Small Set Research Articles

Stability of Llarull's theorem in all dimensions

Llarull's theorem characterizes the round sphere Sn among all spin manifolds whose scalar curvature is bounded from below by n(n−1). In this paper we show that if the scalar curvature is bounded from below by n(n−1)−ε, the underlying manifold is C0-close to a finite number of spheres outside a small bad set. This completely solves Gromov's spherical stability problem and is the first instance of a scalar curvature stability result that both holds in all dimensions and is stated without any additional geometrical or topological assumptions.

Cost-optimized probabilistic maintenance for condition monitoring of wind turbines with rare failures

We propose a method, a model, and a form of presenting model results for condition monitoring of a small set of wind turbines with rare failures. The main new ingredient of the method is to sample failure thresholds according to the profit they give to an operating company. The model is a multiple linear regression with seasonal components and external regressors, representing all sensor components except for the selected one. To overcome the scarcity of the training data, we use the median sensor values from all available turbines in their healthy state. The cumulated deviation from the normal behavior model obtained for this median turbine is calibrated for each turbine at the beginning of the test period and after known failures. The proposed form of presenting results is to set a scale for possible costs, control for random maintenance, and show a whole distribution of costs depending on the free model parameters. We make a case study on an open dataset with SCADA data from multiple sensors and show that considering the influence of turbine components is more critical than seasonality. The distribution, the average, and the standard deviation of maintenance costs can be very different for similar minimal costs. Random maintenance can be more profitable than reactive maintenance and other approaches. Our predictive maintenance model outperforms random maintenance and competitors for the whole set of considered turbines, giving substantial savings.

Combination of Transfer Learning and Chemprop Interpreter with Support of Deep Learning for the Energy Levels of Organic Photovoltaic Materials Prediction and Regulation.

It is challenging to build a deep learning predictive model using traditional data mining methods due to the scarcity of available data, and the model's internal decision-making process is often nonintuitive and difficult to explain. In this work, a directed message passing neural network model with transfer learning (TL) and chemprop interpreter is proposed to improve energy levels prediction and visualization for organic photovoltaic materials. The established model shows the best performance, with coefficient of determination reaching 0.787 for HOMO and 0.822 for LUMO in a small testing set after TL, compared to the other four models. Then, the chemprop interpreter analyzes local and global effects of 12 molecular structures on the energy levels for organic materials. After a comprehensive analysis of the energy level effects of nonfullerene Y-series, IT-series, and other organic materials, 12 new IT-series derivatives are designed. 1,1-dicyano-methylene-3-indanone (IC) end group halogenation can reduce HOMO and LUMO energy levels to varying degrees, while IC end group modified by electron-withdrawing aromatic groups can increase HOMO and LUMO energy levels and obtain relatively smaller electrostatic potential (ESP) to reducing intermolecular interactions. The influence of side-chain modification on energy levels is limited. It is worth mentioning that the predicted results of IT-series derivatives match density functional theory calculations. The model also shows good generalization and transferability for predicting the energy levels of other organic electronic materials. This work not only provides a cost-effective model for predicting the energy levels of organic photovoltaic materials but also explains the potential bridge between molecular structure and electronic properties.

Challenges with Literature-Derived Data in Machine Learning for Yield Prediction: A Case Study on Pd-Catalyzed Carbonylation Reactions.

The application of machine learning (ML) to predict reaction yields has shown remarkable accuracy when based on high-throughput computational and experimental data. However, the accuracy significantly diminishes when leveraging literature-derived data, highlighting a gap in the predictive capability of the current ML models. This study, focusing on Pd-catalyzed carbonylation reactions, reveals that even with a data set of 2512 reactions, the best-performing model reaches only an R2 of 0.51. Further investigations show that the models' effectiveness is predominantly confined to predictions within narrow subsets of data, closely related and from the same literature sources, rather than across the broader, heterogeneous data sets available in the literature. The reliance on data similarity, coupled with small sample sizes from the same sources, makes the model highly sensitive to inherent fluctuations typical of small data sets, adversely impacting stability, accuracy, and generalizability. The findings underscore the inherent limitations of current ML techniques in leveraging literature-derived data for predicting chemical reaction yields, highlighting the need for more sophisticated approaches to handle the complexity and diversity of chemical data.

Combination of Coevolutionary Information and Supervised Learning Enables Generation of Cyclic Peptide Inhibitors with Enhanced Potency from a Small Data Set

Combination of Coevolutionary Information and Supervised Learning Enables Generation of Cyclic Peptide Inhibitors with Enhanced Potency from a Small Data Set

Towards Open-Set NLP-Based Multi-Level Planning for Robotic Tasks

This paper outlines a conceptual design for a multi-level natural language-based planning system and describes a demonstrator. The main goal of the demonstrator is to serve as a proof-of-concept by accomplishing end-to-end execution in a real-world environment, and showing a novel way of interfacing an LLM-based planner with open-set semantic maps. The target use-case is executing sequences of tabletop pick-and-place operations using an industrial robot arm and RGB-D camera. The demonstrator processes unstructured user prompts, produces high-level action plans, queries a map for object positions and grasp poses using open-set semantics, then uses the resulting outputs to parametrize and execute a sequence of action primitives. In this paper, the overall system structure, high-level planning using language models, low-level planning through action and motion primitives, as well as the implementation of two different environment modeling schemes—2.5 or fully 3-dimensional—are described in detail. The impacts of quantizing image embeddings on object recall are assessed and high-level planner performance is evaluated using a small reference scene data set. We observe that, for the simple constrained test command data set, the high-level planner is able to achieve a total success rate of 96.40%, while the semantic maps exhibit maximum recall rates of 94.69% and 92.29% for the 2.5d and 3d versions, respectively.

TensCERs: Tension-Constrained Elastic Rods

We study ensembles of elastic rods that are tensioned by a small set of inextensible cables. The cables induce forces that deform the initially straight, but flexible rods into 3D space curves at equilibrium. Rods can be open or closed, knotted, and arranged in arbitrary topologies. We specifically focus on equilibrium states with no contacts among rods. Our setup can thus be seen as a generalization of classical tensegrities that are composed of rigid rods and tensile cables, to also support rods that elastically deform. We show how this generalization leads to a rich design space, where complex target shapes can be achieved with a small set of elastic rods. To explore this space, we present an inverse design optimization algorithm that solves for the length and placement of cables such that the equilibrium state of the rod network best approximates a given set of input curves. We introduce appropriate sparsity terms to minimize the number of required cables, which significantly simplifies fabrication. Using our algorithm, we explore new classes of bending-active 3D structures, including elastic tensegrity knots that only require a few internal cables. We design and fabricate several physical models from basic materials that attain complex 3D shapes with unique structural properties.

Neural network–based transfer learning to improve stiffness modeling of industrial robots with small experimental data sets

AbstractStiffness modeling is an essential subject for the composition of robot control. Accurate stiffness modeling is helpful for improving the control accuracy of industrial robots, particularly under dynamic load circumstances. The classic virtual joint modeling (VJM) method is challenging in predicting the deformation of the end-effector throughout the full workspace due to the nonlinear deformation of the robot joint and its serial articulated structure. This paper proposes a full-space stiffness modeling method for robots based on the integration of a multi-layer perceptual (MLP) model and VJM. To provide enough training data for the MLP model, VJM is used to build a stiffness model with a small set of experimental data to generate 106,400 training data. A model-based transfer learning approach is proposed to improve the model’s accuracy and generalization regarding the difference between generated training data and actual experimental data. The VJM stiffness model is compared with the MLP stiffness model and the existing CNN-based transfer learning model based on the same experimental data. Considering the deformation prediction in the three directions in Cartesian space, the mean absolute error, standard deviation, and maximum error of the MLP model are decreased by at least 24.90%, 14.20%, and 8.50%, respectively, than the VJM. These prediction results demonstrate that the proposed modeling technique can significantly increase the accuracy of robot stiffness modeling, which is essential for position compensation in precise motion control of robots under dynamic load.

Functional characteristics and computational model of abundant hyperactive loci in the human genome.

Enhancers and promoters are classically considered to be bound by a small set of transcription factors (TFs) in a sequence-specific manner. This assumption has come under increasing skepticism as the datasets of ChIP-seq assays of TFs have expanded. In particular, high-occupancy target (HOT) loci attract hundreds of TFs with often no detectable correlation between ChIP-seq peaks and DNA-binding motif presence. Here, we used a set of 1003 TF ChIP-seq datasets (HepG2, K562, H1) to analyze the patterns of ChIP-seq peak co-occurrence in combination with functional genomics datasets. We identified 43,891 HOT loci forming at the promoter (53%) and enhancer (47%) regions. HOT promoters regulate housekeeping genes, whereas HOT enhancers are involved in tissue-specific process regulation. HOT loci form the foundation of human super-enhancers and evolve under strong negative selection, with some of these loci being located in ultraconserved regions. Sequence-based classification analysis of HOT loci suggested that their formation is driven by the sequence features, and the density of mapped ChIP-seq peaks across TF-bound loci correlates with sequence features and the expression level of flanking genes. Based on the affinities to bind to promoters and enhancers we detected five distinct clusters of TFs that form the core of the HOT loci. We report an abundance of HOT loci in the human genome and a commitment of 51% of all TF ChIP-seq binding events to HOT locus formation thus challenging the classical model of enhancer activity and propose a model of HOT locus formation based on the existence of large transcriptional condensates.

Functional characteristics and computational model of abundant hyperactive loci in the human genome

Enhancers and promoters are classically considered to be bound by a small set of transcription factors (TFs) in a sequence-specific manner. This assumption has come under increasing skepticism as the datasets of ChIP-seq assays of TFs have expanded. In particular, high-occupancy target (HOT) loci attract hundreds of TFs with often no detectable correlation between ChIP-seq peaks and DNA-binding motif presence. Here, we used a set of 1003 TF ChIP-seq datasets (HepG2, K562, H1) to analyze the patterns of ChIP-seq peak co-occurrence in combination with functional genomics datasets. We identified 43,891 HOT loci forming at the promoter (53%) and enhancer (47%) regions. HOT promoters regulate housekeeping genes, whereas HOT enhancers are involved in tissue-specific process regulation. HOT loci form the foundation of human super-enhancers and evolve under strong negative selection, with some of these loci being located in ultraconserved regions. Sequence-based classification analysis of HOT loci suggested that their formation is driven by the sequence features, and the density of mapped ChIP-seq peaks across TF-bound loci correlates with sequence features and the expression level of flanking genes. Based on the affinities to bind to promoters and enhancers we detected five distinct clusters of TFs that form the core of the HOT loci. We report an abundance of HOT loci in the human genome and a commitment of 51% of all TF ChIP-seq binding events to HOT locus formation thus challenging the classical model of enhancer activity and propose a model of HOT locus formation based on the existence of large transcriptional condensates.

Predicting and Accelerating Nanomaterial Synthesis Using Machine Learning Featurization.

Materials synthesis optimization is constrained by serial feedback processes that rely on manual tools and intuition across multiple siloed modes of characterization. We automate and generalize feature extraction of reflection high-energy electron diffraction (RHEED) data with machine learning to establish quantitatively predictive relationships in small sets (∼10) of expert-labeled data, saving significant time on subsequently grown samples. These predictive relationships are evaluated in a representative material system (W1-xVxSe2 on c-plane sapphire (0001)) with two aims: 1) predicting grain alignment of the deposited film using pregrowth substrate data and 2) estimating vanadium dopant concentration using in situ RHEED as a proxy for ex situ methods (e.g., X-ray photoelectron spectroscopy). Both tasks are accomplished using the same materials-agnostic features, avoiding specific system retraining and leading to a potential 80% time saving over a 100-sample synthesis campaign. These predictions provide guidance to avoid doomed trials, reduce follow-on characterization, and improve control resolution for materials synthesis.

Coupled Perturbed Approach to Dual Basis Sets for Molecules and Solids. II: Energy and Band Corrections for Periodic Systems.

When trying to reach convergence of quantum chemical calculations toward the complete basis set limit, crystalline solids generally prove to be more challenging than molecules. This is due both to the closer packing of atoms─hence, to linear dependencies─and to the problematic behavior of Ewald techniques used for dealing with the infinite character of Coulomb sums. Thus, a dual basis set approach is even more desirable for periodic systems than for molecules. In such an approach, the self-consistent procedure is implemented in a small basis set, and the effect of the enlargement of the basis set is estimated a posteriori. In this paper, we extend to crystalline solids our previous coupled perturbed dual basis set approach [J. Chem. Theory Comput. 2020, 16, 1, 340-353] in which the basis set enlargement is treated as a perturbation. Among the notable features of this approach are (i) the possibility of obtaining not only a correction to the energy but also to energy bands and electron density; (ii) the absence of a diagonalization step for the full Fock matrix in the large basis set; and (iii) the possibility of extrapolating low order perturbation energy corrections to infinite order. We also present here the first periodic implementation of the dual basis set method of Liang and Head-Gordon [J. Phys. Chem. A 2004, 108, 3206-3210]. The effectiveness of both approaches is, then, compared on a small, but representative, set of solids.

EPCO-29. PATHOMICS ANALYSIS IDENTIFIES POTENTIAL SUBTYPES OF DIFFUSE GLIOMAS IN H&E-STAINED WHOLE-SLIDE IMAGES

Abstract IDH status is the first criteria of diagnostic definition for diffuse gliomas in the 2021 WHO classification. While sufficient number of molecular tools are available to identify IDH1 and/or IDH2 mutations, they impose a time and cost burden on patients. We previously trained deep learning models visually differentiate IDH wild-type (IDHwt) and IDH mutant (IDHmut) gliomas in a small set of H&E-stained whole image slides (WSIs) from TCGA using an Uncertainty-Aware Convolutional Neural Network (CNN) at 10x magnification. In this follow-up study, we aimed to improve our models by expanding our annotations of a more representative subset of the TCGA public data, increasing the sampling magnification to 20x, redesigning the preprocessing filters, adjusting the training pipeline to reduce overfitting, and assessing the confidence in model prediction via uncertainty metrics. METHODS By modifying the pre-processing methods from our pilot study, we increased the number of expert-annotated WSIs. Using a 2:1:2 train/validation/test split, we fine-tuned a ResNet18 deep learning model with a pre-trained feature extractor and Monte Carlo dropouts. To identify image features critical for separating by IDH status, we extracted the learned embeddings and performed post-hoc analyses (PCA, t-SNE, and UMAP). RESULTS The new set of annotations resulted in ~15-fold increase in the number of WSIs (i.e.,>2.5 million tiles), without any data augmentation. Our prototype model demonstrated clear separation of cases according to IDH status (sensitivity = 0.63, specificity = 0.91, weighted F1 = 0.81). CONCLUSION We successfully improved the prediction of IDH status in H&E-stained WSIs and identified potential subtypes of IDHwt and IDHmut diffuse gliomas after significantly increasing the dataset size with appropriate expert annotations. We are currently addressing the data imbalance by annotating additional IDHmut glioma WSIs. Furthermore, we will integrate other biomarkers (1p19q, EGFR etc.) to increase the robustness of histo-pathomics as a surrogate for molecular tests.

The underlying causes of differential migration: assumptions, hypotheses, and predictions.

Mechanisms governing the migratory decisions of birds have long fascinated ecologists and sparked considerable debate. Identifying factors responsible for variation in migration distance, also known as differential migration, has been a popular approach to understanding the mechanisms underlying migratory behaviour more generally. However, research progress has been slowed by the continued testing of overlapping, non-mechanistic, and circular predictions among a small set of historically entrenched hypotheses. We highlight the body size hypothesis and suggest that the predictions commonly tested have impeded progress because body size relationships with migration distance are predictions made by several distinct hypotheses with contrasting mechanisms. The cost of migration itself has not been adequately accounted for in most hypotheses, and we propose two flight efficiency hypotheses with time- and energy-minimizing mechanisms that allow individuals to mitigate the risks inherent to longer migrations. We also advance two conceptual versions of the social dominance hypothesis based on two distinct underlying mechanisms related to distance minimization and food maximization that will help clarify the role of competition in driving migratory decisions. Overall, we describe and refine 12 mechanistic hypotheses proposed to explain differential migration (along with several other special-case hypotheses), seven of which have underlying mechanisms related to food limitation as past research has identified this to be an important driver of differential migration. We also thoroughly reviewed 145 publications to assess the amount of support for 10 critical assumptions underlying alternative hypotheses for differential migration in birds. Our review reveals that surprisingly few studies explicitly evaluate assumptions within a differential migration context. Generating and testing strong predictions and critical assumptions underlying mechanisms of alternative hypotheses will improve our ability to differentiate among these explanations of differential migration. Additionally, future intraspecific progress will be greatest if investigators continue to focus on mechanisms underlying variation in migration distance within rather than among demographic classes, as previous research has found differing mechanisms to be responsible for differential migration among demographic classes. Interspecifically, a thorough comparative analysis that seeks to explain variation in migration distance among species would broaden both our understanding of the mechanisms regulating current differential migration patterns and those that led to the evolution of migration more generally. Collectively, we provide a framework that, together with advances in animal-borne tracking and other technology, can be used to advance our understanding of the causes of differential migration distance, and migratory decisions more generally.

Examining focus and alternative priming: Effects of grammatical role and breadth of the alternative set

Recent work has shown that contrastive accenting plays a crucial role in discourse processing, causing listeners to activate alternatives to focused words and/or suppress non-contrastive semantic associates. However, key theoretical questions remain, relating to how lexical activation, sentence and discourse processing interact. These include the breadth of the alternative set, which could span from a small contextually-relevant set to a large, ‘permissive’ one; and whether these processes are best characterised as activation or suppression mechanisms. There is also little research on whether activation of alternatives differs by the grammatical role of the prime, despite differences in the focus-related properties of subjects versus objects. We present two cross-modal lexical decision experiments showing activation of non-contrastive associates is suppressed with contrastive focus, consistent with a suppression mechanism, at least for objects. Alternatives both semantically related, and unrelated, to the prime, were primed, consistent with a broad, ‘permissive’, alternative set. There were crucial differences in priming patterns for subjects versus objects. The study makes important contributions to our theoretical understanding of the role of focus in discourse processing.

Robust quantum dots charge autotuning using neural network uncertainty

Abstract This study presents a machine learning-based procedure to automate the charge tuning of semiconductor spin qubits with minimal human intervention, addressing one of the significant challenges in scaling up quantum dot technologies. This method exploits artificial neural networks to identify noisy transition lines in stability diagrams, guiding a robust exploration strategy leveraging neural network uncertainty estimations. Tested across three distinct offline experimental datasets representing different single-quantum-dot technologies, this approach achieves a tuning success rate of over 99% in optimal cases, where more than 10% of the success is directly attributable to uncertainty exploitation. The challenging constraints of small training sets containing high diagram-to-diagram variability allowed us to evaluate the capabilities and limits of the proposed procedure.

Application of Prompt Learning Models in Identifying the Collaborative Problem Solving Skills in an Online Task

Collaborative problem solving (CPS) competence is considered one of the essential 21st-century skills. To facilitate the assessment and learning of CPS competence, researchers have proposed a series of frameworks to conceptualize CPS and explored ways to make sense of the complex processes involved in collaborative problem solving. However, encoding explicit behaviors into subskills within the frameworks of CPS skills is still a challenging task. Traditional studies have relied on manual coding to decipher behavioral data for CPS, but such coding methods can be very time-consuming and cannot support real-time analyses. Scholars have begun to explore approaches for constructing automatic coding models. Nevertheless, the existing models built using machine learning or deep learning techniques depend on a large amount of training data and have relatively low accuracy. To address these problems, this paper proposes a prompt-based learning pre-trained model. The model can achieve high performance even with limited training data. In this study, three experiments were conducted, and the results showed that our model not only produced the highest accuracy, macro F1 score, and kappa values on large training sets, but also performed the best on small training sets of the CPS behavioral data. The application of the proposed prompt-based learning pre-trained model contributes to the CPS skills coding task and can also be used for other CSCW coding tasks to replace manual coding.

VRTree: Example‐Based 3D Interactive Tree Modeling in Virtual Reality

AbstractWe present VRTree, an example‐based interactive virtual reality (VR) system designed to efficiently create diverse 3D tree models while faithfully preserving botanical characteristics of real‐world references. Our method employs a novel representation called Hierarchical Branch Lobe (HBL), which captures the hierarchical features of trees and serves as a versatile intermediary for intuitive VR interaction. The HBL representation decomposes a 3D tree into a series of concise examples, each consisting of a small set of main branches, secondary branches, and lobe‐bounded twigs. The core of our system involves two key components: (1) We design an automatic algorithm to extract an initial library of HBL examples from real tree point clouds. These HBL examples can be optionally refined according to user intentions through an interactive editing process. (2) Users can interact with the extracted HBL examples to assemble new tree structures, ensuring the local features align with the target tree species. A shape‐guided procedural growth algorithm then transforms these assembled HBL structures into highly realistic, finegrained 3D tree models. Extensive experiments and user studies demonstrate that VRTree outperforms current state‐of‐the‐art approaches, offering a highly effective and easy‐to‐use VR tool for tree modeling.

High-quality multimodal MRI with simultaneous EEG using conductive ink and polymer-thick film nets

Objective. Combining magnetic resonance imaging (MRI) and electroencephalography (EEG) provides a powerful tool for investigating brain function at varying spatial and temporal scales. Simultaneous acquisition of both modalities can provide unique information that a single modality alone cannot reveal. However, current simultaneous EEG-fMRI studies are limited to a small set of MRI sequences due to the image quality and safety limitations of commercially available MR-conditional EEG nets. We tested whether the Inknet2, a high-resistance polymer thick film based EEG net that uses conductive ink, could enable the acquisition of a variety of MR image modalities with minimal artifacts by reducing the radiofrequency-shielding caused by traditional MR-conditional nets.Approach. We first performed simulations to model the effect of the EEG nets on the magnetic field and image quality. We then performed phantom scans to test image quality with a conventional copper EEG net, with the new Inknet2, and without any EEG net. Finally, we scanned five human subjects at 3 Tesla (3 T) and three human subjects at 7 Tesla (7 T) with and without the Inknet2 to assess structural and functional MRI image quality.Main results. Across these simulations, phantom scans, and human studies, the Inknet2 induced fewer artifacts than the conventional net and produced image quality similar to scans with no net present.Significance. Our results demonstrate that high-quality structural and functional multimodal imaging across a variety of MRI pulse sequences at both 3 T and 7 T is achievable with an EEG net made with conductive ink and polymer thick film technology.

Direct testing of natural twister ribozymes from over a thousand organisms reveals a broad tolerance for structural imperfections.

Twister ribozymes are an extensively studied class of nucleolytic RNAs. Thousands of natural twisters have been proposed using sequence homology and structural descriptors. Yet, most of these candidates have not been validated experimentally. To address this gap, we developed Cleavage High-Throughput Assay (CHiTA), a high-throughput pipeline utilizing massively parallel oligonucleotide synthesis and next-generation sequencing to test putative ribozymes en masse in a scarless fashion. As proof of principle, we applied CHiTA to a small set of known active and mutant ribozymes. We then used CHiTA to test two large sets of naturally occurring twister ribozymes: over 1600 previously reported putative twisters and ∼1000 new candidate twisters. The new candidates were identified computationally in ∼1000 organisms, representing a massive increase in the number of ribozyme-harboring organisms. Approximately 94% of the twisters we tested were active and cleaved site-specifically. Analysis of their structural features revealed that many substitutions and helical imperfections can be tolerated. We repeated our computational search with structural descriptors updated from this analysis, whereupon we identified and confirmed the first intrinsically active twister ribozyme in mammals. CHiTA broadly expands the number of active twister ribozymes found in nature and provides a powerful method for functional analyses of other RNAs.