pwc-archive/papers-with-abstracts huggingface dataset:
Contextualizing biological perturbation experiments through language
Authors: Menghua Wu, Russell Littman, Jacob Levine, Lin Qiu, Tommaso Biancalani, David Richmond, Jan-Christian Huetter
Date: 2025-02-28 00:00:00
Tasks: Efficient Exploration

High-content perturbation experiments allow scientists to probe biomolecular systems at unprecedented resolution, but experimental and analysis costs pose significant barriers to widespread adoption. Machine learning has the potential to guide efficient exploration of the perturbation space and extract novel insights from these data. However, current approaches neglect the semantic richness of the relevant biology, and their objectives are misaligned with downstream biological analyses. In this paper, we hypothesize that large language models (LLMs) present a natural medium for representing complex biological relationships and rationalizing experimental outcomes. We propose PerturbQA, a benchmark for structured reasoning over perturbation experiments. Unlike current benchmarks that primarily interrogate existing knowledge, PerturbQA is inspired by open problems in perturbation modeling: prediction of differential expression and change of direction for unseen perturbations, and gene set enrichment. We evaluate state-of-the-art machine learning and statistical approaches for modeling perturbations, as well as standard LLM reasoning strategies, and we find that current methods perform poorly on PerturbQA. As a proof of feasibility, we introduce Summer (SUMMarize, retrievE, and answeR, a simple, domain-informed LLM framework that matches or exceeds the current state-of-the-art. Our code and data are publicly available at https://github.com/genentech/PerturbQA.
Modeling cell differentiation in neuroblastoma: insights into development, malignancy, and treatment relapse
Authors: Simon F. Martina-Perez, Luke A. Heirene, Jennifer C. Kasemeier, Paul M. Kulesa, Ruth E. Baker
Date: 2025-02-28 00:00:00
Tasks: Bayesian Inference, Diversity

Neuroblastoma is a paediatric extracranial solid cancer that arises from the developing sympathetic nervous system and is characterised by an abnormal distribution of cell types in tumours compared to healthy infant tissues. In this paper, we propose a new mathematical model of cell differentiation during sympathoadrenal development. By performing Bayesian inference of the model parameters using clinical data from patient samples, we show that the model successfully accounts for the observed differences in cell type heterogeneity among healthy adrenal tissues and four common types of neuroblastomas. Using a phenotypically structured model, we show that alterations in healthy differentiation dynamics are related to cell malignancy, and tumour volume growth. We use this model to analyse the evolution of malignant traits in a tumour. Our findings suggest that normal development dynamics make the embryonic sympathetic nervous system more robust to perturbations and accumulation of malignancies, and that the diversity of differentiation dynamics found in the neuroblastoma subtypes lead to unique risk profiles for neuroblastoma relapse after treatment.
Using quantile time series and historical simulation to forecast financial risk multiple steps ahead
Authors: Richard Gerlach, Antonio Naimoli, Giuseppe Storti
Date: 2025-02-28 00:00:00
Tasks: Time Series

A method for quantile-based, semi-parametric historical simulation estimation of multiple step ahead Value-at-Risk (VaR) and Expected Shortfall (ES) models is developed. It uses the quantile loss function, analogous to how the quasi-likelihood is employed by standard historical simulation methods. The returns data are scaled by the estimated quantile series, then resampling is employed to estimate the forecast distribution one and multiple steps ahead, allowing tail risk forecasting. The proposed method is applicable to any data or model where the relationship between VaR and ES does not change over time and can be extended to allow a measurement equation incorporating realized measures, thus including Realized GARCH and Realized CAViaR type models. Its finite sample properties, and its comparison with existing historical simulation methods, are evaluated via a simulation study. A forecasting study assesses the relative accuracy of the 1% and 2.5% VaR and ES one-day-ahead and ten-day-ahead forecasting results for the proposed class of models compared to several competitors.
Chronologically Consistent Large Language Models
Authors: Songrun He, Linying Lv, Asaf Manela, Jimmy Wu
Date: 2025-02-28 00:00:00
Tasks: Language Modeling, Language Modelling

Large language models are increasingly used in social sciences, but their training data can introduce lookahead bias and training leakage. A good chronologically consistent language model requires efficient use of training data to maintain accuracy despite time-restricted data. Here, we overcome this challenge by training a suite of chronologically consistent large language models, ChronoBERT and ChronoGPT, which incorporate only the text data that would have been available at each point in time. Despite this strict temporal constraint, our models achieve strong performance on natural language processing benchmarks, outperforming or matching widely used models (e.g., BERT), and remain competitive with larger open-weight models. Lookahead bias is model and application-specific because even if a chronologically consistent language model has poorer language comprehension, a regression or prediction model applied on top of the language model can compensate. In an asset pricing application predicting next-day stock returns from financial news, we find that ChronoBERT's real-time outputs achieve a Sharpe ratio comparable to state-of-the-art models, indicating that lookahead bias is modest. Our results demonstrate a scalable, practical framework to mitigate training leakage, ensuring more credible backtests and predictions across finance and other social science domains.
Short-Rate Derivatives in a Higher-for-Longer Environment
Authors: Aram Karakhanyan, Takis Konstantopoulos, Matthew Lorig, Evgenii Samutichev
Date: 2025-02-28 00:00:00

We introduce a class of short-rate models that exhibit a ``higher for longer'' phenomenon. Specifically, the short-rate is modeled as a general time-homogeneous one-factor Markov diffusion on a finite interval. The lower endpoint is assumed to be regular, exit or natural according to boundary classification while the upper endpoint is assumed to be regular with absorbing behavior. In this setting, we give an explicit expression for price of a zero-coupon bond (as well as more general interest rate derivatives) in terms of the transition density of the short-rate under a new probability measure, and the solution of a non-linear ordinary differential equation (ODE). We then narrow our focus to a class of models for which the transition density and ODE can be solved explicitly. For models within this class, we provide conditions under which the lower endpoint is regular, exit and natural. Finally, we study two specific models -- one in which the lower endpoint is exit and another in which the lower endpoint is natural. In these two models, we give an explicit solution of transition density of the short-rate as a (generalized) eigenfunction expansion. We provide plots of the transition density, (generalized) eigenfunctions, bond prices and the associated yield curve.
Do Sell-side Analyst Reports Have Investment Value?
Authors: Linying Lv
Date: 2025-02-27 00:00:00

This paper documents new investment value in analyst reports. Analyst narratives embedded with large language models strongly forecast future stock returns, generating significant alpha beyond established analyst-based and fundamental-based factors. The return predictability arises primarily from reports that convey negative sentiment but forecast favorable long-term prospects, suggesting systematic market overreaction to near-term negative news. The effect is more pronounced for large, mature firms and for reports authored by skilled, experienced analysts. A Shapley value decomposition reveals that analysts' strategic outlook contributes the most to portfolio performance, especially forward-looking discussions on fundamentals. Beyond demonstrating untapped value in qualitative information, this paper illustrates the broader potential of artificial intelligence to augment, rather than replace, expert human judgment in financial markets.
Forecasting Monthly Residential Natural Gas Demand Using Just-In-Time-Learning Modeling
Authors: Burak Alakent, Erkan Isikli, Cigdem Kadaifci, Tonguc S. Taspinar
Date: 2025-02-28 00:00:00
Tasks: GPR, Time Series

Natural gas (NG) is relatively a clean source of energy, particularly compared to fossil fuels, and worldwide consumption of NG has been increasing almost linearly in the last two decades. A similar trend can also be seen in Turkey, while another similarity is the high dependence on imports for the continuous NG supply. It is crucial to accurately forecast future NG demand (NGD) in Turkey, especially, for import contracts; in this respect, forecasts of monthly NGD for the following year are of utmost importance. In the current study, the historical monthly NG consumption data between 2014 and 2024 provided by SOCAR, the local residential NG distribution company for two cities in Turkey, Bursa and Kayseri, was used to determine out-of-sample monthly NGD forecasts for a period of one year and nine months using various time series models, including SARIMA and ETS models, and a novel proposed machine learning method. The proposed method, named Just-in-Time-Learning-Gaussian Process Regression (JITL-GPR), uses a novel feature representation for the past NG demand values; instead of using past demand values as column-wise separate features, they are placed on a two-dimensional (2-D) grid of year-month values. For each test point, a kernel function, tailored for the NGD predictions, is used in GPR to predict the query point. Since a model is constructed separately for each test point, the proposed method is, indeed, an example of JITL. The JITL-GPR method is easy to use and optimize, and offers a reduction in forecast errors compared to traditional time series methods and a state-of-the-art combination model; therefore, it is a promising tool for NGD forecasting in similar settings.
Collective Reasoning Among LLMs A Framework for Answer Validation Without Ground Truth
Authors: Seyed Pouyan Mousavi Davoudi, Alireza Shafiee Fard, Alireza Amiri-Margavi
Date: 2025-02-28 00:00:00
Tasks: Large Language Model

We present a collaborative framework where multiple large language models, namely GPT-4-0125-preview, Meta-LLaMA-3-70B-Instruct, Claude-3-Opus, and Gemini-1.5-Flash, work together to generate and respond to complex PhD-level probability questions in the absence of definitive ground truth. This study explores how inter-model consensus enhances response reliability and serves as a proxy for assessing the quality of generated questions. To quantify agreement and consistency, we employ statistical methods including chi-square tests, Fleiss' Kappa, and confidence interval analysis, measuring both response precision and question clarity. Our findings highlight that Claude and Gemini generate well-structured and less ambiguous questions, leading to higher inter-model agreement. This is reflected in their narrower confidence intervals and stronger alignment with answering models. Conversely, LLaMA demonstrates increased variability and lower reliability in question formulation, as indicated by broader confidence intervals and reduced consensus rates. These results suggest that multi-model collaboration not only enhances the reliability of responses but also provides a valuable framework for assessing and improving question quality in the absence of explicit ground truth. This research offers meaningful insights into optimizing AI-driven reasoning through collaborative large-language model interactions.
The two filter formula reconsidered: Smoothing in partially observed Gauss--Markov models without information parametrization
Authors: Filip Tronarp
Date: 2025-02-28 00:00:00

In this article, the two filter formula is re-examined in the setting of partially observed Gauss--Markov models. It is traditionally formulated as a filter running backward in time, where the Gaussian density is parametrized in ``information form''. However, the quantity in the backward recursion is strictly speaking not a distribution, but a likelihood. Taking this observation seriously, a recursion over log-quadratic likelihoods is formulated instead, which obviates the need for ``information'' parametrization. In particular, it greatly simplifies the square-root formulation of the algorithm. Furthermore, formulae are given for producing the forward Markov representation of the a posteriori distribution over paths from the proposed likelihood representation.
Human-AI Collaboration: Trade-offs Between Performance and Preferences
Authors: Lukas William Mayer, Sheer Karny, Jackie Ayoub, Miao Song, Danyang Tian, Ehsan Moradi-Pari, Mark Steyvers
Date: 2025-02-28 00:00:00

Despite the growing interest in collaborative AI, designing systems that seamlessly integrate human input remains a major challenge. In this study, we developed a task to systematically examine human preferences for collaborative agents. We created and evaluated five collaborative AI agents with strategies that differ in the manner and degree they adapt to human actions. Participants interacted with a subset of these agents, evaluated their perceived traits, and selected their preferred agent. We used a Bayesian model to understand how agents' strategies influence the Human-AI team performance, AI's perceived traits, and the factors shaping human-preferences in pairwise agent comparisons. Our results show that agents who are more considerate of human actions are preferred over purely performance-maximizing agents. Moreover, we show that such human-centric design can improve the likability of AI collaborators without reducing performance. We find evidence for inequality-aversion effects being a driver of human choices, suggesting that people prefer collaborative agents which allow them to meaningfully contribute to the team. Taken together, these findings demonstrate how collaboration with AI can benefit from development efforts which include both subjective and objective metrics.
Evidence of conceptual mastery in the application of rules by Large Language Models
Authors: José Luiz Nunes, Guilherme FCF Almeida, Brian Flanagan
Date: 2025-03-02 00:00:00
Tasks: Decision Making

In this paper we leverage psychological methods to investigate LLMs' conceptual mastery in applying rules. We introduce a novel procedure to match the diversity of thought generated by LLMs to that observed in a human sample. We then conducted two experiments comparing rule-based decision-making in humans and LLMs. Study 1 found that all investigated LLMs replicated human patterns regardless of whether they are prompted with scenarios created before or after their training cut-off. Moreover, we found unanticipated differences between the two sets of scenarios among humans. Surprisingly, even these differences were replicated in LLM responses. Study 2 turned to a contextual feature of human rule application: under forced time delay, human samples rely more heavily on a rule's text than on other considerations such as a rule's purpose.. Our results revealed that some models (Gemini Pro and Claude 3) responded in a human-like manner to a prompt describing either forced delay or time pressure, while others (GPT-4o and Llama 3.2 90b) did not. We argue that the evidence gathered suggests that LLMs have mastery over the concept of rule, with implications for both legal decision making and philosophical inquiry.
Solving Satisfiability Modulo Counting Exactly with Probabilistic Circuits
Authors: Jinzhao Li, Nan Jiang, Yexiang Xue
Date: 2025-03-02 00:00:00
Tasks: Computational Efficiency

Satisfiability Modulo Counting (SMC) is a recently proposed general language to reason about problems integrating statistical and symbolic Artificial Intelligence. An SMC problem is an extended SAT problem in which the truth values of a few Boolean variables are determined by probabilistic inference. Approximate solvers may return solutions that violate constraints. Directly integrating available SAT solvers and probabilistic inference solvers gives exact solutions but results in slow performance because of many back-and-forth invocations of both solvers. We propose KOCO-SMC, an integrated exact SMC solver that efficiently tracks lower and upper bounds in the probabilistic inference process. It enhances computational efficiency by enabling early estimation of probabilistic inference using only partial variable assignments, whereas existing methods require full variable assignments. In the experiment, we compare KOCO-SMC with currently available approximate and exact SMC solvers on large-scale datasets and real-world applications. The proposed KOCO-SMC finds exact solutions with much less time.
Multi-Agent Reinforcement Learning with Long-Term Performance Objectives for Service Workforce Optimization
Authors: Kareem Eissa, Rayal Prasad, Sarith Mohan, Ankur Kapoor, Dorin Comaniciu, Vivek Singh
Date: 2025-03-03 00:00:00
Tasks: Benchmarking, Decision Making, Deep Reinforcement Learning, Multi-agent Reinforcement Learning, reinforcement-learning, Reinforcement Learning

Workforce optimization plays a crucial role in efficient organizational operations where decision-making may span several different administrative and time scales. For instance, dispatching personnel to immediate service requests while managing talent acquisition with various expertise sets up a highly dynamic optimization problem. Existing work focuses on specific sub-problems such as resource allocation and facility location, which are solved with heuristics like local-search and, more recently, deep reinforcement learning. However, these may not accurately represent real-world scenarios where such sub-problems are not fully independent. Our aim is to fill this gap by creating a simulator that models a unified workforce optimization problem. Specifically, we designed a modular simulator to support the development of reinforcement learning methods for integrated workforce optimization problems. We focus on three interdependent aspects: personnel dispatch, workforce management, and personnel positioning. The simulator provides configurable parameterizations to help explore dynamic scenarios with varying levels of stochasticity and non-stationarity. To facilitate benchmarking and ablation studies, we also include heuristic and RL baselines for the above mentioned aspects.
Hybrid Metaheuristic Vehicle Routing Problem for Security Dispatch Operations
Authors: Nguyen Gia Hien Vu, Yifan Tang, Rey Lim, G. Gary Wang
Date: 2025-03-03 00:00:00

This paper investigates the optimization of the Vehicle Routing Problem for Security Dispatch (VRPSD). VRPSD focuses on security and patrolling applications which involve challenging constraints including precise timing and strict time windows. We propose three algorithms based on different metaheuristics, which are Adaptive Large Neighborhood Search (ALNS), Tabu Search (TS), and Threshold Accepting (TA). The first algorithm combines single-phase ALNS with TA, the second employs a multiphase ALNS with TA, and the third integrates multiphase ALNS, TS, and TA. Experiments are conducted on an instance comprising 251 customer requests. The results demonstrate that the third algorithm, the hybrid multiphase ALNS-TS-TA algorithm, delivers the best performance. This approach simultaneously leverages the large-area search capabilities of ALNS for exploration and effectively escapes local optima when the multiphase ALNS is coupled with TS and TA. Furthermore, in our experiments, the hybrid multiphase ALNS-TS-TA algorithm is the only one that shows potential for improving results with increased computation time across all attempts.
Constrained multi-fidelity Bayesian optimization with automatic stop condition
Authors: Zahra Zanjani Foumani, Ramin Bostanabad
Date: 2025-03-03 00:00:00
Tasks: Bayesian Optimization

Bayesian optimization (BO) is increasingly employed in critical applications to find the optimal design with minimal cost. While BO is known for its sample efficiency, relying solely on costly high-fidelity data can still result in high costs. This is especially the case in constrained search spaces where BO must not only optimize but also ensure feasibility. A related issue in the BO literature is the lack of a systematic stopping criterion. To solve these challenges, we develop a constrained cost-aware multi-fidelity BO (CMFBO) framework whose goal is to minimize overall sampling costs by utilizing inexpensive low-fidelity sources while ensuring feasibility. In our case, the constraints can change across the data sources and may be even black-box functions. We also introduce a systematic stopping criterion that addresses the long-lasting issue associated with BO's convergence assessment. Our framework is publicly available on GitHub through the GP+ Python package and herein we validate it's efficacy on multiple benchmark problems.
Can Large Language Models Help Experimental Design for Causal Discovery?
Authors: Junyi Li, Yongqiang Chen, Chenxi Liu, Qianyi Cai, Tongliang Liu, Bo Han, Kun Zhang, Hui Xiong
Date: 2025-03-03 00:00:00
Tasks: Causal Discovery, Experimental Design, Large Language Model, scientific discovery, World Knowledge

Designing proper experiments and selecting optimal intervention targets is a longstanding problem in scientific or causal discovery. Identifying the underlying causal structure from observational data alone is inherently difficult. Obtaining interventional data, on the other hand, is crucial to causal discovery, yet it is usually expensive and time-consuming to gather sufficient interventional data to facilitate causal discovery. Previous approaches commonly utilize uncertainty or gradient signals to determine the intervention targets. However, numerical-based approaches may yield suboptimal results due to the inaccurate estimation of the guiding signals at the beginning when with limited interventional data. In this work, we investigate a different approach, whether we can leverage Large Language Models (LLMs) to assist with the intervention targeting in causal discovery by making use of the rich world knowledge about the experimental design in LLMs. Specifically, we present Large Language Model Guided Intervention Targeting (LeGIT) -- a robust framework that effectively incorporates LLMs to augment existing numerical approaches for the intervention targeting in causal discovery. Across 4 realistic benchmark scales, LeGIT demonstrates significant improvements and robustness over existing methods and even surpasses humans, which demonstrates the usefulness of LLMs in assisting with experimental design for scientific discovery.