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Dec 12

TempME: Towards the Explainability of Temporal Graph Neural Networks via Motif Discovery

Temporal graphs are widely used to model dynamic systems with time-varying interactions. In real-world scenarios, the underlying mechanisms of generating future interactions in dynamic systems are typically governed by a set of recurring substructures within the graph, known as temporal motifs. Despite the success and prevalence of current temporal graph neural networks (TGNN), it remains uncertain which temporal motifs are recognized as the significant indications that trigger a certain prediction from the model, which is a critical challenge for advancing the explainability and trustworthiness of current TGNNs. To address this challenge, we propose a novel approach, called Temporal Motifs Explainer (TempME), which uncovers the most pivotal temporal motifs guiding the prediction of TGNNs. Derived from the information bottleneck principle, TempME extracts the most interaction-related motifs while minimizing the amount of contained information to preserve the sparsity and succinctness of the explanation. Events in the explanations generated by TempME are verified to be more spatiotemporally correlated than those of existing approaches, providing more understandable insights. Extensive experiments validate the superiority of TempME, with up to 8.21% increase in terms of explanation accuracy across six real-world datasets and up to 22.96% increase in boosting the prediction Average Precision of current TGNNs.

  • 2 authors
·
Oct 30, 2023

Feature Learning for Stock Price Prediction Shows a Significant Role of Analyst Rating

To reject the Efficient Market Hypothesis a set of 5 technical indicators and 23 fundamental indicators was identified to establish the possibility of generating excess returns on the stock market. Leveraging these data points and various classification machine learning models, trading data of the 505 equities on the US S&P500 over the past 20 years was analysed to develop a classifier effective for our cause. From any given day, we were able to predict the direction of change in price by 1% up to 10 days in the future. The predictions had an overall accuracy of 83.62% with a precision of 85% for buy signals and a recall of 100% for sell signals. Moreover, we grouped equities by their sector and repeated the experiment to see if grouping similar assets together positively effected the results but concluded that it showed no significant improvements in the performance rejecting the idea of sector-based analysis. Also, using feature ranking we could identify an even smaller set of 6 indicators while maintaining similar accuracies as that from the original 28 features and also uncovered the importance of buy, hold and sell analyst ratings as they came out to be the top contributors in the model. Finally, to evaluate the effectiveness of the classifier in real-life situations, it was backtested on FAANG equities using a modest trading strategy where it generated high returns of above 60% over the term of the testing dataset. In conclusion, our proposed methodology with the combination of purposefully picked features shows an improvement over the previous studies, and our model predicts the direction of 1% price changes on the 10th day with high confidence and with enough buffer to even build a robotic trading system.

  • 2 authors
·
Mar 12, 2021

A Disease-Centric Vision-Language Foundation Model for Precision Oncology in Kidney Cancer

The non-invasive assessment of increasingly incidentally discovered renal masses is a critical challenge in urologic oncology, where diagnostic uncertainty frequently leads to the overtreatment of benign or indolent tumors. In this study, we developed and validated RenalCLIP using a dataset of 27,866 CT scans from 8,809 patients across nine Chinese medical centers and the public TCIA cohort, a visual-language foundation model for characterization, diagnosis and prognosis of renal mass. The model was developed via a two-stage pre-training strategy that first enhances the image and text encoders with domain-specific knowledge before aligning them through a contrastive learning objective, to create robust representations for superior generalization and diagnostic precision. RenalCLIP achieved better performance and superior generalizability across 10 core tasks spanning the full clinical workflow of kidney cancer, including anatomical assessment, diagnostic classification, and survival prediction, compared with other state-of-the-art general-purpose CT foundation models. Especially, for complicated task like recurrence-free survival prediction in the TCIA cohort, RenalCLIP achieved a C-index of 0.726, representing a substantial improvement of approximately 20% over the leading baselines. Furthermore, RenalCLIP's pre-training imparted remarkable data efficiency; in the diagnostic classification task, it only needs 20% training data to achieve the peak performance of all baseline models even after they were fully fine-tuned on 100% of the data. Additionally, it achieved superior performance in report generation, image-text retrieval and zero-shot diagnosis tasks. Our findings establish that RenalCLIP provides a robust tool with the potential to enhance diagnostic accuracy, refine prognostic stratification, and personalize the management of patients with kidney cancer.

  • 20 authors
·
Aug 22

PD-Quant: Post-Training Quantization based on Prediction Difference Metric

Post-training quantization (PTQ) is a neural network compression technique that converts a full-precision model into a quantized model using lower-precision data types. Although it can help reduce the size and computational cost of deep neural networks, it can also introduce quantization noise and reduce prediction accuracy, especially in extremely low-bit settings. How to determine the appropriate quantization parameters (e.g., scaling factors and rounding of weights) is the main problem facing now. Existing methods attempt to determine these parameters by minimize the distance between features before and after quantization, but such an approach only considers local information and may not result in the most optimal quantization parameters. We analyze this issue and ropose PD-Quant, a method that addresses this limitation by considering global information. It determines the quantization parameters by using the information of differences between network prediction before and after quantization. In addition, PD-Quant can alleviate the overfitting problem in PTQ caused by the small number of calibration sets by adjusting the distribution of activations. Experiments show that PD-Quant leads to better quantization parameters and improves the prediction accuracy of quantized models, especially in low-bit settings. For example, PD-Quant pushes the accuracy of ResNet-18 up to 53.14% and RegNetX-600MF up to 40.67% in weight 2-bit activation 2-bit. The code is released at https://github.com/hustvl/PD-Quant.

  • 6 authors
·
Dec 14, 2022

DrugReasoner: Interpretable Drug Approval Prediction with a Reasoning-augmented Language Model

Drug discovery is a complex and resource-intensive process, making early prediction of approval outcomes critical for optimizing research investments. While classical machine learning and deep learning methods have shown promise in drug approval prediction, their limited interpretability constraints their impact. Here, we present DrugReasoner, a reasoning-based large language model (LLM) built on the LLaMA architecture and fine-tuned with group relative policy optimization (GRPO) to predict the likelihood of small-molecule approval. DrugReasoner integrates molecular descriptors with comparative reasoning against structurally similar approved and unapproved compounds, generating predictions alongside step-by-step rationales and confidence scores. DrugReasoner achieved robust performance with an AUC of 0.732 and an F1 score of 0.729 on the validation set and 0.725 and 0.718 on the test set, respectively. These results outperformed conventional baselines, including logistic regression, support vector machine, and k-nearest neighbors and had competitive performance relative to XGBoost. On an external independent dataset, DrugReasoner outperformed both baseline and the recently developed ChemAP model, achieving an AUC of 0.728 and an F1-score of 0.774, while maintaining high precision and balanced sensitivity, demonstrating robustness in real-world scenarios. These findings demonstrate that DrugReasoner not only delivers competitive predictive accuracy but also enhances transparency through its reasoning outputs, thereby addressing a key bottleneck in AI-assisted drug discovery. This study highlights the potential of reasoning-augmented LLMs as interpretable and effective tools for pharmaceutical decision-making.

  • 6 authors
·
Aug 25 2

DrivAerNet: A Parametric Car Dataset for Data-Driven Aerodynamic Design and Graph-Based Drag Prediction

This study introduces DrivAerNet, a large-scale high-fidelity CFD dataset of 3D industry-standard car shapes, and RegDGCNN, a dynamic graph convolutional neural network model, both aimed at aerodynamic car design through machine learning. DrivAerNet, with its 4000 detailed 3D car meshes using 0.5 million surface mesh faces and comprehensive aerodynamic performance data comprising of full 3D pressure, velocity fields, and wall-shear stresses, addresses the critical need for extensive datasets to train deep learning models in engineering applications. It is 60\% larger than the previously available largest public dataset of cars, and is the only open-source dataset that also models wheels and underbody. RegDGCNN leverages this large-scale dataset to provide high-precision drag estimates directly from 3D meshes, bypassing traditional limitations such as the need for 2D image rendering or Signed Distance Fields (SDF). By enabling fast drag estimation in seconds, RegDGCNN facilitates rapid aerodynamic assessments, offering a substantial leap towards integrating data-driven methods in automotive design. Together, DrivAerNet and RegDGCNN promise to accelerate the car design process and contribute to the development of more efficient vehicles. To lay the groundwork for future innovations in the field, the dataset and code used in our study are publicly accessible at https://github.com/Mohamedelrefaie/DrivAerNet

  • 3 authors
·
Mar 12, 2024

End-To-End Prediction of Knee Osteoarthritis Progression With Multi-Modal Transformers

Knee Osteoarthritis (KOA) is a highly prevalent chronic musculoskeletal condition with no currently available treatment. The manifestation of KOA is heterogeneous and prediction of its progression is challenging. Current literature suggests that the use of multi-modal data and advanced modeling methods, such as the ones based on Deep Learning, has promise in tackling this challenge. To date, however, the evidence on the efficacy of this approach is limited. In this study, we leveraged recent advances in Deep Learning and, using a Transformer approach, developed a unified framework for the multi-modal fusion of knee imaging data. Subsequently, we analyzed its performance across a range of scenarios by investigating multiple progression horizons -- from short-term to long-term. We report our findings using a large cohort (n=2421-3967) derived from the Osteoarthritis Initiative dataset. We show that structural knee MRI allows identifying radiographic KOA progressors on par with multi-modal fusion approaches, achieving an area under the ROC curve (ROC AUC) of 0.70-0.76 and Average Precision (AP) of 0.15-0.54 in 2-8 year horizons. Progression within 1 year was better predicted with a multi-modal method using X-ray, structural, and compositional MR images -- ROC AUC of 0.76(0.04), AP of 0.13(0.04) -- or via clinical data. Our follow-up analysis generally shows that prediction from the imaging data is more accurate for post-traumatic subjects, and we further investigate which subject subgroups may benefit the most. The present study provides novel insights into multi-modal imaging of KOA and brings a unified data-driven framework for studying its progression in an end-to-end manner, providing new tools for the design of more efficient clinical trials. The source code of our framework and the pre-trained models are made publicly available.

  • 4 authors
·
Jul 3, 2023

Smart Timing for Mining: A Deep Learning Framework for Bitcoin Hardware ROI Prediction

Bitcoin mining hardware acquisition requires strategic timing due to volatile markets, rapid technological obsolescence, and protocol-driven revenue cycles. Despite mining's evolution into a capital-intensive industry, there is little guidance on when to purchase new Application-Specific Integrated Circuit (ASIC) hardware, and no prior computational frameworks address this decision problem. We address this gap by formulating hardware acquisition as a time series classification task, predicting whether purchasing ASIC machines yields profitable (Return on Investment (ROI) >= 1), marginal (0 < ROI < 1), or unprofitable (ROI <= 0) returns within one year. We propose MineROI-Net, an open source Transformer-based architecture designed to capture multi-scale temporal patterns in mining profitability. Evaluated on data from 20 ASIC miners released between 2015 and 2024 across diverse market regimes, MineROI-Net outperforms LSTM-based and TSLANet baselines, achieving 83.7% accuracy and 83.1% macro F1-score. The model demonstrates strong economic relevance, achieving 93.6% precision in detecting unprofitable periods and 98.5% precision for profitable ones, while avoiding misclassification of profitable scenarios as unprofitable and vice versa. These results indicate that MineROI-Net offers a practical, data-driven tool for timing mining hardware acquisitions, potentially reducing financial risk in capital-intensive mining operations. The model is available through: https://github.com/AMAAI-Lab/MineROI-Net.

Uncertainty quantification for improving radiomic-based models in radiation pneumonitis prediction

Background and Objective: Radiation pneumonitis (RP) is a side effect of thoracic radiation therapy. Recently, Machine learning (ML) models enhanced with radiomic and dosiomic features provide better predictions by incorporating spatial information beyond DVHs. However, to improve the clinical decision process, we propose to use uncertainty quantification (UQ) to improve the confidence in model prediction. This study evaluates the impact of post hoc UQ methods on the discriminative performance and calibration of ML models for RP prediction. Methods: This study evaluated four ML models: logistic regression (LR), support vector machines (SVM), extreme gradient boosting (XGB), and random forest (RF), using radiomic, dosiomic, and dosimetric features to predict RP. We applied UQ methods, including Patt scaling, isotonic regression, Venn-ABERS predictor, and Conformal Prediction, to quantify uncertainty. Model performance was assessed through Area Under the Receiver Operating Characteristic curve (AUROC), Area Under the Precision-Recall Curve (AUPRC), and Adaptive Calibration Error (ACE) using Leave-One-Out Cross-Validation (LOO-CV). Results: UQ methods enhanced predictive performance, particularly for high-certainty predictions, while also improving calibration. Radiomic and dosiomic features increased model accuracy but introduced calibration challenges, especially for non-linear models like XGB and RF. Performance gains from UQ methods were most noticeable at higher certainty thresholds. Conclusion: Integrating UQ into ML models with radiomic and dosiomic features improves both predictive accuracy and calibration, supporting more reliable clinical decision-making. The findings emphasize the value of UQ methods in enhancing applicability of predictive models for RP in healthcare settings.

  • 3 authors
·
Dec 27, 2024

The Mira-Titan Universe IV. High Precision Power Spectrum Emulation

Modern cosmological surveys are delivering datasets characterized by unprecedented quality and statistical completeness; this trend is expected to continue into the future as new ground- and space-based surveys come online. In order to maximally extract cosmological information from these observations, matching theoretical predictions are needed. At low redshifts, the surveys probe the nonlinear regime of structure formation where cosmological simulations are the primary means of obtaining the required information. The computational cost of sufficiently resolved large-volume simulations makes it prohibitive to run very large ensembles. Nevertheless, precision emulators built on a tractable number of high-quality simulations can be used to build very fast prediction schemes to enable a variety of cosmological inference studies. We have recently introduced the Mira-Titan Universe simulation suite designed to construct emulators for a range of cosmological probes. The suite covers the standard six cosmological parameters {omega_m,omega_b, sigma_8, h, n_s, w_0} and, in addition, includes massive neutrinos and a dynamical dark energy equation of state, {omega_{nu}, w_a}. In this paper we present the final emulator for the matter power spectrum based on 111 cosmological simulations, each covering a (2.1Gpc)^3 volume and evolving 3200^3 particles. An additional set of 1776 lower-resolution simulations and TimeRG perturbation theory results for the power spectrum are used to cover scales straddling the linear to mildly nonlinear regimes. The emulator provides predictions at the two to three percent level of accuracy over a wide range of cosmological parameters and is publicly released as part of this paper.

  • 9 authors
·
Jul 25, 2022

OncoReason: Structuring Clinical Reasoning in LLMs for Robust and Interpretable Survival Prediction

Predicting cancer treatment outcomes requires models that are both accurate and interpretable, particularly in the presence of heterogeneous clinical data. While large language models (LLMs) have shown strong performance in biomedical NLP, they often lack structured reasoning capabilities critical for high-stakes decision support. We present a unified, multi-task learning framework that aligns autoregressive LLMs with clinical reasoning for outcome prediction on the MSK-CHORD dataset. Our models are trained to jointly perform binary survival classification, continuous survival time regression, and natural language rationale generation. We evaluate three alignment strategies: (1) standard supervised fine-tuning (SFT), (2) SFT with Chain-of-Thought (CoT) prompting to elicit step-by-step reasoning, and (3) Group Relative Policy Optimization (GRPO), a reinforcement learning method that aligns model outputs to expert-derived reasoning trajectories. Experiments with LLaMa3-8B and Med42-8B backbones demonstrate that CoT prompting improves F1 by +6.0 and reduces MAE by 12%, while GRPO achieves state-of-the-art interpretability and predictive performance across BLEU, ROUGE, and BERTScore. We further show that existing biomedical LLMs often fail to produce valid reasoning traces due to architectural constraints. Our findings underscore the importance of reasoning-aware alignment in multi-task clinical modeling and set a new benchmark for interpretable, trustworthy LLMs in precision oncology.

  • 4 authors
·
Oct 20

Gene-DML: Dual-Pathway Multi-Level Discrimination for Gene Expression Prediction from Histopathology Images

Accurately predicting gene expression from histopathology images offers a scalable and non-invasive approach to molecular profiling, with significant implications for precision medicine and computational pathology. However, existing methods often underutilize the cross-modal representation alignment between histopathology images and gene expression profiles across multiple representational levels, thereby limiting their prediction performance. To address this, we propose Gene-DML, a unified framework that structures latent space through Dual-pathway Multi-Level discrimination to enhance correspondence between morphological and transcriptional modalities. The multi-scale instance-level discrimination pathway aligns hierarchical histopathology representations extracted at local, neighbor, and global levels with gene expression profiles, capturing scale-aware morphological-transcriptional relationships. In parallel, the cross-level instance-group discrimination pathway enforces structural consistency between individual (image/gene) instances and modality-crossed (gene/image, respectively) groups, strengthening the alignment across modalities. By jointly modelling fine-grained and structural-level discrimination, Gene-DML is able to learn robust cross-modal representations, enhancing both predictive accuracy and generalization across diverse biological contexts. Extensive experiments on public spatial transcriptomics datasets demonstrate that Gene-DML achieves state-of-the-art performance in gene expression prediction. The code and checkpoints will be released soon.

  • 4 authors
·
Jul 19

Can Transformers Do Enumerative Geometry?

How can Transformers model and learn enumerative geometry? What is a robust procedure for using Transformers in abductive knowledge discovery within a mathematician-machine collaboration? In this work, we introduce a Transformer-based approach to computational enumerative geometry, specifically targeting the computation of psi-class intersection numbers on the moduli space of curves. By reformulating the problem as a continuous optimization task, we compute intersection numbers across a wide value range from 10^{-45} to 10^{45}. To capture the recursive nature inherent in these intersection numbers, we propose the Dynamic Range Activator (DRA), a new activation function that enhances the Transformer's ability to model recursive patterns and handle severe heteroscedasticity. Given precision requirements for computing the intersections, we quantify the uncertainty of the predictions using Conformal Prediction with a dynamic sliding window adaptive to the partitions of equivalent number of marked points. To the best of our knowledge, there has been no prior work on modeling recursive functions with such a high-variance and factorial growth. Beyond simply computing intersection numbers, we explore the enumerative "world-model" of Transformers. Our interpretability analysis reveals that the network is implicitly modeling the Virasoro constraints in a purely data-driven manner. Moreover, through abductive hypothesis testing, probing, and causal inference, we uncover evidence of an emergent internal representation of the the large-genus asymptotic of psi-class intersection numbers. These findings suggest that the network internalizes the parameters of the asymptotic closed-form and the polynomiality phenomenon of psi-class intersection numbers in a non-linear manner.

  • 3 authors
·
Aug 27, 2024

Grape detection, segmentation and tracking using deep neural networks and three-dimensional association

Agricultural applications such as yield prediction, precision agriculture and automated harvesting need systems able to infer the crop state from low-cost sensing devices. Proximal sensing using affordable cameras combined with computer vision has seen a promising alternative, strengthened after the advent of convolutional neural networks (CNNs) as an alternative for challenging pattern recognition problems in natural images. Considering fruit growing monitoring and automation, a fundamental problem is the detection, segmentation and counting of individual fruits in orchards. Here we show that for wine grapes, a crop presenting large variability in shape, color, size and compactness, grape clusters can be successfully detected, segmented and tracked using state-of-the-art CNNs. In a test set containing 408 grape clusters from images taken on a trellis-system based vineyard, we have reached an F 1 -score up to 0.91 for instance segmentation, a fine separation of each cluster from other structures in the image that allows a more accurate assessment of fruit size and shape. We have also shown as clusters can be identified and tracked along video sequences recording orchard rows. We also present a public dataset containing grape clusters properly annotated in 300 images and a novel annotation methodology for segmentation of complex objects in natural images. The presented pipeline for annotation, training, evaluation and tracking of agricultural patterns in images can be replicated for different crops and production systems. It can be employed in the development of sensing components for several agricultural and environmental applications.

  • 4 authors
·
Jul 26, 2019

UniSite: The First Cross-Structure Dataset and Learning Framework for End-to-End Ligand Binding Site Detection

The detection of ligand binding sites for proteins is a fundamental step in Structure-Based Drug Design. Despite notable advances in recent years, existing methods, datasets, and evaluation metrics are confronted with several key challenges: (1) current datasets and methods are centered on individual protein-ligand complexes and neglect that diverse binding sites may exist across multiple complexes of the same protein, introducing significant statistical bias; (2) ligand binding site detection is typically modeled as a discontinuous workflow, employing binary segmentation and subsequent clustering algorithms; (3) traditional evaluation metrics do not adequately reflect the actual performance of different binding site prediction methods. To address these issues, we first introduce UniSite-DS, the first UniProt (Unique Protein)-centric ligand binding site dataset, which contains 4.81 times more multi-site data and 2.08 times more overall data compared to the previously most widely used datasets. We then propose UniSite, the first end-to-end ligand binding site detection framework supervised by set prediction loss with bijective matching. In addition, we introduce Average Precision based on Intersection over Union (IoU) as a more accurate evaluation metric for ligand binding site prediction. Extensive experiments on UniSite-DS and several representative benchmark datasets demonstrate that IoU-based Average Precision provides a more accurate reflection of prediction quality, and that UniSite outperforms current state-of-the-art methods in ligand binding site detection. The dataset and codes will be made publicly available at https://github.com/quanlin-wu/unisite.

  • 4 authors
·
Jun 3

pyhgf: A neural network library for predictive coding

Bayesian models of cognition have gained considerable traction in computational neuroscience and psychiatry. Their scopes are now expected to expand rapidly to artificial intelligence, providing general inference frameworks to support embodied, adaptable, and energy-efficient autonomous agents. A central theory in this domain is predictive coding, which posits that learning and behaviour are driven by hierarchical probabilistic inferences about the causes of sensory inputs. Biological realism constrains these networks to rely on simple local computations in the form of precision-weighted predictions and prediction errors. This can make this framework highly efficient, but its implementation comes with unique challenges on the software development side. Embedding such models in standard neural network libraries often becomes limiting, as these libraries' compilation and differentiation backends can force a conceptual separation between optimization algorithms and the systems being optimized. This critically departs from other biological principles such as self-monitoring, self-organisation, cellular growth and functional plasticity. In this paper, we introduce pyhgf: a Python package backed by JAX and Rust for creating, manipulating and sampling dynamic networks for predictive coding. We improve over other frameworks by enclosing the network components as transparent, modular and malleable variables in the message-passing steps. The resulting graphs can implement arbitrary computational complexities as beliefs propagation. But the transparency of core variables can also translate into inference processes that leverage self-organisation principles, and express structure learning, meta-learning or causal discovery as the consequence of network structural adaptation to surprising inputs. The code, tutorials and documentation are hosted at: https://github.com/ilabcode/pyhgf.

  • 7 authors
·
Oct 11, 2024

CogDPM: Diffusion Probabilistic Models via Cognitive Predictive Coding

Predictive Coding (PC) is a theoretical framework in cognitive science suggesting that the human brain processes cognition through spatiotemporal prediction of the visual world. Existing studies have developed spatiotemporal prediction neural networks based on the PC theory, emulating its two core mechanisms: Correcting predictions from residuals and hierarchical learning. However, these models do not show the enhancement of prediction skills on real-world forecasting tasks and ignore the Precision Weighting mechanism of PC theory. The precision weighting mechanism posits that the brain allocates more attention to signals with lower precision, contributing to the cognitive ability of human brains. This work introduces the Cognitive Diffusion Probabilistic Models (CogDPM), which demonstrate the connection between diffusion probabilistic models and PC theory. CogDPM features a precision estimation method based on the hierarchical sampling capabilities of diffusion models and weight the guidance with precision weights estimated by the inherent property of diffusion models. We experimentally show that the precision weights effectively estimate the data predictability. We apply CogDPM to real-world prediction tasks using the United Kindom precipitation and ERA surface wind datasets. Our results demonstrate that CogDPM outperforms both existing domain-specific operational models and general deep prediction models by providing more proficient forecasting.

  • 5 authors
·
May 3, 2024

Text4Seg++: Advancing Image Segmentation via Generative Language Modeling

Multimodal Large Language Models (MLLMs) have shown exceptional capabilities in vision-language tasks. However, effectively integrating image segmentation into these models remains a significant challenge. In this work, we propose a novel text-as-mask paradigm that casts image segmentation as a text generation problem, eliminating the need for additional decoders and significantly simplifying the segmentation process. Our key innovation is semantic descriptors, a new textual representation of segmentation masks where each image patch is mapped to its corresponding text label. We first introduce image-wise semantic descriptors, a patch-aligned textual representation of segmentation masks that integrates naturally into the language modeling pipeline. To enhance efficiency, we introduce the Row-wise Run-Length Encoding (R-RLE), which compresses redundant text sequences, reducing the length of semantic descriptors by 74% and accelerating inference by 3times, without compromising performance. Building upon this, our initial framework Text4Seg achieves strong segmentation performance across a wide range of vision tasks. To further improve granularity and compactness, we propose box-wise semantic descriptors, which localizes regions of interest using bounding boxes and represents region masks via structured mask tokens called semantic bricks. This leads to our refined model, Text4Seg++, which formulates segmentation as a next-brick prediction task, combining precision, scalability, and generative efficiency. Comprehensive experiments on natural and remote sensing datasets show that Text4Seg++ consistently outperforms state-of-the-art models across diverse benchmarks without any task-specific fine-tuning, while remaining compatible with existing MLLM backbones. Our work highlights the effectiveness, scalability, and generalizability of text-driven image segmentation within the MLLM framework.

  • 9 authors
·
Sep 8

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

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

Modeling of learning curves with applications to pos tagging

An algorithm to estimate the evolution of learning curves on the whole of a training data base, based on the results obtained from a portion and using a functional strategy, is introduced. We approximate iteratively the sought value at the desired time, independently of the learning technique used and once a point in the process, called prediction level, has been passed. The proposal proves to be formally correct with respect to our working hypotheses and includes a reliable proximity condition. This allows the user to fix a convergence threshold with respect to the accuracy finally achievable, which extends the concept of stopping criterion and seems to be effective even in the presence of distorting observations. Our aim is to evaluate the training effort, supporting decision making in order to reduce the need for both human and computational resources during the learning process. The proposal is of interest in at least three operational procedures. The first is the anticipation of accuracy gain, with the purpose of measuring how much work is needed to achieve a certain degree of performance. The second relates the comparison of efficiency between systems at training time, with the objective of completing this task only for the one that best suits our requirements. The prediction of accuracy is also a valuable item of information for customizing systems, since we can estimate in advance the impact of settings on both the performance and the development costs. Using the generation of part-of-speech taggers as an example application, the experimental results are consistent with our expectations.

  • 3 authors
·
Feb 4, 2024

Sparse Linear Regression is Easy on Random Supports

Sparse linear regression is one of the most basic questions in machine learning and statistics. Here, we are given as input a design matrix X in R^{N times d} and measurements or labels {y} in R^N where {y} = {X} {w}^* + {xi}, and {xi} is the noise in the measurements. Importantly, we have the additional constraint that the unknown signal vector {w}^* is sparse: it has k non-zero entries where k is much smaller than the ambient dimension. Our goal is to output a prediction vector {w} that has small prediction error: 1{N}cdot |{X} {w}^* - {X} {w}|^2_2. Information-theoretically, we know what is best possible in terms of measurements: under most natural noise distributions, we can get prediction error at most epsilon with roughly N = O(k log d/epsilon) samples. Computationally, this currently needs d^{Omega(k)} run-time. Alternately, with N = O(d), we can get polynomial-time. Thus, there is an exponential gap (in the dependence on d) between the two and we do not know if it is possible to get d^{o(k)} run-time and o(d) samples. We give the first generic positive result for worst-case design matrices {X}: For any {X}, we show that if the support of {w}^* is chosen at random, we can get prediction error epsilon with N = poly(k, log d, 1/epsilon) samples and run-time poly(d,N). This run-time holds for any design matrix {X} with condition number up to 2^{poly(d)}. Previously, such results were known for worst-case {w}^*, but only for random design matrices from well-behaved families, matrices that have a very low condition number (poly(log d); e.g., as studied in compressed sensing), or those with special structural properties.

  • 3 authors
·
Nov 8

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

PAC Prediction Sets for Large Language Models of Code

Prediction sets have recently been shown to be a promising strategy for quantifying the uncertainty of deep neural networks in a way that provides theoretical guarantees. However, existing techniques have largely targeted settings where the space of labels is simple, so prediction sets can be arbitrary subsets of labels. For structured prediction problems where the space of labels is exponential in size, even prediction sets containing a small fraction of all labels can be exponentially large. In the context of code generation, we propose a solution that considers a restricted set of prediction sets that can compactly be represented as partial programs, which are programs with portions replaced with holes. Given a trained code generation model, our algorithm leverages a programming language's abstract syntax tree to generate a set of programs such that the correct program is in the set with high-confidence. Valuable applications of our algorithm include a Codex-style code generator with holes in uncertain parts of the generated code, which provides a partial program with theoretical guarantees. We evaluate our approach on PICARD (a T5 model for SQL semantic parsing) and Codex (a GPT model for over a dozen programming languages, including Python), demonstrating that our approach generates compact PAC prediction sets. This is the first research contribution that generates PAC prediction sets for generative code models.

  • 3 authors
·
Feb 17, 2023

Balancing Computational Efficiency and Forecast Error in Machine Learning-based Time-Series Forecasting: Insights from Live Experiments on Meteorological Nowcasting

Machine learning for time-series forecasting remains a key area of research. Despite successful application of many machine learning techniques, relating computational efficiency to forecast error remains an under-explored domain. This paper addresses this topic through a series of real-time experiments to quantify the relationship between computational cost and forecast error using meteorological nowcasting as an example use-case. We employ a variety of popular regression techniques (XGBoost, FC-MLP, Transformer, and LSTM) for multi-horizon, short-term forecasting of three variables (temperature, wind speed, and cloud cover) for multiple locations. During a 5-day live experiment, 4000 data sources were streamed for training and inferencing 144 models per hour. These models were parameterized to explore forecast error for two computational cost minimization methods: a novel auto-adaptive data reduction technique (Variance Horizon) and a performance-based concept drift-detection mechanism. Forecast error of all model variations were benchmarked in real-time against a state-of-the-art numerical weather prediction model. Performance was assessed using classical and novel evaluation metrics. Results indicate that using the Variance Horizon reduced computational usage by more than 50\%, while increasing between 0-15\% in error. Meanwhile, performance-based retraining reduced computational usage by up to 90\% while also improving forecast error by up to 10\%. Finally, the combination of both the Variance Horizon and performance-based retraining outperformed other model configurations by up to 99.7\% when considering error normalized to computational usage.

  • 5 authors
·
Sep 26, 2023

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

Give Me FP32 or Give Me Death? Challenges and Solutions for Reproducible Reasoning

Large Language Models (LLMs) are now integral across various domains and have demonstrated impressive performance. Progress, however, rests on the premise that benchmark scores are both accurate and reproducible. We demonstrate that the reproducibility of LLM performance is fragile: changing system configuration such as evaluation batch size, GPU count, and GPU version can introduce significant difference in the generated responses. This issue is especially pronounced in reasoning models, where minor rounding differences in early tokens can cascade into divergent chains of thought, ultimately affecting accuracy. For instance, under bfloat16 precision with greedy decoding, a reasoning model like DeepSeek-R1-Distill-Qwen-7B can exhibit up to 9% variation in accuracy and 9,000 tokens difference in response length due to differences in GPU count, type, and evaluation batch size. We trace the root cause of this variability to the non-associative nature of floating-point arithmetic under limited numerical precision. This work presents the first systematic investigation into how numerical precision affects reproducibility in LLM inference. Through carefully controlled experiments across various hardware, software, and precision settings, we quantify when and how model outputs diverge. Our analysis reveals that floating-point precision -- while critical for reproducibility -- is often neglected in evaluation practices. Inspired by this, we develop a lightweight inference pipeline, dubbed LayerCast, that stores weights in 16-bit precision but performs all computations in FP32, balancing memory efficiency with numerical stability. Code is available at https://github.com/nanomaoli/llm_reproducibility.

  • 10 authors
·
Jun 11 2

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

Generalized Correctness Models: Learning Calibrated and Model-Agnostic Correctness Predictors from Historical Patterns

Generating accurate and calibrated confidence estimates is critical for deploying LLMs in high-stakes or user-facing applications, and remains an open challenge. Prior research has often framed confidence as a problem of eliciting a model's "self-knowledge", i.e., the ability of an LLM to judge whether its own answers are correct; this approach implicitly assumes that there is some privileged information about the answer's correctness that is accessible to the model itself. However, our experiments reveal that an LLM attempting to predict the correctness of its own outputs generally performs no better than an unrelated LLM. Moreover, we hypothesize that a key factor in building a "Correctness Model" (CM) is exposure to a target model's historical predictions. We propose multiple methods to inject this historical correctness information, creating a Generalized Correctness Model (GCM). We first show that GCMs can be trained on the correctness data from many LLMs and learn patterns for correctness prediction applicable across datasets and models. We then use CMs as a lens for studying the source of correctness prediction ability and its generalization, systematically controlling their training data and finding that answer phrasing is a strong predictor for correctness. We further explore alternative methods of injecting history without training an LLM, finding that including history as in-context examples can help improve correctness prediction, and post-hoc calibration can provide complementary reductions in calibration error. We evaluate GCMs based on Qwen3-8B across 5 model families and the MMLU and TriviaQA datasets, as well as on a downstream selective prediction task, finding that reliable LLM confidence estimation is a generalizable and model-agnostic skill learned by systematically encoding correctness history rather than a model-specific skill reliant on self-introspection.

  • 5 authors
·
Sep 29 2

On the Existence of Simpler Machine Learning Models

It is almost always easier to find an accurate-but-complex model than an accurate-yet-simple model. Finding optimal, sparse, accurate models of various forms (linear models with integer coefficients, decision sets, rule lists, decision trees) is generally NP-hard. We often do not know whether the search for a simpler model will be worthwhile, and thus we do not go to the trouble of searching for one. In this work, we ask an important practical question: can accurate-yet-simple models be proven to exist, or shown likely to exist, before explicitly searching for them? We hypothesize that there is an important reason that simple-yet-accurate models often do exist. This hypothesis is that the size of the Rashomon set is often large, where the Rashomon set is the set of almost-equally-accurate models from a function class. If the Rashomon set is large, it contains numerous accurate models, and perhaps at least one of them is the simple model we desire. In this work, we formally present the Rashomon ratio as a new gauge of simplicity for a learning problem, depending on a function class and a data set. The Rashomon ratio is the ratio of the volume of the set of accurate models to the volume of the hypothesis space, and it is different from standard complexity measures from statistical learning theory. Insight from studying the Rashomon ratio provides an easy way to check whether a simpler model might exist for a problem before finding it, namely whether several different machine learning methods achieve similar performance on the data. In that sense, the Rashomon ratio is a powerful tool for understanding why and when an accurate-yet-simple model might exist. If, as we hypothesize in this work, many real-world data sets admit large Rashomon sets, the implications are vast: it means that simple or interpretable models may often be used for high-stakes decisions without losing accuracy.

  • 3 authors
·
Aug 5, 2019

Why Has Predicting Downstream Capabilities of Frontier AI Models with Scale Remained Elusive?

Predictable behavior from scaling advanced AI systems is an extremely desirable property. Although a well-established literature exists on how pretraining performance scales, the literature on how particular downstream capabilities scale is significantly muddier. In this work, we take a step back and ask: why has predicting specific downstream capabilities with scale remained elusive? While many factors are certainly responsible, we identify a new factor that makes modeling scaling behavior on widely used multiple-choice question-answering benchmarks challenging. Using five model families and twelve well-established multiple-choice benchmarks, we show that downstream performance is computed from negative log likelihoods via a sequence of transformations that progressively degrade the statistical relationship between performance and scale. We then reveal the mechanism causing this degradation: downstream metrics require comparing the correct choice against a small number of specific incorrect choices, meaning accurately predicting downstream capabilities requires predicting not just how probability mass concentrates on the correct choice with scale, but also how probability mass fluctuates on specific incorrect choices with scale. We empirically study how probability mass on the correct choice co-varies with probability mass on incorrect choices with increasing compute, suggesting that scaling laws for incorrect choices might be achievable. Our work also explains why pretraining scaling laws are commonly regarded as more predictable than downstream capabilities and contributes towards establishing scaling-predictable evaluations of frontier AI models.

  • 9 authors
·
Jun 6, 2024

Low-Precision Training of Large Language Models: Methods, Challenges, and Opportunities

Large language models (LLMs) have achieved impressive performance across various domains. However, the substantial hardware resources required for their training present a significant barrier to efficiency and scalability. To mitigate this challenge, low-precision training techniques have been widely adopted, leading to notable advancements in training efficiency. Despite these gains, low-precision training involves several componentsx2013such as weights, activations, and gradientsx2013each of which can be represented in different numerical formats. The resulting diversity has created a fragmented landscape in low-precision training research, making it difficult for researchers to gain a unified overview of the field. This survey provides a comprehensive review of existing low-precision training methods. To systematically organize these approaches, we categorize them into three primary groups based on their underlying numerical formats, which is a key factor influencing hardware compatibility, computational efficiency, and ease of reference for readers. The categories are: (1) fixed-point and integer-based methods, (2) floating-point-based methods, and (3) customized format-based methods. Additionally, we discuss quantization-aware training approaches, which share key similarities with low-precision training during forward propagation. Finally, we highlight several promising research directions to advance this field. A collection of papers discussed in this survey is provided in https://github.com/Hao840/Awesome-Low-Precision-Training.

  • 9 authors
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May 2 3

Evaluating language models as risk scores

Current question-answering benchmarks predominantly focus on accuracy in realizable prediction tasks. Conditioned on a question and answer-key, does the most likely token match the ground truth? Such benchmarks necessarily fail to evaluate LLMs' ability to quantify ground-truth outcome uncertainty. In this work, we focus on the use of LLMs as risk scores for unrealizable prediction tasks. We introduce folktexts, a software package to systematically generate risk scores using LLMs, and evaluate them against US Census data products. A flexible API enables the use of different prompting schemes, local or web-hosted models, and diverse census columns that can be used to compose custom prediction tasks. We evaluate 17 recent LLMs across five proposed benchmark tasks. We find that zero-shot risk scores produced by multiple-choice question-answering have high predictive signal but are widely miscalibrated. Base models consistently overestimate outcome uncertainty, while instruction-tuned models underestimate uncertainty and produce over-confident risk scores. In fact, instruction-tuning polarizes answer distribution regardless of true underlying data uncertainty. This reveals a general inability of instruction-tuned LLMs to express data uncertainty using multiple-choice answers. A separate experiment using verbalized chat-style risk queries yields substantially improved calibration across instruction-tuned models. These differences in ability to quantify data uncertainty cannot be revealed in realizable settings, and highlight a blind-spot in the current evaluation ecosystem that folktexts covers.

  • 3 authors
·
Jul 19, 2024

Temperature-scaling surprisal estimates improve fit to human reading times -- but does it do so for the "right reasons"?

A wide body of evidence shows that human language processing difficulty is predicted by the information-theoretic measure surprisal, a word's negative log probability in context. However, it is still unclear how to best estimate these probabilities needed for predicting human processing difficulty -- while a long-standing belief held that models with lower perplexity would provide more accurate estimates of word predictability, and therefore lead to better reading time predictions, recent work has shown that for very large models, psycholinguistic predictive power decreases. One reason could be that language models might be more confident of their predictions than humans, because they have had exposure to several magnitudes more data. In this paper, we test what effect temperature-scaling of large language model (LLM) predictions has on surprisal estimates and their predictive power of reading times of English texts. Firstly, we show that calibration of large language models typically improves with model size, i.e. poorer calibration cannot account for poorer fit to reading times. Secondly, we find that temperature-scaling probabilities lead to a systematically better fit to reading times (up to 89% improvement in delta log likelihood), across several reading time corpora. Finally, we show that this improvement in fit is chiefly driven by words that are composed of multiple subword tokens.

  • 3 authors
·
Nov 15, 2023

Wisdom of the Silicon Crowd: LLM Ensemble Prediction Capabilities Match Human Crowd Accuracy

Human forecasting accuracy in practice relies on the 'wisdom of the crowd' effect, in which predictions about future events are significantly improved by aggregating across a crowd of individual forecasters. Past work on the forecasting ability of large language models (LLMs) suggests that frontier LLMs, as individual forecasters, underperform compared to the gold standard of a human crowd forecasting tournament aggregate. In Study 1, we expand this research by using an LLM ensemble approach consisting of a crowd of twelve LLMs. We compare the aggregated LLM predictions on 31 binary questions to that of a crowd of 925 human forecasters from a three-month forecasting tournament. Our main analysis shows that the LLM crowd outperforms a simple no-information benchmark and is statistically equivalent to the human crowd. We also observe an acquiescence effect, with mean model predictions being significantly above 50%, despite an almost even split of positive and negative resolutions. Moreover, in Study 2, we test whether LLM predictions (of GPT-4 and Claude 2) can be improved by drawing on human cognitive output. We find that both models' forecasting accuracy benefits from exposure to the median human prediction as information, improving accuracy by between 17% and 28%: though this leads to less accurate predictions than simply averaging human and machine forecasts. Our results suggest that LLMs can achieve forecasting accuracy rivaling that of human crowd forecasting tournaments: via the simple, practically applicable method of forecast aggregation. This replicates the 'wisdom of the crowd' effect for LLMs, and opens up their use for a variety applications throughout society.

  • 4 authors
·
Feb 29, 2024

Task-Specific Skill Localization in Fine-tuned Language Models

Pre-trained language models can be fine-tuned to solve diverse NLP tasks, including in few-shot settings. Thus fine-tuning allows the model to quickly pick up task-specific ``skills,'' but there has been limited study of where these newly-learnt skills reside inside the massive model. This paper introduces the term skill localization for this problem and proposes a solution. Given the downstream task and a model fine-tuned on that task, a simple optimization is used to identify a very small subset of parameters (sim0.01% of model parameters) responsible for (>95%) of the model's performance, in the sense that grafting the fine-tuned values for just this tiny subset onto the pre-trained model gives performance almost as well as the fine-tuned model. While reminiscent of recent works on parameter-efficient fine-tuning, the novel aspects here are that: (i) No further re-training is needed on the subset (unlike, say, with lottery tickets). (ii) Notable improvements are seen over vanilla fine-tuning with respect to calibration of predictions in-distribution (40-90% error reduction) as well as the quality of predictions out-of-distribution (OOD). In models trained on multiple tasks, a stronger notion of skill localization is observed, where the sparse regions corresponding to different tasks are almost disjoint, and their overlap (when it happens) is a proxy for task similarity. Experiments suggest that localization via grafting can assist certain forms of continual learning.

  • 4 authors
·
Feb 13, 2023