arXiv subjects

Ming Song

Publications and source records attributed to Ming Song.

8 recordsLinked to original sources

arXiv2026

CellPath-Bench: A Multidimensional Benchmark for Whole-Slide Cellular Representations in Pathology Foundation Models

Pathology foundation models (PFMs) are increasingly used as general-purpose backbones, yet existing benchmarks cannot systematically diagnose their whole-slide cellular representation capabilities, including the decodability of cell-type information and the transferability of such information across tissue sections, datasets, and anatomical organs. We introduce CellPath-Bench, a cellular-resolution benchmark that evaluates frozen PFMs themselves. Following quality control of 52 candidate Xenium datasets, we construct a panel of 25 spatially aligned H\&E--Xenium tissue sections spanning 11 organs and 7,079,283 cells, harmonized into fine- and coarse-grained taxonomies. CellPath-Bench samples frozen WSI feature maps at registered nuclear coordinates and evaluates them using standardized multiclass linear probes. Cell Representation Advantage (CRA) measures the within-section advantage of nucleus-anchored representations over patch-level mean pooling, while Cell Representation Transferability (CRT) characterizes the generalization of cell-type decodability across tissue sections, datasets, and organs. We benchmark 30 pathology-specific and general-purpose foundation models through 304,920 runs across spatial readouts, magnifications, taxonomic granularities, and evaluation protocols. The results reveal substantial model-dependent differences in cell-type decodability and its cross-domain generalization, yielding distinct multidimensional capability profiles. CellPath-Bench provides a standardized framework for auditing cellular information in frozen PFM representations.

cs.AI↗

arXiv2026

Benchmarking Pathology Foundation Models for Spatial Domain Understanding

Pathology foundation models (PFMs) have emerged as a core approach for learning transferable representations from whole slide images (WSIs), and they are typically benchmarked through downstream clinical endpoints. While such task level evaluations are indispensable, they offer limited insight into what the representations themselves encode, particularly whether PFM embeddings can distinguish meaningful tissue regions and capture their spatial relationships. We present SpaPath-Bench, a representation level benchmark designed to diagnose spatial representation capability in PFMs. SpaPath-Bench formulates spatial domain identification (SDI) on paired whole slide image and spatial transcriptomics (ST) data as a diagnostic task. It curates 42 public paired WSI and ST slides, enables large scale evaluation across 19 encoders and seven SDI methods, and measures partition quality using three complementary criteria: unsupervised spatial coherence, transcriptomics referenced agreement, and expert referenced agreement. Across 83K runs, SpaPath-Bench reveals that different pretraining paradigms capture distinct aspects of tissue spatial architecture, and it provides practical guidance for building the next generation of spatially aware computational pathology models. Code and data pipelines are publicly available at https://bokai-zhao.github.io/SpaPath-benchboard/.

cs.CV↗

arXiv2025

Neural Proteomics Fields for Super-resolved Spatial Proteomics Prediction

Spatial proteomics maps protein distributions in tissues, providing transformative insights for life sciences. However, current sequencing-based technologies suffer from low spatial resolution, and substantial inter-tissue variability in protein expression further compromises the performance of existing molecular data prediction methods. In this work, we introduce the novel task of spatial super-resolution for sequencing-based spatial proteomics (seq-SP) and, to the best of our knowledge, propose the first deep learning model for this task--Neural Proteomics Fields (NPF). NPF formulates seq-SP as a protein reconstruction problem in continuous space by training a dedicated network for each tissue. The model comprises a Spatial Modeling Module, which learns tissue-specific protein spatial distributions, and a Morphology Modeling Module, which extracts tissue-specific morphological features. Furthermore, to facilitate rigorous evaluation, we establish an open-source benchmark dataset, Pseudo-Visium SP, for this task. Experimental results demonstrate that NPF achieves state-of-the-art performance with fewer learnable parameters, underscoring its potential for advancing spatial proteomics research. Our code and dataset are publicly available at https://github.com/Bokai-Zhao/NPF.

q-bio.QM↗

arXiv2024

Yi-Lightning Technical Report

This technical report presents Yi-Lightning, our latest flagship large language model (LLM). It achieves exceptional performance, ranking 6th overall on Chatbot Arena, with particularly strong results (2nd to 4th place) in specialized categories including Chinese, Math, Coding, and Hard Prompts. Yi-Lightning leverages an enhanced Mixture-of-Experts (MoE) architecture, featuring advanced expert segmentation and routing mechanisms coupled with optimized KV-caching techniques. Our development process encompasses comprehensive pre-training, supervised fine-tuning (SFT), and reinforcement learning from human feedback (RLHF), where we devise deliberate strategies for multi-stage training, synthetic data construction, and reward modeling. Furthermore, we implement RAISE (Responsible AI Safety Engine), a four-component framework to address safety issues across pre-training, post-training, and serving phases. Empowered by our scalable super-computing infrastructure, all these innovations substantially reduce training, deployment and inference costs while maintaining high-performance standards. With further evaluations on public academic benchmarks, Yi-Lightning demonstrates competitive performance against top-tier LLMs, while we observe a notable disparity between traditional, static benchmark results and real-world, dynamic human preferences. This observation prompts a critical reassessment of conventional benchmarks' utility in guiding the development of more intelligent and powerful AI systems for practical applications. Yi-Lightning is now available through our developer platform at https://platform.lingyiwanwu.com.

cs.CL↗

arXiv2023

Digital twin brain: a bridge between biological intelligence and artificial intelligence

In recent years, advances in neuroscience and artificial intelligence have paved the way for unprecedented opportunities for understanding the complexity of the brain and its emulation by computational systems. Cutting-edge advancements in neuroscience research have revealed the intricate relationship between brain structure and function, while the success of artificial neural networks highlights the importance of network architecture. Now is the time to bring them together to better unravel how intelligence emerges from the brain's multiscale repositories. In this review, we propose the Digital Twin Brain (DTB) as a transformative platform that bridges the gap between biological and artificial intelligence. It consists of three core elements: the brain structure that is fundamental to the twinning process, bottom-layer models to generate brain functions, and its wide spectrum of applications. Crucially, brain atlases provide a vital constraint, preserving the brain's network organization within the DTB. Furthermore, we highlight open questions that invite joint efforts from interdisciplinary fields and emphasize the far-reaching implications of the DTB. The DTB can offer unprecedented insights into the emergence of intelligence and neurological disorders, which holds tremendous promise for advancing our understanding of both biological and artificial intelligence, and ultimately propelling the development of artificial general intelligence and facilitating precision mental healthcare.

q-bio.NC↗

arXiv2018

Subdivisions of the posteromedial cortex in disorders of consciousness

Evidence suggests that disruptions of the posteromedial cortex (PMC) and posteromedial corticothalamic connectivity contribute to disorders of consciousness (DOCs). While most previous studies treated the PMC as a whole, this structure is functionally heterogeneous. The present study investigated whether particular subdivisions of the PMC are specifically associated with DOCs. Participants were DOC patients, 21 vegetative state/unresponsive wakefulness syndrome (VS/UWS), 12 minimally conscious state (MCS), and 29 healthy controls. Individual PMC and thalamus were divided into distinct subdivisions by their fiber tractograpy to each other and default mode regions, and white matter integrity and brain activity between/within subdivisions were assessed. The thalamus was represented mainly in the dorsal and posterior portions of the PMC, and the white matter tracts connecting these subdivisions to the thalamus had less integrity in VS/UWS patients than in MCS patients and healthy controls, as well as in patients who did not recover after 12 months than in patients who did. The structural substrates were validated by finding impaired functional fluctuations within this PMC subdivision. This study is the first to show that tracts from dorsal and posterior subdivisions of the PMC to the thalamus contribute to DOCs.

q-bio.NC↗

arXiv2018

Prognostication of chronic disorders of consciousness using brain functional networks and clinical characteristics

Disorders of consciousness are a heterogeneous mixture of different diseases or injuries. Although some indicators and models have been proposed for prognostication, any single method when used alone carries a high risk of false prediction. This study aimed to develop a multidomain prognostic model that combines resting state functional MRI with three clinical characteristics to predict one year outcomes at the single-subject level. The model discriminated between patients who would later recover consciousness and those who would not with an accuracy of around 90% on three datasets from two medical centers. It was also able to identify the prognostic importance of different predictors, including brain functions and clinical characteristics. To our knowledge, this is the first implementation reported of a multidomain prognostic model based on resting state functional MRI and clinical characteristics in chronic disorders of consciousness. We therefore suggest that this novel prognostic model is accurate, robust, and interpretable.

q-bio.NC↗

arXiv2017

A Scalable and Adaptive Method for Finding Semantically Equivalent Cue Words of Uncertainty

Scientific knowledge is constantly subject to a variety of changes due to new discoveries, alternative interpretations, and fresh perspectives. Understanding uncertainties associated with various stages of scientific inquiries is an integral part of scientists' domain expertise and it serves as the core of their meta-knowledge of science. Despite the growing interest in areas such as computational linguistics, systematically characterizing and tracking the epistemic status of scientific claims and their evolution in scientific disciplines remains a challenge. We present a unifying framework for the study of uncertainties explicitly and implicitly conveyed in scientific publications. The framework aims to accommodate a wide range of uncertain types, from speculations to inconsistencies and controversies. We introduce a scalable and adaptive method to recognize semantically equivalent cues of uncertainty across different fields of research and accommodate individual analysts' unique perspectives. We demonstrate how the new method can be used to expand a small seed list of uncertainty cue words and how the validity of the expanded candidate cue words are verified. We visualize the mixture of the original and expanded uncertainty cue words to reveal the diversity of expressions of uncertainty. These cue words offer a novel resource for the study of uncertainty in scientific assertions.

cs.DL↗