Fractional ridge regression: a fast, interpretable reparameterization of ridge regression

Distributed representations of behavior-derived object dimensions in the human visual system

Object vision is commonly thought to involve a hierarchy of brain regions processing increasingly complex image features, with high-level visual cortex supporting object recognition and categorization. However, object vision supports diverse behavioral goals, suggesting basic limitations of this category-centric framework. To address these limitations, we mapped a series of dimensions derived from a large-scale analysis of human similarity judgments directly onto the brain. Our results reveal broadly distributed representations of behaviorally-relevant information, demonstrating selectivity to a wide variety of novel dimensions while capturing known selectivities for visual features and categories. Behavior-derived dimensions were superior to categories at predicting brain responses, yielding mixed selectivity in much of visual cortex and sparse selectivity in category-selective clusters. This framework reconciles seemingly disparate findings regarding regional specialization, explaining category selectivity as a special case of sparse response profiles among representational dimensions, suggesting a more expansive view on visual processing in the human brain.

Smart Water Quality Monitoring with IoT Wireless Sensor Networks

Traditional laboratory-based water quality monitoring and testing approaches are soon to be outdated, mainly because of the need for real-time feedback and immediate responses to emergencies. The more recent wireless sensor network (WSN)-based techniques are evolving to alleviate the problems of monitoring, coverage, and energy management, among others. The inclusion of the Internet of Things (IoT) in WSN techniques can further lead to their improvement in delivering, in real time, effective and efficient water-monitoring systems, reaping from the benefits of IoT wireless systems. However, they still suffer from the inability to deliver accurate real-time data, a lack of reconfigurability, the need to be deployed in ad hoc harsh environments, and their limited acceptability within industry. Electronic sensors are required for them to be effectively incorporated into the IoT WSN water-quality-monitoring system. Very few electronic sensors exist for parameter measurement. This necessitates the incorporation of artificial intelligence (AI) sensory techniques for smart water-quality-monitoring systems for indicators without actual electronic sensors by relating with available sensor data. This approach is in its infancy and is still not yet accepted nor standardized by the industry. This work presents a smart water-quality-monitoring framework featuring an intelligent IoT WSN monitoring system. The system uses AI sensors for indicators without electronic sensors, as the design of electronic sensors is lagging behind monitoring systems. In particular, machine learning algorithms are used to predict E. coli concentrations in water. Six different machine learning models (ridge regression, random forest regressor, stochastic gradient boosting, support vector machine, k-nearest neighbors, and AdaBoost regressor) are used on a sourced dataset. From the results, the best-performing model on average during testing was the AdaBoost regressor (a MAE¯ of 14.37 counts/100 mL), and the worst-performing model was stochastic gradient boosting (a MAE¯ of 42.27 counts/100 mL). The development and application of such a system is not trivial. The best-performing water parameter set (Set A) contained pH, conductivity, chloride, turbidity, nitrates, and chlorophyll.

Improving predictions: Enhancing in-hospital mortality forecast for ICU patients with sepsis-induced coagulopathy using a stacking ensemble model

The incidence of sepsis-induced coagulopathy (SIC) is high, leading to increased mortality rates and prolonged hospitalization and intensive care unit (ICU) stays. Early identification of SIC patients at risk of in-hospital mortality can improve patient prognosis. The objective of this study is to develop and validate machine learning (ML) models to dynamically predict in-hospital mortality risk in SIC patients. A ML model is established based on the Medical Information Mart for Intensive Care IV (MIMIC-IV) database to predict in-hospital mortality in SIC patients. Utilizing univariate feature selection for feature screening. The optimal model was determined by calculating the area under the curve (AUC) with a 95% confidence interval (CI). The optimal model was interpreted using Shapley Additive Explanation (SHAP) values. Among the 3112 SIC patients included in MIMIC-IV, a total of 757 (25%) patients experienced mortality during their ICU stay. Univariate feature selection helps us to pick out the 20 most critical variables from the original feature. Among the 10 developed machine learning models, the stacking ensemble model exhibited the highest AUC (0.795, 95% CI: 0.763-0.827). Anion gap and age emerged as the most significant features for predicting the mortality risk in SIC. In this study, an ML model was constructed that exhibited excellent performance in predicting in-hospital mortality risk in SIC patients. Specifically, the stacking ensemble model demonstrated superior predictive ability.

Driving and suppressing the human language network using large language models

Transformer models such as GPT generate human-like language and are predictive of human brain responses to language. Here, using functional-MRI-measured brain responses to 1,000 diverse sentences, we first show that a GPT-based encoding model can predict the magnitude of the brain response associated with each sentence. We then use the model to identify new sentences that are predicted to drive or suppress responses in the human language network. We show that these model-selected novel sentences indeed strongly drive and suppress the activity of human language areas in new individuals. A systematic analysis of the model-selected sentences reveals that surprisal and well-formedness of linguistic input are key determinants of response strength in the language network. These results establish the ability of neural network models to not only mimic human language but also non-invasively control neural activity in higher-level cortical areas, such as the language network.

Decoding face recognition abilities in the human brain

Why are some individuals better at recognizing faces? Uncovering the neural mechanisms supporting face recognition ability has proven elusive. To tackle this challenge, we used a multimodal data-driven approach combining neuroimaging, computational modeling, and behavioral tests. We recorded the high-density electroencephalographic brain activity of individuals with extraordinary face recognition abilities-super-recognizers-and typical recognizers in response to diverse visual stimuli. Using multivariate pattern analyses, we decoded face recognition abilities from 1 s of brain activity with up to 80% accuracy. To better understand the mechanisms subtending this decoding, we compared representations in the brains of our participants with those in artificial neural network models of vision and semantics, as well as with those involved in human judgments of shape and meaning similarity. Compared to typical recognizers, we found stronger associations between early brain representations of super-recognizers and midlevel representations of vision models as well as shape similarity judgments. Moreover, we found stronger associations between late brain representations of super-recognizers and representations of the artificial semantic model as well as meaning similarity judgments. Overall, these results indicate that important individual variations in brain processing, including neural computations extending beyond purely visual processes, support differences in face recognition abilities. They provide the first empirical evidence for an association between semantic computations and face recognition abilities. We believe that such multimodal data-driven approaches will likely play a critical role in further revealing the complex nature of idiosyncratic face recognition in the human brain.

Driving and suppressing the human language network using large language models

Transformer models such as GPT generate human-like language and are highly predictive of human brain responses to language. Here, using fMRI-measured brain responses to 1,000 diverse sentences, we first show that a GPT-based encoding model can predict the magnitude of brain response associated with each sentence. Then, we use the model to identify new sentences that are predicted to drive or suppress responses in the human language network. We show that these model-selected novel sentences indeed strongly drive and suppress activity of human language areas in new individuals. A systematic analysis of the model-selected sentences reveals that surprisal and well-formedness of linguistic input are key determinants of response strength in the language network. These results establish the ability of neural network models to not only mimic human language but also noninvasively control neural activity in higher-level cortical areas, like the language network.

Human brain responses are modulated when exposed to optimized natural images or synthetically generated images

Understanding how human brains interpret and process information is important. Here, we investigated the selectivity and inter-individual differences in human brain responses to images via functional MRI. In our first experiment, we found that images predicted to achieve maximal activations using a group level encoding model evoke higher responses than images predicted to achieve average activations, and the activation gain is positively associated with the encoding model accuracy. Furthermore, anterior temporal lobe face area (aTLfaces) and fusiform body area 1 had higher activation in response to maximal synthetic images compared to maximal natural images. In our second experiment, we found that synthetic images derived using a personalized encoding model elicited higher responses compared to synthetic images from group-level or other subjects' encoding models. The finding of aTLfaces favoring synthetic images than natural images was also replicated. Our results indicate the possibility of using data-driven and generative approaches to modulate macro-scale brain region responses and probe inter-individual differences in and functional specialization of the human visual system.

Data-driven decision-making for precision diagnosis of digestive diseases

Modern omics technologies can generate massive amounts of biomedical data, providing unprecedented opportunities for individualized precision medicine. However, traditional statistical methods cannot effectively process and utilize such big data. To meet this new challenge, machine learning algorithms have been developed and applied rapidly in recent years, which are capable of reducing dimensionality, extracting features, organizing data and forming automatable data-driven clinical decision systems. Data-driven clinical decision-making have promising applications in precision medicine and has been studied in digestive diseases, including early diagnosis and screening, molecular typing, staging and stratification of digestive malignancies, as well as precise diagnosis of Crohn's disease, auxiliary diagnosis of imaging and endoscopy, differential diagnosis of cystic lesions, etiology discrimination of acute abdominal pain, stratification of upper gastrointestinal bleeding (UGIB), and real-time diagnosis of esophageal motility function, showing good application prospects. Herein, we reviewed the recent progress of data-driven clinical decision making in precision diagnosis of digestive diseases and discussed the limitations of data-driven decision making after a brief introduction of methods for data-driven decision making.

Risk factor mining and prediction of urine protein progression in chronic kidney disease: a machine learning- based study

BACKGROUND

Chronic kidney disease (CKD) is a global public health concern. Therefore, to provide timely intervention for non-hospitalized high-risk patients and rationally allocate limited clinical resources is important to mine the key factors when designing a CKD prediction model.

METHODS

This study included data from 1,358 patients with CKD pathologically confirmed during the period from December 2017 to September 2020 at Zhongshan Hospital. A CKD prediction interpretation framework based on machine learning was proposed. From among 100 variables, 17 were selected for the model construction through a recursive feature elimination with logistic regression feature screening. Several machine learning classifiers, including extreme gradient boosting, gaussian-based naive bayes, a neural network, ridge regression, and linear model logistic regression (LR), were trained, and an ensemble model was developed to predict 24-hour urine protein. The detailed relationship between the risk of CKD progression and these predictors was determined using a global interpretation. A patient-specific analysis was conducted using a local interpretation.

RESULTS

The results showed that LR achieved the best performance, with an area under the curve (AUC) of 0.850 in a single machine learning model. The ensemble model constructed using the voting integration method further improved the AUC to 0.856. The major predictors of moderate-to-severe severity included lower levels of 25-OH-vitamin, albumin, transferrin in males, and higher levels of cystatin C.

CONCLUSIONS

Compared with the clinical single kidney function evaluation indicators (eGFR, Scr), the machine learning model proposed in this study improved the prediction accuracy of CKD progression by 17.6% and 24.6%, respectively, and the AUC was improved by 0.250 and 0.236, respectively. Our framework can achieve a good predictive interpretation and provide effective clinical decision support.

Color-biased regions in the ventral visual pathway are food selective

Color-biased regions have been found between face- and place-selective areas in the ventral visual pathway. To investigate the function of the color-biased regions in a pathway responsible for object recognition, we analyzed the natural scenes dataset (NSD), a large 7T fMRI dataset from 8 participants who each viewed up to 30,000 trials of images of colored natural scenes over more than 30 scanning sessions. In a whole-brain analysis, we correlated the average color saturation of the images with voxel responses, revealing color-biased regions that diverge into two streams, beginning in V4 and extending medially and laterally relative to the fusiform face area in both hemispheres. We drew regions of interest (ROIs) for the two streams and found that the images for each ROI that evoked the largest responses had certain characteristics: they contained food, circular objects, warmer hues, and had higher color saturation. Further analyses showed that food images were the strongest predictor of activity in these regions, implying the existence of medial and lateral ventral food streams (VFSs). We found that color also contributed independently to voxel responses, suggesting that the medial and lateral VFSs use both color and form to represent food. Our findings illustrate how high-resolution datasets such as the NSD can be used to disentangle the multifaceted contributions of many visual features to the neural representations of natural scenes.

Personalized visual encoding model construction with small data

Quantifying population heterogeneity in brain stimuli-response mapping may allow insight into variability in bottom-up neural systems that can in turn be related to individual's behavior or pathological state. Encoding models that predict brain responses to stimuli are one way to capture this relationship. However, they generally need a large amount of fMRI data to achieve optimal accuracy. Here, we propose an ensemble approach to create encoding models for novel individuals with relatively little data by modeling each subject's predicted response vector as a linear combination of the other subjects' predicted response vectors. We show that these ensemble encoding models trained with hundreds of image-response pairs, achieve accuracy not different from models trained on 20,000 image-response pairs. Importantly, the ensemble encoding models preserve patterns of inter-individual differences in the image-response relationship. We also show the proposed approach is robust against domain shift by validating on data with a different scanner and experimental setup. Additionally, we show that the ensemble encoding models are able to discover the inter-individual differences in various face areas' responses to images of animal vs human faces using a recently developed NeuroGen framework. Our approach shows the potential to use existing densely-sampled data, i.e. large amounts of data collected from a single individual, to efficiently create accurate, personalized encoding models and, subsequently, personalized optimal synthetic images for new individuals scanned under different experimental conditions.

Improving the accuracy of single-trial fMRI response estimates using GLMsingle

Advances in artificial intelligence have inspired a paradigm shift in human neuroscience, yielding large-scale functional magnetic resonance imaging (fMRI) datasets that provide high-resolution brain responses to thousands of naturalistic visual stimuli. Because such experiments necessarily involve brief stimulus durations and few repetitions of each stimulus, achieving sufficient signal-to-noise ratio can be a major challenge. We address this challenge by introducing GLMsingle, a scalable, user-friendly toolbox available in MATLAB and Python that enables accurate estimation of single-trial fMRI responses (glmsingle.org). Requiring only fMRI time-series data and a design matrix as inputs, GLMsingle integrates three techniques for improving the accuracy of trial-wise general linear model (GLM) beta estimates. First, for each voxel, a custom hemodynamic response function (HRF) is identified from a library of candidate functions. Second, cross-validation is used to derive a set of noise regressors from voxels unrelated to the experiment. Third, to improve the stability of beta estimates for closely spaced trials, betas are regularized on a voxel-wise basis using ridge regression. Applying GLMsingle to the Natural Scenes Dataset and BOLD5000, we find that GLMsingle substantially improves the reliability of beta estimates across visually-responsive cortex in all subjects. Comparable improvements in reliability are also observed in a smaller-scale auditory dataset from the StudyForrest experiment. These improvements translate into tangible benefits for higher-level analyses relevant to systems and cognitive neuroscience. We demonstrate that GLMsingle: (i) helps decorrelate response estimates between trials nearby in time; (ii) enhances representational similarity between subjects within and across datasets; and (iii) boosts one-versus-many decoding of visual stimuli. GLMsingle is a publicly available tool that can significantly improve the quality of past, present, and future neuroimaging datasets sampling brain activity across many experimental conditions.

Feature-reweighted representational similarity analysis: A method for improving the fit between computational models, brains, and behavior

Representational Similarity Analysis (RSA) has emerged as a popular method for relating representational spaces from human brain activity, behavioral data, and computational models. RSA is based on the comparison of representational (dis-)similarity matrices (RDM or RSM), which characterize the pairwise (dis-)similarities of all conditions across all features (e.g. fMRI voxels or units of a model). However, classical RSA treats each feature as equally important. This 'equal weights' assumption contrasts with the flexibility of multivariate decoding, which reweights individual features for predicting a target variable. As a consequence, classical RSA may lead researchers to underestimate the correspondence between a model and a brain region and, in case of model comparison, may lead them to select an inferior model. The aim of this work is twofold: First, we sought to broadly test feature-reweighted RSA (FR-RSA) applied to computational models and reveal the extent to which reweighting model features improves RSM correspondence and affects model selection. Previous work suggested that reweighting can improve model selection in RSA but it has remained unclear to what extent these results generalize across datasets and data modalities. To draw more general conclusions, we utilized a range of publicly available datasets and three popular deep neural networks (DNNs). Second, we propose voxel-reweighted RSA, a novel use case of FR-RSA that reweights fMRI voxels, mirroring the rationale of multivariate decoding of optimally combining voxel activity patterns. We found that reweighting individual model units markedly improved the fit between model RSMs and target RSMs derived from several fMRI and behavioral datasets and affected model selection, highlighting the importance of considering FR-RSA. For voxel-reweighted RSA, improvements in RSM correspondence were even more pronounced, demonstrating the utility of this novel approach. We additionally show that classical noise ceilings can be exceeded when FR-RSA is applied and propose an updated approach for their computation. Taken together, our results broadly validate the use of FR-RSA for improving the fit between computational models, brain, and behavioral data, possibly allowing us to better adjudicate between competing computational models. Further, our results suggest that FR-RSA applied to brain measurement channels could become an important new method to assess the correspondence between representational spaces.

A massive 7T fMRI dataset to bridge cognitive neuroscience and artificial intelligence

Extensive sampling of neural activity during rich cognitive phenomena is critical for robust understanding of brain function. Here we present the Natural Scenes Dataset (NSD), in which high-resolution functional magnetic resonance imaging responses to tens of thousands of richly annotated natural scenes were measured while participants performed a continuous recognition task. To optimize data quality, we developed and applied novel estimation and denoising techniques. Simple visual inspections of the NSD data reveal clear representational transformations along the ventral visual pathway. Further exemplifying the inferential power of the dataset, we used NSD to build and train deep neural network models that predict brain activity more accurately than state-of-the-art models from computer vision. NSD also includes substantial resting-state and diffusion data, enabling network neuroscience perspectives to constrain and enhance models of perception and memory. Given its unprecedented scale, quality and breadth, NSD opens new avenues of inquiry in cognitive neuroscience and artificial intelligence.

NeuroGen: Activation optimized image synthesis for discovery neuroscience

Functional MRI (fMRI) is a powerful technique that has allowed us to characterize visual cortex responses to stimuli, yet such experiments are by nature constructed based on a priori hypotheses, limited to the set of images presented to the individual while they are in the scanner, are subject to noise in the observed brain responses, and may vary widely across individuals. In this work, we propose a novel computational strategy, which we call NeuroGen, to overcome these limitations and develop a powerful tool for human vision neuroscience discovery. NeuroGen combines an fMRI-trained neural encoding model of human vision with a deep generative network to synthesize images predicted to achieve a target pattern of macro-scale brain activation. We demonstrate that the reduction of noise that the encoding model provides, coupled with the generative network’s ability to produce images of high fidelity, results in a robust discovery architecture for visual neuroscience. By using only a small number of synthetic images created by NeuroGen, we demonstrate that we can detect and amplify differences in regional and individual human brain response patterns to visual stimuli. We then verify that these discoveries are reflected in the several thousand observed image responses measured with fMRI. We further demonstrate that NeuroGen can create synthetic images predicted to achieve regional response patterns not achievable by the best-matching natural images. The NeuroGen framework extends the utility of brain encoding models and opens up a new avenue for exploring, and possibly precisely controlling, the human visual system.