pwc-archive/papers-with-abstracts huggingface dataset:
Learnable Group Transform: Enhancing Genotype-to-Phenotype Prediction for Rice Breeding with Small, Structured Datasets
Authors: Yunxuan Dong, Siyuan Chen, Jisen Zhang
Date: 2025-03-14 00:00:00
Tasks: Prediction

Genotype-to-Phenotype (G2P) prediction plays a pivotal role in crop breeding, enabling the identification of superior genotypes based on genomic data. Rice (Oryza sativa), one of the most important staple crops, faces challenges in improving yield and resilience due to the complex genetic architecture of agronomic traits and the limited sample size in breeding datasets. Current G2P prediction methods, such as GWAS and linear models, often fail to capture complex non-linear relationships between genotypes and phenotypes, leading to suboptimal prediction accuracy. Additionally, population stratification and overfitting are significant obstacles when models are applied to small datasets with diverse genetic backgrounds. This study introduces the Learnable Group Transform (LGT) method, which aims to overcome these challenges by combining the advantages of traditional linear models with advanced machine learning techniques. LGT utilizes a group-based transformation of genotype data to capture spatial relationships and genetic structures across diverse rice populations, offering flexibility to generalize even with limited data. Through extensive experiments on the Rice529 dataset, a panel of 529 rice accessions, LGT demonstrated substantial improvements in prediction accuracy for multiple agronomic traits, including yield and plant height, compared to state-of-the-art baselines such as linear models and recent deep learning approaches. Notably, LGT achieved an R^2 improvement of up to 15\% for yield prediction, significantly reducing error and demonstrating its ability to extract meaningful signals from high-dimensional, noisy genomic data. These results highlight the potential of LGT as a powerful tool for genomic prediction in rice breeding, offering a promising solution for accelerating the identification of high-yielding and resilient rice varieties.
OPTIMUS: Predicting Multivariate Outcomes in Alzheimer's Disease Using Multi-modal Data amidst Missing Values
Authors: Christelle Schneuwly Diaz, Duy-Thanh Vu, Julien Bodelet, Duy-Cat Can, Guillaume Blanc, Haiting Jiang, Lin Yao, Guiseppe Pantaleo, ADNI, Oliver Y. Chén
Date: 2025-03-14 00:00:00
Tasks: Disease Prediction, Imputation, Missing Values, Prediction

Alzheimer's disease, a neurodegenerative disorder, is associated with neural, genetic, and proteomic factors while affecting multiple cognitive and behavioral faculties. Traditional AD prediction largely focuses on univariate disease outcomes, such as disease stages and severity. Multimodal data encode broader disease information than a single modality and may, therefore, improve disease prediction; but they often contain missing values. Recent "deeper" machine learning approaches show promise in improving prediction accuracy, yet the biological relevance of these models needs to be further charted. Integrating missing data analysis, predictive modeling, multimodal data analysis, and explainable AI, we propose OPTIMUS, a predictive, modular, and explainable machine learning framework, to unveil the many-to-many predictive pathways between multimodal input data and multivariate disease outcomes amidst missing values. OPTIMUS first applies modality-specific imputation to uncover data from each modality while optimizing overall prediction accuracy. It then maps multimodal biomarkers to multivariate outcomes using machine-learning and extracts biomarkers respectively predictive of each outcome. Finally, OPTIMUS incorporates XAI to explain the identified multimodal biomarkers. Using data from 346 cognitively normal subjects, 608 persons with mild cognitive impairment, and 251 AD patients, OPTIMUS identifies neural and transcriptomic signatures that jointly but differentially predict multivariate outcomes related to executive function, language, memory, and visuospatial function. Our work demonstrates the potential of building a predictive and biologically explainable machine-learning framework to uncover multimodal biomarkers that capture disease profiles across varying cognitive landscapes. The results improve our understanding of the complex many-to-many pathways in AD.
Auto-Associative Memories for Direct Signalling of Visual Angle During Object Approaches
Authors: Matthias S. Keil
Date: 2025-03-13 00:00:00
Tasks: Object

Being hit by a ball is usually not a pleasant experience. While a ball may not be fatal, other objects can be. To protect themselves, many organisms, from humans to insects, have developed neuronal mechanisms to signal approaching objects such as predators and obstacles. The study of these neuronal circuits is still ongoing, both experimentally and theoretically. Many computational proposals rely on temporal contrast integration, as it encodes how the visual angle of an approaching object changes with time. However, mechanisms based on contrast integration are severely limited when the observer is also moving, as it is difficult to distinguish the background-induced temporal contrast from that of an approaching object. Here, I present results of a new mechanism for signaling object approaches, based on modern content-addressable (auto-associative) memories. Auto-associative memories were first proposed by Hopfield in 1982, and are a class of simple neuronal networks which transform incomplete or noisy input patterns to complete and noise-free output patterns. The memory holds different sizes of a generic pattern template that is efficient for segregating an approaching object from irrelevant background motion. Therefore, the model's output correlates directly with angular size. Generally, the new mechanism performs on a par with previously published models. The overall performance was systematically evaluated based on the network's responses to artificial and real-world video footage.
Optimal Transport for Brain-Image Alignment: Unveiling Redundancy and Synergy in Neural Information Processing
Authors: Yang Xiao, Wang Lu, Jie Ji, Ruimeng Ye, Gen Li, Xiaolong Ma, Bo Hui
Date: 2025-03-09 00:00:00
Tasks: Dimensionality Reduction, Large Language Model

The design of artificial neural networks (ANNs) is inspired by the structure of the human brain, and in turn, ANNs offer a potential means to interpret and understand brain signals. Existing methods primarily align brain signals with real-world signals using Mean Squared Error (MSE), which solely focuses on local point-wise alignment, and ignores global matching, leading to coarse interpretations and inaccuracies in brain signal decoding. In this paper, we address these issues through optimal transport (OT) and theoretically demonstrate why OT provides a more effective alignment strategy than MSE. Specifically, we construct a transport plan between brain voxel embeddings and image embeddings, enabling more precise matching. By controlling the amount of transport, we mitigate the influence of redundant information. We apply our alignment model directly to the Brain Captioning task by feeding brain siginals into a large language model (LLM) instead of images. Our approach achieves state-of-the-art performance across ten evaluation metrics, surpassing the previous best method by an average of 6.11\% in single-subject training and 3.81\% in cross-subject training. Additionally, we have uncovered several insightful conclusions that align with existing brain research. We unveil the redundancy and synergy of brain information processing through region masking and data dimensionality reduction visualization experiments. We believe our approach paves the way for a more precise understanding of brain signals in the future. The code is available soon.
Synthetic Categorical Restructuring large Or How AIs Gradually Extract Efficient Regularities from Their Experience of the World
Authors: Michael Pichat, William Pogrund, Paloma Pichat, Armanouche Gasparian, Samuel Demarchi, Martin Corbet, Alois Georgeon, Theo Dasilva, Michael Veillet-Guillem
Date: 2025-02-25 00:00:00

How do language models segment their internal experience of the world of words to progressively learn to interact with it more efficiently? This study in the neuropsychology of artificial intelligence investigates the phenomenon of synthetic categorical restructuring, a process through which each successive perceptron neural layer abstracts and combines relevant categorical sub-dimensions from the thought categories of its previous layer. This process shapes new, even more efficient categories for analyzing and processing the synthetic system's own experience of the linguistic external world to which it is exposed. Our genetic neuron viewer, associated with this study, allows visualization of the synthetic categorical restructuring phenomenon occurring during the transition from perceptron layer 0 to 1 in GPT2-XL.
How causal perspectives can inform problems in computational neuroscience
Authors: Eric W. Bridgeford, Brian S. Caffo, Maya B. Mathur, Russell A. Poldrack
Date: 2025-03-12 00:00:00
Tasks: Experimental Design

Over the past two decades, considerable strides have been made in advancing neuroscience techniques, yet the translation of these advancements into clinically relevant insights for human mental health remains a challenge. This review addresses a fundamental issue in neuroscience - attributing causality - and advocates for the development of robust causal frameworks. We systematically introduce the necessary definitions and concepts, emphasizing the implicit role of causal frameworks in neuroscience investigations. We illustrate how persistent challenges in neuroscience, such as batch effects and selection biases, can be conceptualized and approached using causal frameworks. Through theoretical development and real-world examples, we show how these causal perspectives highlight numerous shortcomings of existing data collection strategies and analytical approaches. We demonstrate how causal frameworks can inform both experimental design and analysis, particularly for observational studies where traditional randomization is infeasible. Using neuroimaging as a detailed case study, we explore the advantages, shortcomings, and implications for generalizability that these perspectives afford to existing and novel research paradigms. Together, we believe that this perspective offers a framework for conceptualizing, framing, and inspiring innovative approaches to problems in neuroscience.
Taxonomic Reasoning for Rare Arthropods: Combining Dense Image Captioning and RAG for Interpretable Classification
Authors: Nathaniel Lesperance, Sujeevan Ratnasingham, Graham W. Taylor
Date: 2025-03-13 00:00:00
Tasks: Image Captioning, RAG, Retrieval-augmented Generation

In the context of pressing climate change challenges and the significant biodiversity loss among arthropods, automated taxonomic classification from organismal images is a subject of intense research. However, traditional AI pipelines based on deep neural visual architectures such as CNNs or ViTs face limitations such as degraded performance on the long-tail of classes and the inability to reason about their predictions. We integrate image captioning and retrieval-augmented generation (RAG) with large language models (LLMs) to enhance biodiversity monitoring, showing particular promise for characterizing rare and unknown arthropod species. While a naive Vision-Language Model (VLM) excels in classifying images of common species, the RAG model enables classification of rarer taxa by matching explicit textual descriptions of taxonomic features to contextual biodiversity text data from external sources. The RAG model shows promise in reducing overconfidence and enhancing accuracy relative to naive LLMs, suggesting its viability in capturing the nuances of taxonomic hierarchy, particularly at the challenging family and genus levels. Our findings highlight the potential for modern vision-language AI pipelines to support biodiversity conservation initiatives, emphasizing the role of comprehensive data curation and collaboration with citizen science platforms to improve species identification, unknown species characterization and ultimately inform conservation strategies.
Exploration of Hepatitis B Virus Infection Dynamics through Virology-Informed Neural Network: A Novel Artificial Intelligence Approach
Authors: Bikram Das, Rupchand Sutradhar, D C Dalal
Date: 2025-03-12 00:00:00
Tasks: Virology

In this work, we introduce Virology-Informed Neural Networks (VINNs), a powerful tool for capturing the intricate dynamics of viral infection when data of some compartments of the model are not available. VINNs, an extension of the widely known Physics-Informed Neural Networks (PINNs), offer an alternative approach to traditional numerical methods for solving system of differential equations. We apply this VINN technique on a recently proposed hepatitis B virus (HBV) infection dynamics model to predict the transmission of the infection within the liver more accurately. This model consists of four compartments, namely uninfected and infected hepatocytes, rcDNA-containing capsids, and free viruses, along with the consideration of capsid recycling. Leveraging the power of VINNs, we study the impacts of variations in parameter range, experimental noise, data variability, network architecture, and learning rate in this work. In order to demonstrate the robustness and effectiveness of VINNs, we employ this approach on the data collected from nine HBV-infceted chimpanzees, and it is observed that VINNs can effectively estimate the model parameters. VINNs reliably capture the dynamics of infection spread and accurately predict their future progression using real-world data. Furthermore, VINNs efficiently identify the most influential parameters in HBV dynamics based solely on experimental data from the capsid component. It is also expected that this framework can be extended beyond viral dynamics, providing a powerful tool for uncovering hidden patterns and complex interactions across various scientific and engineering domains.
Pricing American Parisian Options under General Time-Inhomogeneous Markov Models
Authors: Yuhao Liu, Nian Yang, Gongqiu Zhang
Date: 2025-03-14 00:00:00

This paper develops general approaches for pricing various types of American-style Parisian options (down-in/-out, perpetual/finite-maturity) with general payoff functions based on continuous-time Markov chain (CTMC) approximation under general 1D time-inhomogeneous Markov models. For the down-in types, by conditioning on the Parisian stopping time, we reduce the pricing problem to that of a series of vanilla American options with different maturities and their prices integrated with the distribution function of the Parisian stopping time yield the American Parisian down-in option price. This facilitates an efficient application of CTMC approximation to obtain the approximate option price by calculating the required quantities. For the perpetual down-in cases under time-homogeneous models, significant computational cost can be reduced. The down-out cases are more complicated, for which we use the state augmentation approach to record the excursion duration and then the approximate option price is obtained by solving a series of variational inequalities recursively with the Lemke's pivoting method. We show the convergence of CTMC approximation for all the types of American Parisian options under general time-inhomogeneous Markov models, and the accuracy and efficiency of our algorithms are confirmed with extensive numerical experiments.
Combined climate stress testing of supply-chain networks and the financial system with nation-wide firm-level emission estimates
Authors: Zlata Tabachová, Christian Diem, Johannes Stangl, András Borsos, Stefan Thurner
Date: 2025-02-25 00:00:00

On the way towards carbon neutrality, climate stress testing provides estimates for the physical and transition risks that climate change poses to the economy and the financial system. Missing firm-level CO2 emissions data severely impedes the assessment of transition risks originating from carbon pricing. Based on the individual emissions of all Hungarian firms (410,523), as estimated from their fossil fuel purchases, we conduct a stress test of both actual and hypothetical carbon pricing policies. Using a simple 1:1 economic ABM and introducing the new carbon-to-profit ratio, we identify firms that become unprofitable and default, and estimate the respective loan write-offs. We find that 45% of all companies are directly exposed to carbon pricing. At a price of 45 EUR/t, direct economic losses of 1.3% of total sales and bank equity losses of 1.2% are expected. Secondary default cascades in supply chain networks could increase these losses by 300% to 4000%, depending on firms' ability to substitute essential inputs. To reduce transition risks, firms should reduce their dependence on essential inputs from supply chains with high CO2 exposure. We discuss the implications of different policy implementations on these transition risks.
Tactical Asset Allocation with Macroeconomic Regime Detection
Authors: Daniel Cunha Oliveira, Dylan Sandfelder, André Fujita, Xiaowen Dong, Mihai Cucuringu
Date: 2025-03-14 00:00:00

This paper extends the tactical asset allocation literature by incorporating regime modeling using techniques from machine learning. We propose a novel model that classifies current regimes, forecasts the distribution of future regimes, and integrates these forecasts with the historical performance of individual assets to optimize portfolio allocations. Utilizing a macroeconomic data set from the FRED-MD database, our approach employs a modified k-means algorithm to ensure consistent regime classification over time. We then leverage these regime predictions to estimate expected returns and volatilities, which are subsequently mapped into portfolio allocations using various sizing schemes. Our method outperforms traditional benchmarks such as equal-weight, buy-and-hold, and random regime models. Additionally, we are the first to apply a regime detection model from a large macroeconomic dataset to tactical asset allocation, demonstrating significant improvements in portfolio performance. Our work presents several key contributions, including a novel data-driven regime detection algorithm tailored for uncertainty in forecasted regimes and applying the FRED-MD data set for tactical asset allocation.
CRPS-Based Targeted Sequential Design with Application in Chemical Space
Authors: Lea Friedli, Athénaïs Gautier, Anna Broccard, David Ginsbourger
Date: 2025-03-14 00:00:00

Sequential design of real and computer experiments via Gaussian Process (GP) models has proven useful for parsimonious, goal-oriented data acquisition purposes. In this work, we focus on acquisition strategies for a GP model that needs to be accurate within a predefined range of the response of interest. Such an approach is useful in various fields including synthetic chemistry, where finding molecules with particular properties is essential for developing useful materials and effective medications. GP modeling and sequential design of experiments have been successfully applied to a plethora of domains, including molecule research. Our main contribution here is to use the threshold-weighted Continuous Ranked Probability Score (CRPS) as a basic building block for acquisition functions employed within sequential design. We study pointwise and integral criteria relying on two different weighting measures and benchmark them against competitors, demonstrating improved performance with respect to considered goals. The resulting acquisition strategies are applicable to a wide range of fields and pave the way to further developing sequential design relying on scoring rules.
Introducing Verification Task of Set Consistency with Set-Consistency Energy Networks
Authors: Mooho Song, Jay-Yoon Lee
Date: 2025-03-12 00:00:00
Tasks: Natural Language Inference

Examining logical inconsistencies among multiple statements (such as collections of sentences or question-answer pairs) is a crucial challenge in machine learning, particularly for ensuring the safety and reliability of models. Traditional methods that rely on pairwise comparisons often fail to capture inconsistencies that only emerge when more than two statements are evaluated collectively. To address this gap, we introduce the task of set-consistency verification, an extension of natural language inference (NLI) that assesses the logical coherence of entire sets rather than isolated pairs. Building on this task, we present the Set-Consistency Energy Network (SC-Energy), a novel model that employs a contrastive loss framework to learn the compatibility among a collection of statements. Our approach not only efficiently verifies inconsistencies and pinpoints the specific statements responsible for logical contradictions, but also significantly outperforms existing methods including prompting-based LLM models. Furthermore, we release two new datasets: Set-LConVQA and Set-SNLI for set-consistency verification task.
Predicting Treatment Response in Body Dysmorphic Disorder with Interpretable Machine Learning
Authors: Omar Costilla-Reyes, Morgan Talbot
Date: 2025-03-13 00:00:00
Tasks: Interpretable Machine Learning

Body Dysmorphic Disorder (BDD) is a highly prevalent and frequently underdiagnosed condition characterized by persistent, intrusive preoccupations with perceived defects in physical appearance. In this extended analysis, we employ multiple machine learning approaches to predict treatment outcomes -- specifically treatment response and remission -- with an emphasis on interpretability to ensure clinical relevance and utility. Across the various models investigated, treatment credibility emerged as the most potent predictor, surpassing traditional markers such as baseline symptom severity or comorbid conditions. Notably, while simpler models (e.g., logistic regression and support vector machines) achieved competitive predictive performance, decision tree analyses provided unique insights by revealing clinically interpretable threshold values in credibility scores. These thresholds can serve as practical guideposts for clinicians when tailoring interventions or allocating treatment resources. We further contextualize our findings within the broader literature on BDD, addressing technology-based therapeutics, digital interventions, and the psychosocial determinants of treatment engagement. An extensive array of references situates our results within current research on BDD prevalence, suicidality risks, and digital innovation. Our work underscores the potential of integrating rigorous statistical methodologies with transparent machine learning models. By systematically identifying modifiable predictors -- such as treatment credibility -- we propose a pathway toward more targeted, personalized, and ultimately efficacious interventions for individuals with BDD.