage for spatial transcriptomics prediction. Yuankai Huo arxiv 2605.14104"
},
{
"id": "paper-2605.16104",
"title": "StateXDiff: Cell State-Contextualized Multimodal Diffusion for Single-Cell Perturbation Prediction",
"url": "/paper-tracking/archive/#paper-2605.16104-2026-05-18",
"section": "Paper Tracking Ā· Spatial Single-Cell Study",
"venue": "2026-05-18",
"date": "2026-05-15",
"content": "Predicting drug-induced cellular state changes at single-cell resolution under out-of-distribution conditions with limited multimodal information. StateXDiff: cell State-contextualized multimodal Diffusion framework integrating transcriptomic and pseudo-protein representations with mechanism-aware drug templates via latent conditional diffusion. arxiv 2605.16104"
},
{
"id": "paper-2605.13527",
"title": "MMSkills: Towards Multimodal Skills for General Visual Agents",
"url": "/paper-tracking/archive/#paper-2605.13527-2026-05-18",
"section": "Paper Tracking Ā· Vision-Language Models",
"venue": "2026-05-18",
"date": "2026-05-13",
"content": "Visual agents need reusable multimodal procedural knowledge that binds actions to visual state recognition and decision-making, beyond text-only skills. \"MMSkills: framework for representing, generating, and utilizing reusable multimodal procedures for visual agents. Each skill couples textual procedures with runtime state cards and multi-view keyframes, generated via trajectory-to-skill generator and consulted via branch loading. Yong Yu arxiv 2605.13527"
},
{
"id": "paper-2605.14906",
"title": "MemLens: Benchmarking Multimodal Long-Term Memory in Large Vision-Language Models",
"url": "/paper-tracking/archive/#paper-2605.14906-2026-05-18",
"section": "Paper Tracking Ā· Vision-Language Models",
"venue": "2026-05-18",
"date": "2026-05-13",
"content": "No benchmark systematically compares long-context LVLMs and memory-augmented agents on multimodal multi-session conversations requiring visual evidence. \"MemLens\": benchmark with 789 questions across five memory abilities (information extraction, multi-session reasoning, temporal reasoning, knowledge update, answer refusal) at four context lengths (32K-256K tokens) Simon See arxiv 2605.14906"
},
{
"id": "paper-2605.15128",
"title": "MemEye: A Visual-Centric Evaluation Framework for Multimodal Agent Memory",
"url": "/paper-tracking/archive/#paper-2605.15128-2026-05-18",
"section": "Paper Tracking Ā· Vision-Language Models",
"venue": "2026-05-18",
"date": "2026-05-13",
"content": "Existing multimodal agent memory evaluations fail to assess whether agents preserve fine-grained visual evidence needed for reasoning over time. \"MemEye: a visual-centric evaluation framework measuring visual evidence granularity and reasoning complexity in multimodal agent memory\" Ruixiang Tang arxiv 2605.15128"
},
{
"id": "paper-2605.14269",
"title": "PhyMotion: Structured 3D Motion Reward for Physics-Grounded Human Video Generation",
"url": "/paper-tracking/archive/#paper-2605.14269-2026-05-18",
"section": "Paper Tracking Ā· World Models",
"venue": "2026-05-18",
"date": "2026-05-13",
"content": "Existing video rewards fail to reliably score human motion realism because they operate in 2D pixel space without explicitly modeling 3D body physics and constraints. \"PhyMotion\": physics-grounded motion reward that recovers SMPL meshes, retargets to MuJoCo simulator, and evaluates motion via three axes (kinematic plausibility, contact/balance, dynamic feasibility) Mohit Bansal arxiv 2605.14269"
},
{
"id": "paper-2605.15141",
"title": "Causal Forcing++: Scalable Few-Step Autoregressive Diffusion Distillation for Real-Time Interactive Video Generation",
"url": "/paper-tracking/archive/#paper-2605.15141-2026-05-18",
"section": "Paper Tracking Ā· World Models",
"venue": "2026-05-18",
"date": "2026-05-14",
"content": "Existing AR diffusion distillation methods require 4+ sampling steps; frame-wise 1ā2 step generation needs efficient, scalable student initialization. \"Causal Forcing++\": AR diffusion distillation pipeline using causal consistency distillation for few-step student initialization, avoiding expensive full PF-ODE trajectory precomputation. Jun Zhu arxiv 2605.15141"
},
{
"id": "paper-2605.15182",
"title": "Warp-as-History: Generalizable Camera-Controlled Video Generation from One Training Video",
"url": "/paper-tracking/archive/#paper-2605.15182-2026-05-18",
"section": "Paper Tracking Ā· World Models",
"venue": "2026-05-18",
"date": "2026-05-13",
"content": "Existing camera-controlled video generation methods require large-scale camera-annotated data or expensive test-time optimization; no simple way to leverage pretrained video models' latent camera-control capability. \"Warp-as-History\": converts camera-induced geometric warps into camera-warped pseudo-history fed through pretrained video models' native history pathway, with target-frame positional alignment and visible-token selection. Tong He arxiv 2605.15182"
}
]