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Recent advances in biological technologies, such as multi-way chromosome conformation capture (3C), require development of methods for analysis of multi-way interactions. Hypergraphs are mathematically tractable objects that can be utilized…
Retention time drift caused by fluctuations in physical factors such as temperature ramping rate and carrier gas flow rate is ubiquitous in chromatographic measurements. Proper peak identification and alignment across different…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
The spatial organization of chromatin within the nucleus plays a crucial role in gene expression and genome function. However, the quantitative relationship between this organization and nuclear biochemical processes remains under debate.…
In semi-supervised segmentation, capturing meaningful semantic structures from unlabeled data is essential. This is particularly challenging in histopathology image analysis, where objects are densely distributed. To address this issue, we…
Background: It is well known that the development of cancer is caused by the accumulation of somatic mutations within the genome. For oncogenes specifically, current research suggests that there is a small set of "driver" mutations that are…
The measure between heterogeneous data is still an open problem. Many research works have been developed to learn a common subspace where the similarity between different modalities can be calculated directly. However, most of existing…
High-resolution point clouds~(HRPCD) anomaly detection~(AD) plays a critical role in precision machining and high-end equipment manufacturing. Despite considerable 3D-AD methods that have been proposed recently, they still cannot meet the…
The spatial transcriptomics (ST) data produced by recent biotechnologies, such as CosMx and Xenium, contain huge amount of information about cancer tissue samples, which has great potential for cancer research via detection of community: a…
Hyperspectral anomaly detection (HAD), a crucial approach for many civilian and military applications, seeks to identify pixels with spectral signatures that are anomalous relative to a preponderance of background signatures. Significant…
Recent advances in computational pathology have leveraged vision-language models to learn joint representations of Hematoxylin and Eosin (HE) images with spatial transcriptomic (ST) profiles. However, existing approaches typically align HE…
The past decade has seen a revolution in genomic technologies that enable a flood of genome-wide profiling of chromatin marks. Recent literature tried to understand gene regulation by predicting gene expression from large-scale chromatin…
Alzheimer's disease (AD) emerges from a complex interplay of molecular, cellular, and network-level disturbances that are not easily captured by traditional reductionist frameworks. Conventional analyses of gene expression often rely on…
Blood cell identification is critical for hematological analysis as it aids physicians in diagnosing various blood-related diseases. In real-world scenarios, blood cell image datasets often present the issues of domain shift and data…
Multidimensional separations data have the capacity to reveal detailed information about complex biological samples. However, data analysis has been an ongoing challenge in the area since the peaks that represent chemical factors may drift…
A directed hypergraph, which consists of nodes and hyperarcs, is a higher-order data structure that naturally models directional group interactions (e.g., chemical reactions of molecules). Although there have been extensive studies on local…
Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polymer simulations, microscopy and mass spectrometry to dissect…
Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene…
Graph anomaly detection is critical in domains such as healthcare and economics, where identifying deviations can prevent substantial losses. Existing unsupervised approaches strive to learn a single model capable of detecting both…