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Feb 25

CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Prediction

Drug toxicity remains a major challenge in pharmaceutical development. Recent machine learning models have improved in silico toxicity prediction, but their reliance on annotated data and lack of interpretability limit their applicability. This limits their ability to capture organ-specific toxicities driven by complex biological mechanisms. Large language models (LLMs) offer a promising alternative through step-by-step reasoning and integration of textual data, yet prior approaches lack biological context and transparent rationale. To address this issue, we propose CoTox, a novel framework that integrates LLM with chain-of-thought (CoT) reasoning for multi-toxicity prediction. CoTox combines chemical structure data, biological pathways, and gene ontology (GO) terms to generate interpretable toxicity predictions through step-by-step reasoning. Using GPT-4o, we show that CoTox outperforms both traditional machine learning and deep learning model. We further examine its performance across various LLMs to identify where CoTox is most effective. Additionally, we find that representing chemical structures with IUPAC names, which are easier for LLMs to understand than SMILES, enhances the model's reasoning ability and improves predictive performance. To demonstrate its practical utility in drug development, we simulate the treatment of relevant cell types with drug and incorporated the resulting biological context into the CoTox framework. This approach allow CoTox to generate toxicity predictions aligned with physiological responses, as shown in case study. This result highlights the potential of LLM-based frameworks to improve interpretability and support early-stage drug safety assessment. The code and prompt used in this work are available at https://github.com/dmis-lab/CoTox.

  • 7 authors
·
Aug 5, 2025 2

Multimodal Multitask Representation Learning for Pathology Biobank Metadata Prediction

Metadata are general characteristics of the data in a well-curated and condensed format, and have been proven to be useful for decision making, knowledge discovery, and also heterogeneous data organization of biobank. Among all data types in the biobank, pathology is the key component of the biobank and also serves as the gold standard of diagnosis. To maximize the utility of biobank and allow the rapid progress of biomedical science, it is essential to organize the data with well-populated pathology metadata. However, manual annotation of such information is tedious and time-consuming. In the study, we develop a multimodal multitask learning framework to predict four major slide-level metadata of pathology images. The framework learns generalizable representations across tissue slides, pathology reports, and case-level structured data. We demonstrate improved performance across all four tasks with the proposed method compared to a single modal single task baseline on two test sets, one external test set from a distinct data source (TCGA) and one internal held-out test set (TTH). In the test sets, the performance improvements on the averaged area under receiver operating characteristic curve across the four tasks are 16.48% and 9.05% on TCGA and TTH, respectively. Such pathology metadata prediction system may be adopted to mitigate the effort of expert annotation and ultimately accelerate the data-driven research by better utilization of the pathology biobank.

  • 5 authors
·
Sep 17, 2019

AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale Clinical Tool Learning

Clinical calculators play a vital role in healthcare by offering accurate evidence-based predictions for various purposes such as prognosis. Nevertheless, their widespread utilization is frequently hindered by usability challenges, poor dissemination, and restricted functionality. Augmenting large language models with extensive collections of clinical calculators presents an opportunity to overcome these obstacles and improve workflow efficiency, but the scalability of the manual curation process poses a significant challenge. In response, we introduce AgentMD, a novel language agent capable of curating and applying clinical calculators across various clinical contexts. Using the published literature, AgentMD has automatically curated a collection of 2,164 diverse clinical calculators with executable functions and structured documentation, collectively named RiskCalcs. Manual evaluations show that RiskCalcs tools achieve an accuracy of over 80% on three quality metrics. At inference time, AgentMD can automatically select and apply the relevant RiskCalcs tools given any patient description. On the newly established RiskQA benchmark, AgentMD significantly outperforms chain-of-thought prompting with GPT-4 (87.7% vs. 40.9% in accuracy). Additionally, we also applied AgentMD to real-world clinical notes for analyzing both population-level and risk-level patient characteristics. In summary, our study illustrates the utility of language agents augmented with clinical calculators for healthcare analytics and patient care.

  • 11 authors
·
Feb 20, 2024

FantasyWorld: Geometry-Consistent World Modeling via Unified Video and 3D Prediction

High-quality 3D world models are pivotal for embodied intelligence and Artificial General Intelligence (AGI), underpinning applications such as AR/VR content creation and robotic navigation. Despite the established strong imaginative priors, current video foundation models lack explicit 3D grounding capabilities, thus being limited in both spatial consistency and their utility for downstream 3D reasoning tasks. In this work, we present FantasyWorld, a geometry-enhanced framework that augments frozen video foundation models with a trainable geometric branch, enabling joint modeling of video latents and an implicit 3D field in a single forward pass. Our approach introduces cross-branch supervision, where geometry cues guide video generation and video priors regularize 3D prediction, thus yielding consistent and generalizable 3D-aware video representations. Notably, the resulting latents from the geometric branch can potentially serve as versatile representations for downstream 3D tasks such as novel view synthesis and navigation, without requiring per-scene optimization or fine-tuning. Extensive experiments show that FantasyWorld effectively bridges video imagination and 3D perception, outperforming recent geometry-consistent baselines in multi-view coherence and style consistency. Ablation studies further confirm that these gains stem from the unified backbone and cross-branch information exchange.

  • 5 authors
·
Sep 25, 2025

Reasoning-Enhanced Large Language Models for Molecular Property Prediction

Molecular property prediction is crucial for drug discovery and materials science, yet existing approaches suffer from limited interpretability, poor cross-task generalization, and lack of chemical reasoning capabilities. Traditional machine learning models struggle with task transferability, while specialized molecular language models provide little insight into their decision-making processes. To address these limitations, we propose MPPReasoner, a multimodal large language model that incorporates chemical reasoning for molecular property prediction. Our approach, built upon Qwen2.5-VL-7B-Instruct, integrates molecular images with SMILES strings to enable comprehensive molecular understanding. We develop a two-stage training strategy: supervised fine-tuning (SFT) using 16,000 high-quality reasoning trajectories generated through expert knowledge and multiple teacher models, followed by Reinforcement Learning from Principle-Guided Rewards (RLPGR). RLPGR employs verifiable, rule-based rewards that systematically evaluate chemical principle application, molecular structure analysis, and logical consistency through computational verification. Extensive experiments across 8 datasets demonstrate significant performance improvements, with MPPReasoner outperforming the best baselines by 7.91\% and 4.53\% on in-distribution and out-of-distribution tasks respectively. MPPReasoner exhibits exceptional cross-task generalization and generates chemically sound reasoning paths that provide valuable insights into molecular property analysis, substantially enhancing both interpretability and practical utility for chemists. Code is available at https://anonymous.4open.science/r/MPPReasoner-12687.

  • 12 authors
·
Oct 11, 2025

DISPROTBENCH: A Disorder-Aware, Task-Rich Benchmark for Evaluating Protein Structure Prediction in Realistic Biological Contexts

Recent advances in protein structure prediction have achieved near-atomic accuracy for well-folded proteins. However, current benchmarks inadequately assess model performance in biologically challenging contexts, especially those involving intrinsically disordered regions (IDRs), limiting their utility in applications such as drug discovery, disease variant interpretation, and protein interface design. We introduce DisProtBench, a comprehensive benchmark for evaluating protein structure prediction models (PSPMs) under structural disorder and complex biological conditions. DisProtBench spans three key axes: (1) Data complexity, covering disordered regions, G protein-coupled receptor (GPCR) ligand pairs, and multimeric complexes; (2) Task diversity, benchmarking twelve leading PSPMs across structure-based tasks with unified classification, regression, and interface metrics; and (3) Interpretability, via the DisProtBench Portal, which provides precomputed 3D structures and visual error analyses. Our results reveal significant variability in model robustness under disorder, with low-confidence regions linked to functional prediction failures. Notably, global accuracy metrics often fail to predict task performance in disordered settings, emphasizing the need for function-aware evaluation. DisProtBench establishes a reproducible, extensible, and biologically grounded framework for assessing next-generation PSPMs in realistic biomedical scenarios.

  • 9 authors
·
Jun 18, 2025

Detecting and recognizing characters in Greek papyri with YOLOv8, DeiT and SimCLR

Purpose: The capacity to isolate and recognize individual characters from facsimile images of papyrus manuscripts yields rich opportunities for digital analysis. For this reason the `ICDAR 2023 Competition on Detection and Recognition of Greek Letters on Papyri' was held as part of the 17th International Conference on Document Analysis and Recognition. This paper discusses our submission to the competition. Methods: We used an ensemble of YOLOv8 models to detect and classify individual characters and employed two different approaches for refining the character predictions, including a transformer based DeiT approach and a ResNet-50 model trained on a large corpus of unlabelled data using SimCLR, a self-supervised learning method. Results: Our submission won the recognition challenge with a mAP of 42.2%, and was runner-up in the detection challenge with a mean average precision (mAP) of 51.4%. At the more relaxed intersection over union threshold of 0.5, we achieved the highest mean average precision and mean average recall results for both detection and classification. Conclusion: The results demonstrate the potential for these techniques for automated character recognition on historical manuscripts. We ran the prediction pipeline on more than 4,500 images from the Oxyrhynchus Papyri to illustrate the utility of our approach, and we release the results publicly in multiple formats.

  • 2 authors
·
Jan 23, 2024

Reflections from the 2024 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry

Here, we present the outcomes from the second Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry, which engaged participants across global hybrid locations, resulting in 34 team submissions. The submissions spanned seven key application areas and demonstrated the diverse utility of LLMs for applications in (1) molecular and material property prediction; (2) molecular and material design; (3) automation and novel interfaces; (4) scientific communication and education; (5) research data management and automation; (6) hypothesis generation and evaluation; and (7) knowledge extraction and reasoning from scientific literature. Each team submission is presented in a summary table with links to the code and as brief papers in the appendix. Beyond team results, we discuss the hackathon event and its hybrid format, which included physical hubs in Toronto, Montreal, San Francisco, Berlin, Lausanne, and Tokyo, alongside a global online hub to enable local and virtual collaboration. Overall, the event highlighted significant improvements in LLM capabilities since the previous year's hackathon, suggesting continued expansion of LLMs for applications in materials science and chemistry research. These outcomes demonstrate the dual utility of LLMs as both multipurpose models for diverse machine learning tasks and platforms for rapid prototyping custom applications in scientific research.

  • 141 authors
·
Nov 20, 2024 2

Tomayto, Tomahto. Beyond Token-level Answer Equivalence for Question Answering Evaluation

The predictions of question answering (QA)systems are typically evaluated against manually annotated finite sets of one or more answers. This leads to a coverage limitation that results in underestimating the true performance of systems, and is typically addressed by extending over exact match (EM) with pre-defined rules or with the token-level F1 measure. In this paper, we present the first systematic conceptual and data-driven analysis to examine the shortcomings of token-level equivalence measures. To this end, we define the asymmetric notion of answer equivalence (AE), accepting answers that are equivalent to or improve over the reference, and publish over 23k human judgments for candidates produced by multiple QA systems on SQuAD. Through a careful analysis of this data, we reveal and quantify several concrete limitations of the F1 measure, such as a false impression of graduality, or missing dependence on the question. Since collecting AE annotations for each evaluated model is expensive, we learn a BERT matching (BEM) measure to approximate this task. Being a simpler task than QA, we find BEM to provide significantly better AE approximations than F1, and to more accurately reflect the performance of systems. Finally, we demonstrate the practical utility of AE and BEM on the concrete application of minimal accurate prediction sets, reducing the number of required answers by up to x2.6.

  • 5 authors
·
Feb 15, 2022

Lucy-SKG: Learning to Play Rocket League Efficiently Using Deep Reinforcement Learning

A successful tactic that is followed by the scientific community for advancing AI is to treat games as problems, which has been proven to lead to various breakthroughs. We adapt this strategy in order to study Rocket League, a widely popular but rather under-explored 3D multiplayer video game with a distinct physics engine and complex dynamics that pose a significant challenge in developing efficient and high-performance game-playing agents. In this paper, we present Lucy-SKG, a Reinforcement Learning-based model that learned how to play Rocket League in a sample-efficient manner, outperforming by a notable margin the two highest-ranking bots in this game, namely Necto (2022 bot champion) and its successor Nexto, thus becoming a state-of-the-art agent. Our contributions include: a) the development of a reward analysis and visualization library, b) novel parameterizable reward shape functions that capture the utility of complex reward types via our proposed Kinesthetic Reward Combination (KRC) technique, and c) design of auxiliary neural architectures for training on reward prediction and state representation tasks in an on-policy fashion for enhanced efficiency in learning speed and performance. By performing thorough ablation studies for each component of Lucy-SKG, we showed their independent effectiveness in overall performance. In doing so, we demonstrate the prospects and challenges of using sample-efficient Reinforcement Learning techniques for controlling complex dynamical systems under competitive team-based multiplayer conditions.

  • 4 authors
·
May 25, 2023

Utility-Probability Duality of Neural Networks

It is typically understood that the training of modern neural networks is a process of fitting the probability distribution of desired output. However, recent paradoxical observations in a number of language generation tasks let one wonder if this canonical probability-based explanation can really account for the empirical success of deep learning. To resolve this issue, we propose an alternative utility-based explanation to the standard supervised learning procedure in deep learning. The basic idea is to interpret the learned neural network not as a probability model but as an ordinal utility function that encodes the preference revealed in training data. In this perspective, training of the neural network corresponds to a utility learning process. Specifically, we show that for all neural networks with softmax outputs, the SGD learning dynamic of maximum likelihood estimation (MLE) can be seen as an iteration process that optimizes the neural network toward an optimal utility function. This utility-based interpretation can explain several otherwise-paradoxical observations about the neural networks thus trained. Moreover, our utility-based theory also entails an equation that can transform the learned utility values back to a new kind of probability estimation with which probability-compatible decision rules enjoy dramatic (double-digits) performance improvements. These evidences collectively reveal a phenomenon of utility-probability duality in terms of what modern neural networks are (truly) modeling: We thought they are one thing (probabilities), until the unexplainable showed up; changing mindset and treating them as another thing (utility values) largely reconcile the theory, despite remaining subtleties regarding its original (probabilistic) identity.

  • 2 authors
·
May 24, 2023

Look Before you Leap: Estimating LLM Benchmark Scores from Descriptions

Progress in large language models is constrained by an evaluation bottleneck: build a benchmark, evaluate models and settings, then iterate. We therefore ask a simple question: can we forecast outcomes before running any experiments? We study text-only performance forecasting: estimating a model's score from a redacted task description and intended configuration, with no access to dataset instances. To support systematic study, we curate PRECOG, a corpus of redacted description-performance pairs spanning diverse tasks, domains, and metrics. Experiments show the task is challenging but feasible: models equipped with a retrieval module that excludes source papers achieve moderate prediction performance with well-calibrated uncertainty, reaching mean absolute error as low as 8.7 on the Accuracy subset at high-confidence thresholds. Our analysis indicates that stronger reasoning models engage in diverse, iterative querying, whereas current open-source models lag and often skip retrieval or gather evidence with limited diversity. We further test a zero-leakage setting, forecasting on newly released datasets or experiments before their papers are indexed, where GPT-5 with built-in web search still attains nontrivial prediction accuracy. Overall, our corpus and analyses offer an initial step toward open-ended anticipatory evaluation, supporting difficulty estimation and smarter experiment prioritization.

  • 4 authors
·
Sep 24, 2025

FutureX: An Advanced Live Benchmark for LLM Agents in Future Prediction

Future prediction is a complex task for LLM agents, requiring a high level of analytical thinking, information gathering, contextual understanding, and decision-making under uncertainty. Agents must not only gather and interpret vast amounts of dynamic information but also integrate diverse data sources, weigh uncertainties, and adapt predictions based on emerging trends, just as human experts do in fields like politics, economics, and finance. Despite its importance, no large-scale benchmark exists for evaluating agents on future prediction, largely due to challenges in handling real-time updates and retrieving timely, accurate answers. To address this, we introduce FutureX, a dynamic and live evaluation benchmark specifically designed for LLM agents performing future prediction tasks. FutureX is the largest and most diverse live benchmark for future prediction, supporting real-time daily updates and eliminating data contamination through an automated pipeline for question gathering and answer collection. We evaluate 25 LLM/agent models, including those with reasoning, search capabilities, and integration of external tools such as the open-source Deep Research Agent and closed-source Deep Research models. This comprehensive evaluation assesses agents' adaptive reasoning and performance in dynamic environments. Additionally, we provide in-depth analyses of agents' failure modes and performance pitfalls in future-oriented tasks, including the vulnerability to fake web pages and the temporal validity. Our goal is to establish a dynamic, contamination-free evaluation standard that drives the development of LLM agents capable of performing at the level of professional human analysts in complex reasoning and predictive thinking.

ByteDance-Seed ByteDance Seed
·
Aug 16, 2025 5

Large Language Model Prediction Capabilities: Evidence from a Real-World Forecasting Tournament

Accurately predicting the future would be an important milestone in the capabilities of artificial intelligence. However, research on the ability of large language models to provide probabilistic predictions about future events remains nascent. To empirically test this ability, we enrolled OpenAI's state-of-the-art large language model, GPT-4, in a three-month forecasting tournament hosted on the Metaculus platform. The tournament, running from July to October 2023, attracted 843 participants and covered diverse topics including Big Tech, U.S. politics, viral outbreaks, and the Ukraine conflict. Focusing on binary forecasts, we show that GPT-4's probabilistic forecasts are significantly less accurate than the median human-crowd forecasts. We find that GPT-4's forecasts did not significantly differ from the no-information forecasting strategy of assigning a 50% probability to every question. We explore a potential explanation, that GPT-4 might be predisposed to predict probabilities close to the midpoint of the scale, but our data do not support this hypothesis. Overall, we find that GPT-4 significantly underperforms in real-world predictive tasks compared to median human-crowd forecasts. A potential explanation for this underperformance is that in real-world forecasting tournaments, the true answers are genuinely unknown at the time of prediction; unlike in other benchmark tasks like professional exams or time series forecasting, where strong performance may at least partly be due to the answers being memorized from the training data. This makes real-world forecasting tournaments an ideal environment for testing the generalized reasoning and prediction capabilities of artificial intelligence going forward.

  • 2 authors
·
Oct 17, 2023

SpecDec++: Boosting Speculative Decoding via Adaptive Candidate Lengths

Speculative decoding reduces the inference latency of a target large language model via utilizing a smaller and faster draft model. Its performance depends on a hyperparameter K -- the candidate length, i.e., the number of candidate tokens for the target model to verify in each round. However, previous methods often use simple heuristics to choose K, which may result in sub-optimal performance. We study the choice of the candidate length K and formulate it as a Markov Decision Process. We theoretically show that the optimal policy of this Markov decision process takes the form of a threshold policy, i.e., the current speculation should stop and be verified when the probability of getting a rejection exceeds a threshold value. Motivated by this theory, we propose SpecDec++, an enhanced version of speculative decoding that adaptively determines the candidate length on the fly. We augment the draft model with a trained acceptance prediction head to predict the conditional acceptance probability of the candidate tokens. SpecDec++ will stop the current speculation when the predicted probability that at least one token gets rejected exceeds a threshold. We implement SpecDec++ and apply it to the llama-2-chat 7B & 70B model pair. Our adaptive method achieves a 2.04x speedup on the Alpaca dataset (an additional 7.2% improvement over the baseline speculative decoding). On the GSM8K and HumanEval datasets, our method achieves a 2.26x speedup (9.4% improvement) and 2.23x speedup (11.1% improvement), respectively.

  • 3 authors
·
May 30, 2024

Foresight -- Generative Pretrained Transformer (GPT) for Modelling of Patient Timelines using EHRs

Background: Electronic Health Records hold detailed longitudinal information about each patient's health status and general clinical history, a large portion of which is stored within the unstructured text. Existing approaches focus mostly on structured data and a subset of single-domain outcomes. We explore how temporal modelling of patients from free text and structured data, using deep generative transformers can be used to forecast a wide range of future disorders, substances, procedures or findings. Methods: We present Foresight, a novel transformer-based pipeline that uses named entity recognition and linking tools to convert document text into structured, coded concepts, followed by providing probabilistic forecasts for future medical events such as disorders, substances, procedures and findings. We processed the entire free-text portion from three different hospital datasets totalling 811336 patients covering both physical and mental health. Findings: On tests in two UK hospitals (King's College Hospital, South London and Maudsley) and the US MIMIC-III dataset precision@10 0.68, 0.76 and 0.88 was achieved for forecasting the next disorder in a patient timeline, while precision@10 of 0.80, 0.81 and 0.91 was achieved for forecasting the next biomedical concept. Foresight was also validated on 34 synthetic patient timelines by five clinicians and achieved relevancy of 97% for the top forecasted candidate disorder. As a generative model, it can forecast follow-on biomedical concepts for as many steps as required. Interpretation: Foresight is a general-purpose model for biomedical concept modelling that can be used for real-world risk forecasting, virtual trials and clinical research to study the progression of disorders, simulate interventions and counterfactuals, and educational purposes.

  • 12 authors
·
Dec 13, 2022

Measuring Reasoning Utility in LLMs via Conditional Entropy Reduction

Recent advancements in large language models (LLMs) often rely on generating intermediate reasoning steps to enhance accuracy. However, little work has examined how reasoning utility contributes to the final answer's correctness. Due to the stochastic nature of autoregressive generation, generating more context does not guarantee increased confidence in the answer. If we could predict, during generation, whether a reasoning step will be useful, we could stop early or prune ineffective steps, avoiding distractions in the final decision. We present an oracle study on MATH dataset, using Qwen2.5-32B and GPT-4o to generate reasoning chains, and then employing a separate model (Qwen3-8B) to quantify the utility of these chains for final accuracy. Specifically, we measure the model's uncertainty on the answer span Y at each reasoning step using conditional entropy (expected negative log-likelihood over the vocabulary) with context expanding step by step. Our results show a clear pattern: conditional entropy that decreases over steps is strongly associated with correct answers, whereas flat or increasing entropy often results in wrong answers. We also corroborate that incorrect reasoning paths tend to be longer than correct ones, suggesting that longer reasoning does not necessarily yield better outcomes. These findings serve as a foundation to inspire future work on designing efficient reasoning pipelines that detect and avoid unproductive reasoning early.

  • 1 authors
·
Aug 27, 2025

What's In My Human Feedback? Learning Interpretable Descriptions of Preference Data

Human feedback can alter language models in unpredictable and undesirable ways, as practitioners lack a clear understanding of what feedback data encodes. While prior work studies preferences over certain attributes (e.g., length or sycophancy), automatically extracting relevant features without pre-specifying hypotheses remains challenging. We introduce What's In My Human Feedback? (WIMHF), a method to explain feedback data using sparse autoencoders. WIMHF characterizes both (1) the preferences a dataset is capable of measuring and (2) the preferences that the annotators actually express. Across 7 datasets, WIMHF identifies a small number of human-interpretable features that account for the majority of the preference prediction signal achieved by black-box models. These features reveal a wide diversity in what humans prefer, and the role of dataset-level context: for example, users on Reddit prefer informality and jokes, while annotators in HH-RLHF and PRISM disprefer them. WIMHF also surfaces potentially unsafe preferences, such as that LMArena users tend to vote against refusals, often in favor of toxic content. The learned features enable effective data curation: re-labeling the harmful examples in Arena yields large safety gains (+37%) with no cost to general performance. They also allow fine-grained personalization: on the Community Alignment dataset, we learn annotator-specific weights over subjective features that improve preference prediction. WIMHF provides a human-centered analysis method for practitioners to better understand and use preference data.

  • 4 authors
·
Oct 30, 2025

Stock Price Prediction Using CNN and LSTM-Based Deep Learning Models

Designing robust and accurate predictive models for stock price prediction has been an active area of research for a long time. While on one side, the supporters of the efficient market hypothesis claim that it is impossible to forecast stock prices accurately, many researchers believe otherwise. There exist propositions in the literature that have demonstrated that if properly designed and optimized, predictive models can very accurately and reliably predict future values of stock prices. This paper presents a suite of deep learning based models for stock price prediction. We use the historical records of the NIFTY 50 index listed in the National Stock Exchange of India, during the period from December 29, 2008 to July 31, 2020, for training and testing the models. Our proposition includes two regression models built on convolutional neural networks and three long and short term memory network based predictive models. To forecast the open values of the NIFTY 50 index records, we adopted a multi step prediction technique with walk forward validation. In this approach, the open values of the NIFTY 50 index are predicted on a time horizon of one week, and once a week is over, the actual index values are included in the training set before the model is trained again, and the forecasts for the next week are made. We present detailed results on the forecasting accuracies for all our proposed models. The results show that while all the models are very accurate in forecasting the NIFTY 50 open values, the univariate encoder decoder convolutional LSTM with the previous two weeks data as the input is the most accurate model. On the other hand, a univariate CNN model with previous one week data as the input is found to be the fastest model in terms of its execution speed.

  • 2 authors
·
Oct 21, 2020

Student Answer Forecasting: Transformer-Driven Answer Choice Prediction for Language Learning

Intelligent Tutoring Systems (ITS) enhance personalized learning by predicting student answers to provide immediate and customized instruction. However, recent research has primarily focused on the correctness of the answer rather than the student's performance on specific answer choices, limiting insights into students' thought processes and potential misconceptions. To address this gap, we present MCQStudentBert, an answer forecasting model that leverages the capabilities of Large Language Models (LLMs) to integrate contextual understanding of students' answering history along with the text of the questions and answers. By predicting the specific answer choices students are likely to make, practitioners can easily extend the model to new answer choices or remove answer choices for the same multiple-choice question (MCQ) without retraining the model. In particular, we compare MLP, LSTM, BERT, and Mistral 7B architectures to generate embeddings from students' past interactions, which are then incorporated into a finetuned BERT's answer-forecasting mechanism. We apply our pipeline to a dataset of language learning MCQ, gathered from an ITS with over 10,000 students to explore the predictive accuracy of MCQStudentBert, which incorporates student interaction patterns, in comparison to correct answer prediction and traditional mastery-learning feature-based approaches. This work opens the door to more personalized content, modularization, and granular support.

  • 7 authors
·
May 30, 2024

Language Models (Mostly) Know What They Know

We study whether language models can evaluate the validity of their own claims and predict which questions they will be able to answer correctly. We first show that larger models are well-calibrated on diverse multiple choice and true/false questions when they are provided in the right format. Thus we can approach self-evaluation on open-ended sampling tasks by asking models to first propose answers, and then to evaluate the probability "P(True)" that their answers are correct. We find encouraging performance, calibration, and scaling for P(True) on a diverse array of tasks. Performance at self-evaluation further improves when we allow models to consider many of their own samples before predicting the validity of one specific possibility. Next, we investigate whether models can be trained to predict "P(IK)", the probability that "I know" the answer to a question, without reference to any particular proposed answer. Models perform well at predicting P(IK) and partially generalize across tasks, though they struggle with calibration of P(IK) on new tasks. The predicted P(IK) probabilities also increase appropriately in the presence of relevant source materials in the context, and in the presence of hints towards the solution of mathematical word problems. We hope these observations lay the groundwork for training more honest models, and for investigating how honesty generalizes to cases where models are trained on objectives other than the imitation of human writing.

  • 36 authors
·
Jul 11, 2022

Online Speculative Decoding

Speculative decoding is a pivotal technique to accelerate the inference of large language models (LLMs) by employing a smaller draft model to predict the target model's outputs. However, its efficacy can be limited due to the low predictive accuracy of the draft model, particularly when faced with diverse text inputs and a significant capability gap between the draft and target models. We introduce online speculative decoding (OSD) to address this challenge. The main idea is to continually update (multiple) draft model(s) on observed user query data using the abundant excess computational power in an LLM serving cluster. Given that LLM inference is memory-bounded, the surplus computational power in a typical LLM serving cluster can be repurposed for online retraining of draft models, thereby making the training cost-neutral. Since the query distribution of an LLM service is relatively simple, retraining on query distribution enables the draft model to more accurately predict the target model's outputs, particularly on data originating from query distributions. As the draft model evolves online, it aligns with the query distribution in real time, mitigating distribution shifts. We develop a prototype of online speculative decoding based on online knowledge distillation and evaluate it using both synthetic and real query data on several popular LLMs. The results show a substantial increase in the token acceptance rate by 0.1 to 0.65, which translates into 1.22x to 3.06x latency reduction.

  • 7 authors
·
Oct 11, 2023

Dichotomy of Control: Separating What You Can Control from What You Cannot

Future- or return-conditioned supervised learning is an emerging paradigm for offline reinforcement learning (RL), where the future outcome (i.e., return) associated with an observed action sequence is used as input to a policy trained to imitate those same actions. While return-conditioning is at the heart of popular algorithms such as decision transformer (DT), these methods tend to perform poorly in highly stochastic environments, where an occasional high return can arise from randomness in the environment rather than the actions themselves. Such situations can lead to a learned policy that is inconsistent with its conditioning inputs; i.e., using the policy to act in the environment, when conditioning on a specific desired return, leads to a distribution of real returns that is wildly different than desired. In this work, we propose the dichotomy of control (DoC), a future-conditioned supervised learning framework that separates mechanisms within a policy's control (actions) from those beyond a policy's control (environment stochasticity). We achieve this separation by conditioning the policy on a latent variable representation of the future, and designing a mutual information constraint that removes any information from the latent variable associated with randomness in the environment. Theoretically, we show that DoC yields policies that are consistent with their conditioning inputs, ensuring that conditioning a learned policy on a desired high-return future outcome will correctly induce high-return behavior. Empirically, we show that DoC is able to achieve significantly better performance than DT on environments that have highly stochastic rewards and transition

  • 4 authors
·
Oct 24, 2022

Preference Learning Algorithms Do Not Learn Preference Rankings

Preference learning algorithms (e.g., RLHF and DPO) are frequently used to steer LLMs to produce generations that are more preferred by humans, but our understanding of their inner workings is still limited. In this work, we study the conventional wisdom that preference learning trains models to assign higher likelihoods to more preferred outputs than less preferred outputs, measured via ranking accuracy. Surprisingly, we find that most state-of-the-art preference-tuned models achieve a ranking accuracy of less than 60% on common preference datasets. We furthermore derive the idealized ranking accuracy that a preference-tuned LLM would achieve if it optimized the DPO or RLHF objective perfectly. We demonstrate that existing models exhibit a significant alignment gap -- i.e., a gap between the observed and idealized ranking accuracies. We attribute this discrepancy to the DPO objective, which is empirically and theoretically ill-suited to fix even mild ranking errors in the reference model, and derive a simple and efficient formula for quantifying the difficulty of learning a given preference datapoint. Finally, we demonstrate that ranking accuracy strongly correlates with the empirically popular win rate metric when the model is close to the reference model used in the objective, shedding further light on the differences between on-policy (e.g., RLHF) and off-policy (e.g., DPO) preference learning algorithms.

  • 7 authors
·
May 29, 2024

Value-Incentivized Preference Optimization: A Unified Approach to Online and Offline RLHF

Reinforcement learning from human feedback (RLHF) has demonstrated great promise in aligning large language models (LLMs) with human preference. Depending on the availability of preference data, both online and offline RLHF are active areas of investigation. A key bottleneck is understanding how to incorporate uncertainty estimation in the reward function learned from the preference data for RLHF, regardless of how the preference data is collected. While the principles of optimism or pessimism under uncertainty are well-established in standard reinforcement learning (RL), a practically-implementable and theoretically-grounded form amenable to large language models is not yet available, as standard techniques for constructing confidence intervals become intractable under arbitrary policy parameterizations. In this paper, we introduce a unified approach to online and offline RLHF -- value-incentivized preference optimization (VPO) -- which regularizes the maximum-likelihood estimate of the reward function with the corresponding value function, modulated by a sign to indicate whether the optimism or pessimism is chosen. VPO also directly optimizes the policy with implicit reward modeling, and therefore shares a simpler RLHF pipeline similar to direct preference optimization. Theoretical guarantees of VPO are provided for both online and offline settings, matching the rates of their standard RL counterparts. Moreover, experiments on text summarization and dialog verify the practicality and effectiveness of VPO.

  • 9 authors
·
May 29, 2024

Cognitively Inspired Energy-Based World Models

One of the predominant methods for training world models is autoregressive prediction in the output space of the next element of a sequence. In Natural Language Processing (NLP), this takes the form of Large Language Models (LLMs) predicting the next token; in Computer Vision (CV), this takes the form of autoregressive models predicting the next frame/token/pixel. However, this approach differs from human cognition in several respects. First, human predictions about the future actively influence internal cognitive processes. Second, humans naturally evaluate the plausibility of predictions regarding future states. Based on this capability, and third, by assessing when predictions are sufficient, humans allocate a dynamic amount of time to make a prediction. This adaptive process is analogous to System 2 thinking in psychology. All these capabilities are fundamental to the success of humans at high-level reasoning and planning. Therefore, to address the limitations of traditional autoregressive models lacking these human-like capabilities, we introduce Energy-Based World Models (EBWM). EBWM involves training an Energy-Based Model (EBM) to predict the compatibility of a given context and a predicted future state. In doing so, EBWM enables models to achieve all three facets of human cognition described. Moreover, we developed a variant of the traditional autoregressive transformer tailored for Energy-Based models, termed the Energy-Based Transformer (EBT). Our results demonstrate that EBWM scales better with data and GPU Hours than traditional autoregressive transformers in CV, and that EBWM offers promising early scaling in NLP. Consequently, this approach offers an exciting path toward training future models capable of System 2 thinking and intelligently searching across state spaces.

  • 6 authors
·
Jun 13, 2024 7

TimeSeriesScientist: A General-Purpose AI Agent for Time Series Analysis

Time series forecasting is central to decision-making in domains as diverse as energy, finance, climate, and public health. In practice, forecasters face thousands of short, noisy series that vary in frequency, quality, and horizon, where the dominant cost lies not in model fitting, but in the labor-intensive preprocessing, validation, and ensembling required to obtain reliable predictions. Prevailing statistical and deep learning models are tailored to specific datasets or domains and generalize poorly. A general, domain-agnostic framework that minimizes human intervention is urgently in demand. In this paper, we introduce TimeSeriesScientist (TSci), the first LLM-driven agentic framework for general time series forecasting. The framework comprises four specialized agents: Curator performs LLM-guided diagnostics augmented by external tools that reason over data statistics to choose targeted preprocessing; Planner narrows the hypothesis space of model choice by leveraging multi-modal diagnostics and self-planning over the input; Forecaster performs model fitting and validation and, based on the results, adaptively selects the best model configuration as well as ensemble strategy to make final predictions; and Reporter synthesizes the whole process into a comprehensive, transparent report. With transparent natural-language rationales and comprehensive reports, TSci transforms the forecasting workflow into a white-box system that is both interpretable and extensible across tasks. Empirical results on eight established benchmarks demonstrate that TSci consistently outperforms both statistical and LLM-based baselines, reducing forecast error by an average of 10.4% and 38.2%, respectively. Moreover, TSci produces a clear and rigorous report that makes the forecasting workflow more transparent and interpretable.

  • 7 authors
·
Oct 1, 2025 2

PrefPalette: Personalized Preference Modeling with Latent Attributes

Personalizing AI systems requires understanding not just what users prefer, but the reasons that underlie those preferences - yet current preference models typically treat human judgment as a black box. We introduce PrefPalette, a framework that decomposes preferences into attribute dimensions and tailors its preference prediction to distinct social community values in a human-interpretable manner. PrefPalette operationalizes a cognitive science principle known as multi-attribute decision making in two ways: (1) a scalable counterfactual attribute synthesis step that involves generating synthetic training data to isolate for individual attribute effects (e.g., formality, humor, cultural values), and (2) attention-based preference modeling that learns how different social communities dynamically weight these attributes. This approach moves beyond aggregate preference modeling to capture the diverse evaluation frameworks that drive human judgment. When evaluated on 45 social communities from the online platform Reddit, PrefPalette outperforms GPT-4o by 46.6% in average prediction accuracy. Beyond raw predictive improvements, PrefPalette also shed light on intuitive, community-specific profiles: scholarly communities prioritize verbosity and stimulation, conflict-oriented communities value sarcasm and directness, and support-based communities emphasize empathy. By modeling the attribute-mediated structure of human judgment, PrefPalette delivers both superior preference modeling and transparent, interpretable insights, and serves as a first step toward more trustworthy, value-aware personalized applications.

  • 10 authors
·
Jul 17, 2025 1

Secrets of RLHF in Large Language Models Part II: Reward Modeling

Reinforcement Learning from Human Feedback (RLHF) has become a crucial technology for aligning language models with human values and intentions, enabling models to produce more helpful and harmless responses. Reward models are trained as proxies for human preferences to drive reinforcement learning optimization. While reward models are often considered central to achieving high performance, they face the following challenges in practical applications: (1) Incorrect and ambiguous preference pairs in the dataset may hinder the reward model from accurately capturing human intent. (2) Reward models trained on data from a specific distribution often struggle to generalize to examples outside that distribution and are not suitable for iterative RLHF training. In this report, we attempt to address these two issues. (1) From a data perspective, we propose a method to measure the strength of preferences within the data, based on a voting mechanism of multiple reward models. Experimental results confirm that data with varying preference strengths have different impacts on reward model performance. We introduce a series of novel methods to mitigate the influence of incorrect and ambiguous preferences in the dataset and fully leverage high-quality preference data. (2) From an algorithmic standpoint, we introduce contrastive learning to enhance the ability of reward models to distinguish between chosen and rejected responses, thereby improving model generalization. Furthermore, we employ meta-learning to enable the reward model to maintain the ability to differentiate subtle differences in out-of-distribution samples, and this approach can be utilized for iterative RLHF optimization.

  • 27 authors
·
Jan 11, 2024 4

LiveTradeBench: Seeking Real-World Alpha with Large Language Models

Large language models (LLMs) achieve strong performance across benchmarks--from knowledge quizzes and math reasoning to web-agent tasks--but these tests occur in static settings, lacking real dynamics and uncertainty. Consequently, they evaluate isolated reasoning or problem-solving rather than decision-making under uncertainty. To address this, we introduce LiveTradeBench, a live trading environment for evaluating LLM agents in realistic and evolving markets. LiveTradeBench follows three design principles: (i) Live data streaming of market prices and news, eliminating dependence on offline backtesting and preventing information leakage while capturing real-time uncertainty; (ii) a portfolio-management abstraction that extends control from single-asset actions to multi-asset allocation, integrating risk management and cross-asset reasoning; and (iii) multi-market evaluation across structurally distinct environments--U.S. stocks and Polymarket prediction markets--differing in volatility, liquidity, and information flow. At each step, an agent observes prices, news, and its portfolio, then outputs percentage allocations that balance risk and return. Using LiveTradeBench, we run 50-day live evaluations of 21 LLMs across families. Results show that (1) high LMArena scores do not imply superior trading outcomes; (2) models display distinct portfolio styles reflecting risk appetite and reasoning dynamics; and (3) some LLMs effectively leverage live signals to adapt decisions. These findings expose a gap between static evaluation and real-world competence, motivating benchmarks that test sequential decision making and consistency under live uncertainty.

  • 3 authors
·
Nov 5, 2025 2

Hybrid Preferences: Learning to Route Instances for Human vs. AI Feedback

Learning from human feedback has enabled the alignment of language models (LMs) with human preferences. However, directly collecting human preferences can be expensive, time-consuming, and can have high variance. An appealing alternative is to distill preferences from LMs as a source of synthetic annotations as they are more consistent, cheaper, and scale better than human annotation; however, they are also prone to biases and errors. In this work, we introduce a routing framework that combines inputs from humans and LMs to achieve better annotation quality, while reducing the total cost of human annotation. The crux of our approach is to identify preference instances that will benefit from human annotations. We formulate this as an optimization problem: given a preference dataset and an evaluation metric, we train a performance prediction model to predict a reward model's performance on an arbitrary combination of human and LM annotations and employ a routing strategy that selects a combination that maximizes predicted performance. We train the performance prediction model on MultiPref, a new preference dataset with 10K instances paired with human and LM labels. We show that the selected hybrid mixture of LM and direct human preferences using our routing framework achieves better reward model performance compared to using either one exclusively. We simulate selective human preference collection on three other datasets and show that our method generalizes well to all three. We analyze features from the routing model to identify characteristics of instances that can benefit from human feedback, e.g., prompts with a moderate safety concern or moderate intent complexity. We release the dataset, annotation platform, and source code used in this study to foster more efficient and accurate preference collection in the future.

  • 9 authors
·
Oct 24, 2024 2

Leveraging Domain Knowledge for Efficient Reward Modelling in RLHF: A Case-Study in E-Commerce Opinion Summarization

Reinforcement Learning from Human Feedback (RLHF) has become a dominating strategy in steering Language Models (LMs) towards human values/goals. The key to the strategy is employing a reward model ({varphi}) which can reflect a latent reward model with humans. While this strategy has proven to be effective, the training methodology requires a lot of human preference annotation (usually of the order of tens of thousands) to train {varphi}. Such large-scale preference annotations can be achievable if the reward model can be ubiquitously used. However, human values/goals are subjective and depend on the nature of the task. This poses a challenge in collecting diverse preferences for downstream applications. To address this, we propose a novel methodology to infuse domain knowledge into {varphi}, which reduces the size of preference annotation required. We validate our approach in E-Commerce Opinion Summarization, with a significant reduction in dataset size (just 940 samples) while advancing the state-of-the-art. Our contributions include a novel Reward Modelling technique, a new dataset (PromptOpinSumm) for Opinion Summarization, and a human preference dataset (OpinPref). The proposed methodology opens avenues for efficient RLHF, making it more adaptable to diverse applications with varying human values. We release the artifacts for usage under MIT License.

  • 11 authors
·
Feb 23, 2024

LABOR-LLM: Language-Based Occupational Representations with Large Language Models

Many empirical studies of labor market questions rely on estimating relatively simple predictive models using small, carefully constructed longitudinal survey datasets based on hand-engineered features. Large Language Models (LLMs), trained on massive datasets, encode vast quantities of world knowledge and can be used for the next job prediction problem. However, while an off-the-shelf LLM produces plausible career trajectories when prompted, the probability with which an LLM predicts a particular job transition conditional on career history will not, in general, align with the true conditional probability in a given population. Recently, Vafa et al. (2024) introduced a transformer-based "foundation model", CAREER, trained using a large, unrepresentative resume dataset, that predicts transitions between jobs; it further demonstrated how transfer learning techniques can be used to leverage the foundation model to build better predictive models of both transitions and wages that reflect conditional transition probabilities found in nationally representative survey datasets. This paper considers an alternative where the fine-tuning of the CAREER foundation model is replaced by fine-tuning LLMs. For the task of next job prediction, we demonstrate that models trained with our approach outperform several alternatives in terms of predictive performance on the survey data, including traditional econometric models, CAREER, and LLMs with in-context learning, even though the LLM can in principle predict job titles that are not allowed in the survey data. Further, we show that our fine-tuned LLM-based models' predictions are more representative of the career trajectories of various workforce subpopulations than off-the-shelf LLM models and CAREER. We conduct experiments and analyses that highlight the sources of the gains in the performance of our models for representative predictions.

  • 5 authors
·
Jun 25, 2024

Probing Preference Representations: A Multi-Dimensional Evaluation and Analysis Method for Reward Models

Previous methods evaluate reward models by testing them on a fixed pairwise ranking test set, but they typically do not provide performance information on each preference dimension. In this work, we address the evaluation challenge of reward models by probing preference representations. To confirm the effectiveness of this evaluation method, we construct a Multi-dimensional Reward Model Benchmark (MRMBench), a collection of six probing tasks for different preference dimensions. We design it to favor and encourage reward models that better capture preferences across different dimensions. Furthermore, we introduce an analysis method, inference-time probing, which identifies the dimensions used during the reward prediction and enhances its interpretability. Through extensive experiments, we find that MRMBench strongly correlates with the alignment performance of large language models (LLMs), making it a reliable reference for developing advanced reward models. Our analysis of MRMBench evaluation results reveals that reward models often struggle to capture preferences across multiple dimensions, highlighting the potential of multi-objective optimization in reward modeling. Additionally, our findings show that the proposed inference-time probing method offers a reliable metric for assessing the confidence of reward predictions, which ultimately improves the alignment of LLMs.

  • 13 authors
·
Nov 16, 2025

TruthTensor: Evaluating LLMs through Human Imitation on Prediction Market under Drift and Holistic Reasoning

Evaluating language models and AI agents remains fundamentally challenging because static benchmarks fail to capture real-world uncertainty, distribution shift, and the gap between isolated task accuracy and human-aligned decision-making under evolving conditions. This paper introduces TruthTensor, a novel, reproducible evaluation paradigm that measures reasoning models not only as prediction engines but as human-imitation systems operating in socially-grounded, high-entropy environments. Building on forward-looking, contamination-free tasks, our framework anchors evaluation to live prediction markets and combines probabilistic scoring to provide a holistic view of model behavior. TruthTensor complements traditional correctness metrics with drift-centric diagnostics and explicit robustness checks for reproducibility. It specify human vs. automated evaluation roles, annotation protocols, and statistical testing procedures to ensure interpretability and replicability of results. In experiments across 500+ real markets (political, economic, cultural, technological), TruthTensor demonstrates that models with similar forecast accuracy can diverge markedly in calibration, drift, and risk-sensitivity, underscoring the need to evaluate models along multiple axes (accuracy, calibration, narrative stability, cost, and resource efficiency). TruthTensor therefore operationalizes modern evaluation best practices, clear hypothesis framing, careful metric selection, transparent compute/cost reporting, human-in-the-loop validation, and open, versioned evaluation contracts, to produce defensible assessments of LLMs in real-world decision contexts. We publicly released TruthTensor at https://truthtensor.com.

  • 3 authors
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Jan 19

What-If Analysis of Large Language Models: Explore the Game World Using Proactive Thinking

Large language models (LLMs) excel at processing information reactively but lack the ability to systemically explore hypothetical futures. They cannot ask, "what if we take this action? how will it affect the final outcome" and forecast its potential consequences before acting. This critical gap limits their utility in dynamic, high-stakes scenarios like strategic planning, risk assessment, and real-time decision making. To bridge this gap, we propose WiA-LLM, a new paradigm that equips LLMs with proactive thinking capabilities. Our approach integrates What-If Analysis (WIA), a systematic approach for evaluating hypothetical scenarios by changing input variables. By leveraging environmental feedback via reinforcement learning, WiA-LLM moves beyond reactive thinking. It dynamically simulates the outcomes of each potential action, enabling the model to anticipate future states rather than merely react to the present conditions. We validate WiA-LLM in Honor of Kings (HoK), a complex multiplayer game environment characterized by rapid state changes and intricate interactions. The game's real-time state changes require precise multi-step consequence prediction, making it an ideal testbed for our approach. Experimental results demonstrate WiA-LLM achieves a remarkable 74.2% accuracy in forecasting game-state changes (up to two times gain over baselines). The model shows particularly significant gains in high-difficulty scenarios where accurate foresight is critical. To our knowledge, this is the first work to formally explore and integrate what-if analysis capabilities within LLMs. WiA-LLM represents a fundamental advance toward proactive reasoning in LLMs, providing a scalable framework for robust decision-making in dynamic environments with broad implications for strategic applications.

  • 8 authors
·
Sep 5, 2025