预测ER弱阳性乳腺癌状态的机器学习模型的建立及验证

目的探讨利用机器学习算法预测ER弱阳性乳腺癌的状态。方法收集710例原发性浸润性乳腺癌,其中139例ER阴性(<1%)和311例ER阳性(>10%)乳腺癌作为训练队列,260例ER弱阳性(1%~10%)乳腺癌作为测试队列。深度学习分割模型(LinkNet)用于分割并提取肿瘤细胞的形态特征。基于朴素贝叶斯机器学习算法,利用从训练队列中提取的12个临床病理特征和14个形态特征开发机器学习预测模型,并进行内部验证。利用ROC曲线的曲线下面积(AUC)反映预测模型的性能。利用预测模型对测试队列进行ER状态预测。对比分析两组的临床病理特征、ESR1 mRNA的表达水平和预后。结果ER阴性与ER阳性乳腺癌在组织学类型(P=0.01)、淋巴结转移(P=0.02)、组织学分级(P<0.001)、PR(P<0.001)、HER2(P<0.001)和Ki-67(P<0.001)表达差异有显著性。基于朴素贝叶斯机器学习算法构建预测模型,5倍交叉验证显示,在训练队列中预测模型对ER状态的预测性能优异(AUC=0.91±0.03)。ER状态预测结果显示,260例ER弱阳性乳腺癌中206例(79.23%)被划分为阴性组,54例(20.77%)被划分为阳性组。与ER阳性组相比,ER阴性组组织学分级更高、Ki-67高表达、ESR1 mRNA表达水平低,内分泌治疗获益更少,患者预后更差。结论机器学习模型能够较为精准地对乳腺癌ER表达状态进行预测,为进一步明确ER弱阳性乳腺癌的状态提供了新视角,协助临床医师做出更为精准的治疗决策。

基于人工智能辅助乳腺癌新辅助治疗后肿瘤浸润淋巴细胞评估及可重复性分析

目的对比分析人工智能(artificial intelligence,AI)显微镜辅助和显微镜下视觉评估判读乳腺癌新辅助治疗后肿瘤浸润淋巴细胞(tumor infiltrating lymphocytes,TILs),探讨利用AI结合病理医师判读新辅助治疗后TILs的临床适用性。方法收集行新辅助治疗乳腺癌且未获得完全缓解病例50例,由9名不同级别的病理医师通过视觉评估和AI显微镜辅助评估TILs。采用组内相关系数(intra-group correlation coefficient,ICC)和Bland-Altman散点图进行一致性分析。结果视觉评估组9名病理医师间TILs判读结果差异有统计学意义(P<0.05,ICC=0.741,95%CI=0.656~0.821),仅高级病理医师对TILs判读结果差异较小,中级及初级病理医师的TILs判读结果差异有显著性(P<0.05)。通过AI显微镜辅助判读,不同级别病理医师对TILs判读结果差异无显著(ICC=0.955,95%CI=0.931~0.971),判读结果达到优等一致性。同时,通过对比AI辅助组与视觉评估组对新辅助治疗后TILs判读结果与金标准之间的一致性,发现仅AI辅助组和视觉评估高级病理医师组判读结果与金标准具有良好的一致性。结论AI技术在精准判读TILs中具有良好的应用前景。

基于最优传输理论的联合分布匹配方法及应用

联合分布匹配问题是机器学习和计算机视觉领域的研究热点之一.该问题旨在学习双向映射以匹配两个域的联合分布,目前仍然面临两个重要挑战:第一:两个不同域之间的相关性信息难以被充分利用.第二:联合分布匹配问题难以建模和优化.基于最优传输理论,本文通过最小化两个域间联合分布的Wasserstein距离来解决上述挑战.首先,本文提出一个定理将难以求解的Wasserstein距离原问题转化为一个简单的优化问题,并设计了一个联合Wasserstein自编码器模型(JWAE)来求解该问题.然后,本文将JWAE成功应用在无监督图像翻译和跨域视频合成任务中,并生成高质量的图像和连贯的视频.实验结果表明,JWAE在两种任务中的定性和定量指标上均优于现有方法.比如,在“街景→语义分割”图像翻译任务中,JWAE的IS值比CycleGAN高0.59,FID值比CycleGAN小65.8.在“冬季→夏季”跨域视频合成任务中,JWAE的FID4video值比Slomo-Cycle小2.2.

Recent Progresses in Deep Learning Based Acoustic Models

In this paper,we summarize recent progresses made in deep learning based acoustic models and the motivation and insights behind the surveyed techniques.We first discuss models such as recurrent neural networks(RNNs) and convolutional neural networks(CNNs) that can effectively exploit variablelength contextual information,and their various combination with other models.We then describe models that are optimized end-to-end and emphasize on feature representations learned jointly with the rest of the system,the connectionist temporal classification(CTC) criterion,and the attention-based sequenceto-sequence translation model.We further illustrate robustness issues in speech recognition systems,and discuss acoustic model adaptation,speech enhancement and separation,and robust training strategies.We also cover modeling techniques that lead to more efficient decoding and discuss possible future directions in acoustic model research.

面向非任务型对话系统的人工标注中文数据集

该文针对非任务导向型对话的回复质量构建了一个大规模的人工标注中文数据集,该数据集包含了从社交媒体收集到的超过27 000个对话问题以及超过82 000个对话问题的回复①。为了产生高质量的标注数据,邀请了专业人员根据对话回复的相关性、连贯性、信息性、趣味性,以及是否潜在地具有让对话继续延续的特性进行标注,在标注中定义了一个五级评分方法,分别是:极差的、较差的、一般的、较好的、极好的。为了测试标注产生的数据集是否具有有效性和实用性,以对话回复选择为任务,在标注数据集上测试了多种无监督和有监督模型。实验结果表明,该数据集对于提升对话回复选择的质量有显著效果。

Establishment and validation of a computer-assisted colonic polyp localization system based on deep learning

BACKGROUND Artificial intelligence in colonoscopy is an emerging field,and its application may help colonoscopists improve inspection quality and reduce the rate of missed polyps and adenomas.Several deep learning-based computer-assisted detection(CADe)techniques were established from small single-center datasets,and unrepresentative learning materials might confine their application and generalization in wide practice.Although CADes have been reported to identify polyps in colonoscopic images and videos in real time,their diagnostic performance deserves to be further validated in clinical practice.AIM To train and test a CADe based on multicenter high-quality images of polyps and preliminarily validate it in clinical colonoscopies.METHODS With high-quality screening and labeling from 55 qualified colonoscopists,a dataset consisting of over 71000 images from 20 centers was used to train and test a deep learning-based CADe.In addition,the real-time diagnostic performance of CADe was tested frame by frame in 47 unaltered full-ranged videos that contained 86 histologically confirmed polyps.Finally,we conducted a selfcontrolled observational study to validate the diagnostic performance of CADe in real-world colonoscopy with the main outcome measure of polyps per colonoscopy in Changhai Hospital.RESULTS The CADe was able to identify polyps in the test dataset with 95.0%sensitivity and 99.1%specificity.For colonoscopy videos,all 86 polyps were detected with 92.2%sensitivity and 93.6%specificity in frame-by-frame analysis.In the prospective validation,the sensitivity of CAD in identifying polyps was 98.4%(185/188).Folds,reflections of light and fecal fluid were the main causes of false positives in both the test dataset and clinical colonoscopies.Colonoscopists can detect more polyps(0.90 vs 0.82,P<0.001)and adenomas(0.32 vs 0.30,P=0.045)with the aid of CADe,particularly polyps<5 mm and flat polyps(0.65 vs 0.57,P<0.001;0.74 vs 0.67,P=0.001,respectively).However,high efficacy is not realized in colonoscopies with inadequate bowel preparation and withdrawal time(P=0.32;P=0.16,respectively).CONCLUSION CADe is feasible in the clinical setting and might help endoscopists detect more polyps and adenomas,and further confirmation is warranted.

PhaseFIT:live-organoid phase-fluorescent image transformation via generative AI

Organoid models have provided a powerful platform for mechanistic investigations into fundamental biological processes involved in the development and function of organs.Despite the potential for image-based phenotypic quantification of organoids,their complex 3D structure,and the time-consuming and labor-intensive nature of immunofluorescent staining present significant challenges.In this work,we developed a virtual painting system,PhaseFIT(phase-fluorescent image transformation)utilizing customized and morphologically rich 2.5D intestinal organoids,which generate virtual fluorescent images for phenotypic quantification via accessible and low-cost organoid phase images.This system is driven by a novel segmentation-informed deep generative model that specializes in segmenting overlap and proximity between objects.The model enables an annotation-free digital transformation from phase-contrast to multi-channel fluorescent images.The virtual painting results of nuclei,secretory cell markers,and stem cells demonstrate that PhaseFIT outperforms the existing deep learning-based stain transformation models by generating fine-grained visual content.We further validated the efficiency and accuracy of PhaseFIT to quantify the impacts of three compounds on crypt formation,cell population,and cell stemness.PhaseFIT is the first deep learning-enabled virtual painting system focused on live organoids,enabling large-scale,informative,and efficient organoid phenotypic quantification.PhaseFIT would enable the use of organoids in high-throughput drug screening applications.

SinGRAV: Learning a Generative Radiance Volume from a Single Natural Scene

We present SinGRAV, an attempt to learn a generative radiance volume from multi-view observations of a single natural scene, in stark contrast to existing category-level 3D generative models that learn from images of many object-centric scenes. Inspired by SinGAN, we also learn the internal distribution of the input scene, which necessitates our key designs w.r.t. the scene representation and network architecture. Unlike popular multi-layer perceptrons (MLP)-based architectures, we particularly employ convolutional generators and discriminators, which inherently possess spatial locality bias, to operate over voxelized volumes for learning the internal distribution over a plethora of overlapping regions. On the other hand, localizing the adversarial generators and discriminators over confined areas with limited receptive fields easily leads to highly implausible geometric structures in the spatial. Our remedy is to use spatial inductive bias and joint discrimination on geometric clues in the form of 2D depth maps. This strategy is effective in improving spatial arrangement while incurring negligible additional computational cost. Experimental results demonstrate the ability of SinGRAV in generating plausible and diverse variations from a single scene, the merits of SinGRAV over state-of-the-art generative neural scene models, and the versatility of SinGRAV by its use in a variety of applications. Code and data will be released to facilitate further research.

Encoding biological metaverse: Advancements and challenges in neural fields from macroscopic to microscopic

Neural fields can efficiently encode three-dimensional(3D)scenes,providing a bridge between two-dimensional(2D)images and virtual reality.This method becomes a trendsetter in bringing the metaverse into vivo life.It has initially captured the attention of macroscopic biology,as demonstrated by computed tomography and magnetic resonance imaging,which provide a 3D field of view for diagnostic biological images.Meanwhile,it has also opened up new research opportunities in microscopic imaging,such as achieving clearer de novo protein structure reconstructions.Introducing this method to the field of biology is particularly significant,as it is refining the approach to studying biological images.However,many biologists have yet to fully appreciate the distinctive meaning of neural fields in transforming 2D images into 3D perspectives.This article discusses the application of neural fields in both microscopic and macroscopic biological images and their practical uses in biomedicine,highlighting the broad prospects of neural fields in the future biological metaverse.We stand at the threshold of an exciting new era,where the advancements in neural field technology herald the dawn of exploring the mysteries of life in innovative ways.

Promoting interactions between cognitive science and large language models

Large language models(LLMs)have made unprecedented progress,demonstrating human-like language proficiency and an extraordinary ability to encode complex knowledge.The emergence of high-level cognitive capabilities in LLMs,such as in-context learning and complex reasoning,suggests a path toward the realization of artificial general intelligence(AGI).However,we lack scientific theories and tools to assess and interpret such an emergence of the advanced intelligence of LLMs.Artificial intelligence(AI)has been extensively applied in various areas of fundamental science to accelerate scientific research.

Past review,current progress,and challenges ahead on the cocktail party problem

The cocktail party problem,i.e.,tracing and recognizing the speech of a specific speaker when multiple speakers talk simultaneously,is one of the critical problems yet to be solved to enable the wide application of automatic speech recognition(ASR) systems.In this overview paper,we review the techniques proposed in the last two decades in attacking this problem.We focus our discussions on the speech separation problem given its central role in the cocktail party environment,and describe the conventional single-channel techniques such as computational auditory scene analysis(CASA),non-negative matrix factorization(NMF) and generative models,the conventional multi-channel techniques such as beamforming and multi-channel blind source separation,and the newly developed deep learning-based techniques,such as deep clustering(DPCL),the deep attractor network(DANet),and permutation invariant training(PIT).We also present techniques developed to improve ASR accuracy and speaker identification in the cocktail party environment.We argue effectively exploiting information in the microphone array,the acoustic training set,and the language itself using a more powerful model.Better optimization ob jective and techniques will be the approach to solving the cocktail party problem.

一种预测无机晶体形成能的高精度泛化模型

随着数据科学和材料科学的进步,人们如今可构建出较为准确的人工智能模型,用于材料性质预测.本文中,我们以170,714个无机晶体化合物的高通量第一性原理计算数据集为基础,训练得到了可精确预测无机化合物形成能的机器学习模型.相比于同类工作,本项研究以超大数据集为出发点,构建出无机晶体形成能的高精度泛化模型,可外推至广阔相空间,其中的Dense Net神经网络模型精度可以达到R^(2)=0.982和平均绝对误差(MAE)=0.072 eV atom^(-1).上述模型精度的提升源自一系列新型特征描述符,这些描述符可有效提取出原子与领域原子间的电负性和局域结构等信息,从而精确捕捉到原子间的相互作用.本文为新材料搜索提供了一种高效、低成本的结合能预测手段.

COPPER:a combinatorial optimization problem solver with processing-in-memory architecture

The combinatorial optimization problem(COP),which aims to find the optimal solution in discrete space,is fundamental in various fields.Unfortunately,many COPs are NP-complete,and require much more time to solve as the problem scale increases.Troubled by this,researchers may prefer fast methods even if they are not exact,so approximation algorithms,heuristic algorithms,and machine learning have been proposed.Some works proposed chaotic simulated annealing(CSA)based on the Hopfield neural network and did a good job.However,CSA is not something that current general-purpose processors can handle easily,and there is no special hardware for it.To efficiently perform CSA,we propose a software and hardware co-design.In software,we quantize the weight and output using appropriate bit widths,and then modify the calculations that are not suitable for hardware implementation.In hardware,we design a specialized processing-in-memory hardware architecture named COPPER based on the memristor.COPPER is capable of efficiently running the modified quantized CSA algorithm and supporting the pipeline further acceleration.The results show that COPPER can perform CSA remarkably well in both speed and energy.

基于深度学习的MOOC论坛探索型对话识别方法研究

[目的/意义]大规模在线开放课程论坛具有丰富的用户评论数据。从大量未区分的评论数据中,自动识别出知识密度较高的探索型对话并挖掘其潜在价值,对于改善教师教学质量以及提高学生知识水平具有重要影响。[方法/过程]首先利用GloVe方法训练词向量,加强对文本语义的理解,然后利用卷积神经网络自动学习文本特征,提出一种基于深度学习的探索型对话自动识别模型,并在学堂在线平台《心理学概论》课程论坛标注数据集上进行实证与对比研究。[结果/结论]实验结果显示,利用GloVe方法预训练词向量以及在训练过程中不断对词向量进行学习修正能够提高模型效果。该模型识别探索型对话的F1值为0.94,相较于传统的朴素贝叶斯方法(0.88)、逻辑斯谛回归方法(0.89)、决策树方法(0.88)以及随机森林方法(0.88)取得较大提升,具有较高的实用性和较低的学习成本。

面向本征图像分解的高质量渲染数据集与非局部卷积网络

目的本征图像分解是计算视觉和图形学领域的一个基本问题,旨在将图像中场景的纹理和光照成分分离开来。基于深度学习的本征图像分解方法受限于现有的数据集,存在分解结果过度平滑、在真实数据泛化能力较差等问题。方法首先设计基于图卷积的模块,显式地考虑图像中的非局部信息。同时,为了使训练的网络可以处理更复杂的光照情况,渲染了高质量的合成数据集。此外,引入了一个基于神经网络的反照率图像优化模块,提升获得的反照率图像的局部平滑性。结果将不同方法在所提的数据集上训练,相比之前合成数据集CGIntrinsics进行训练的结果,在IIW(intrinsic images in the wild)测试数据集的平均WHDR(weighted human disagreement rate)降低了7.29%,在SAW(shading annotations in the wild)测试集的AP(average precision)指标上提升了2.74%。同时,所提出的基于图卷积的神经网络,在IIW、SAW数据集上均取得了较好的结果,在视觉结果上显著优于此前的方法。此外,利用本文算法得到的本征结果,在重光照、纹理编辑和光照编辑等图像编辑任务上,取得了更优的结果。结论所提出的数据集质量更高,有利于基于神经网络的本征分解模型的训练。同时,提出的本征分解模型由于显式地结合了非局部先验,得到了更优的本征分解结果,并通过一系列应用任务进一步验证了结果。

DeepNoise: Signal and Noise Disentanglement Based on Classifying Fluorescent Microscopy Images via Deep Learning

The high-content image-based assay is commonly leveraged for identifying the phenotypic impact of genetic perturbations in biology field.However,a persistent issue remains unsolved during experiments:the interferential technical noises caused by systematic errors(e.g.,temperature,reagent concentration,and well location)are always mixed up with the real biological signals,leading to misinterpretation of any conclusion drawn.Here,we reported a mean teacher-based deep learning model(Deep Noise)that can disentangle biological signals from the experimental noises.Specifically,we aimed to classify the phenotypic impact of 1108 different genetic perturbations screened from 125,510 fluorescent microscopy images,which were totally unrecognizable by the human eye.We validated our model by participating in the Recursion Cellular Image Classification Challenge,and Deep Noise achieved an extremely high classification score(accuracy:99.596%),ranking the 2nd place among 866 participating groups.This promising result indicates the successful separation of biological and technical factors,which might help decrease the cost of treatment development and expedite the drug discovery process.The source code of Deep Noise is available at https://github.com/Scu-sen/Recursion-Cellular-Image-Classification-Challenge.