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Jan 7

Adaptive Fusion of Multi-view Remote Sensing data for Optimal Sub-field Crop Yield Prediction

Accurate crop yield prediction is of utmost importance for informed decision-making in agriculture, aiding farmers, and industry stakeholders. However, this task is complex and depends on multiple factors, such as environmental conditions, soil properties, and management practices. Combining heterogeneous data views poses a fusion challenge, like identifying the view-specific contribution to the predictive task. We present a novel multi-view learning approach to predict crop yield for different crops (soybean, wheat, rapeseed) and regions (Argentina, Uruguay, and Germany). Our multi-view input data includes multi-spectral optical images from Sentinel-2 satellites and weather data as dynamic features during the crop growing season, complemented by static features like soil properties and topographic information. To effectively fuse the data, we introduce a Multi-view Gated Fusion (MVGF) model, comprising dedicated view-encoders and a Gated Unit (GU) module. The view-encoders handle the heterogeneity of data sources with varying temporal resolutions by learning a view-specific representation. These representations are adaptively fused via a weighted sum. The fusion weights are computed for each sample by the GU using a concatenation of the view-representations. The MVGF model is trained at sub-field level with 10 m resolution pixels. Our evaluations show that the MVGF outperforms conventional models on the same task, achieving the best results by incorporating all the data sources, unlike the usual fusion results in the literature. For Argentina, the MVGF model achieves an R2 value of 0.68 at sub-field yield prediction, while at field level evaluation (comparing field averages), it reaches around 0.80 across different countries. The GU module learned different weights based on the country and crop-type, aligning with the variable significance of each data source to the prediction task.

  • 14 authors
·
Jan 22, 2024

An Open and Large-Scale Dataset for Multi-Modal Climate Change-aware Crop Yield Predictions

Precise crop yield predictions are of national importance for ensuring food security and sustainable agricultural practices. While AI-for-science approaches have exhibited promising achievements in solving many scientific problems such as drug discovery, precipitation nowcasting, etc., the development of deep learning models for predicting crop yields is constantly hindered by the lack of an open and large-scale deep learning-ready dataset with multiple modalities to accommodate sufficient information. To remedy this, we introduce the CropNet dataset, the first terabyte-sized, publicly available, and multi-modal dataset specifically targeting climate change-aware crop yield predictions for the contiguous United States (U.S.) continent at the county level. Our CropNet dataset is composed of three modalities of data, i.e., Sentinel-2 Imagery, WRF-HRRR Computed Dataset, and USDA Crop Dataset, for over 2200 U.S. counties spanning 6 years (2017-2022), expected to facilitate researchers in developing versatile deep learning models for timely and precisely predicting crop yields at the county-level, by accounting for the effects of both short-term growing season weather variations and long-term climate change on crop yields. Besides, we develop the CropNet package, offering three types of APIs, for facilitating researchers in downloading the CropNet data on the fly over the time and region of interest, and flexibly building their deep learning models for accurate crop yield predictions. Extensive experiments have been conducted on our CropNet dataset via employing various types of deep learning solutions, with the results validating the general applicability and the efficacy of the CropNet dataset in climate change-aware crop yield predictions.

  • 6 authors
·
Jun 10, 2024

DFYP: A Dynamic Fusion Framework with Spectral Channel Attention and Adaptive Operator learning for Crop Yield Prediction

Accurate remote sensing-based crop yield prediction remains a fundamental challenging task due to complex spatial patterns, heterogeneous spectral characteristics, and dynamic agricultural conditions. Existing methods often suffer from limited spatial modeling capacity, weak generalization across crop types and years. To address these challenges, we propose DFYP, a novel Dynamic Fusion framework for crop Yield Prediction, which combines spectral channel attention, edge-adaptive spatial modeling and a learnable fusion mechanism to improve robustness across diverse agricultural scenarios. Specifically, DFYP introduces three key components: (1) a Resolution-aware Channel Attention (RCA) module that enhances spectral representation by adaptively reweighting input channels based on resolution-specific characteristics; (2) an Adaptive Operator Learning Network (AOL-Net) that dynamically selects operators for convolutional kernels to improve edge-sensitive spatial feature extraction under varying crop and temporal conditions; and (3) a dual-branch architecture with a learnable fusion mechanism, which jointly models local spatial details and global contextual information to support cross-resolution and cross-crop generalization. Extensive experiments on multi-year datasets MODIS and multi-crop dataset Sentinel-2 demonstrate that DFYP consistently outperforms current state-of-the-art baselines in RMSE, MAE, and R2 across different spatial resolutions, crop types, and time periods, showcasing its effectiveness and robustness for real-world agricultural monitoring.

  • 5 authors
·
Jul 8, 2025

VITA: Variational Pretraining of Transformers for Climate-Robust Crop Yield Forecasting

Accurate crop yield forecasting is essential for global food security. However, current AI models systematically underperform when yields deviate from historical trends. We attribute this to the lack of rich, physically grounded datasets directly linking atmospheric states to yields. To address this, we introduce VITA (Variational Inference Transformer for Asymmetric data), a variational pretraining framework that learns representations from large satellite-based weather datasets and transfers to the ground-based limited measurements available for yield prediction. VITA is trained using detailed meteorological variables as proxy targets during pretraining and learns to predict latent atmospheric states under a seasonality-aware sinusoidal prior. This allows the model to be fine-tuned using limited weather statistics during deployment. Applied to 763 counties in the U.S. Corn Belt, VITA achieves state-of-the-art performance in predicting corn and soybean yields across all evaluation scenarios, particularly during extreme years, with statistically significant improvements (paired t-test, p < 0.0001). Importantly, VITA outperforms prior frameworks like GNN-RNN without soil data, and bigger foundational models (e.g., Chronos-Bolt) with less compute, making it practical for real-world use--especially in data-scarce regions. This work highlights how domain-aware AI design can overcome data limitations and support resilient agricultural forecasting in a changing climate.

  • 3 authors
·
Aug 5, 2025

A Hybrid Deep Learning-based Approach for Optimal Genotype by Environment Selection

Precise crop yield prediction is essential for improving agricultural practices and ensuring crop resilience in varying climates. Integrating weather data across the growing season, especially for different crop varieties, is crucial for understanding their adaptability in the face of climate change. In the MLCAS2021 Crop Yield Prediction Challenge, we utilized a dataset comprising 93,028 training records to forecast yields for 10,337 test records, covering 159 locations across 28 U.S. states and Canadian provinces over 13 years (2003-2015). This dataset included details on 5,838 distinct genotypes and daily weather data for a 214-day growing season, enabling comprehensive analysis. As one of the winning teams, we developed two novel convolutional neural network (CNN) architectures: the CNN-DNN model, combining CNN and fully-connected networks, and the CNN-LSTM-DNN model, with an added LSTM layer for weather variables. Leveraging the Generalized Ensemble Method (GEM), we determined optimal model weights, resulting in superior performance compared to baseline models. The GEM model achieved lower RMSE (5.55% to 39.88%), reduced MAE (5.34% to 43.76%), and higher correlation coefficients (1.1% to 10.79%) when evaluated on test data. We applied the CNN-DNN model to identify top-performing genotypes for various locations and weather conditions, aiding genotype selection based on weather variables. Our data-driven approach is valuable for scenarios with limited testing years. Additionally, a feature importance analysis using RMSE change highlighted the significance of location, MG, year, and genotype, along with the importance of weather variables MDNI and AP.

  • 4 authors
·
Sep 22, 2023

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

TasselNetV4: A vision foundation model for cross-scene, cross-scale, and cross-species plant counting

Accurate plant counting provides valuable information for agriculture such as crop yield prediction, plant density assessment, and phenotype quantification. Vision-based approaches are currently the mainstream solution. Prior art typically uses a detection or a regression model to count a specific plant. However, plants have biodiversity, and new cultivars are increasingly bred each year. It is almost impossible to exhaust and build all species-dependent counting models. Inspired by class-agnostic counting (CAC) in computer vision, we argue that it is time to rethink the problem formulation of plant counting, from what plants to count to how to count plants. In contrast to most daily objects with spatial and temporal invariance, plants are dynamic, changing with time and space. Their non-rigid structure often leads to worse performance than counting rigid instances like heads and cars such that current CAC and open-world detection models are suboptimal to count plants. In this work, we inherit the vein of the TasselNet plant counting model and introduce a new extension, TasselNetV4, shifting from species-specific counting to cross-species counting. TasselNetV4 marries the local counting idea of TasselNet with the extract-and-match paradigm in CAC. It builds upon a plain vision transformer and incorporates novel multi-branch box-aware local counters used to enhance cross-scale robustness. Two challenging datasets, PAC-105 and PAC-Somalia, are harvested. Extensive experiments against state-of-the-art CAC models show that TasselNetV4 achieves not only superior counting performance but also high efficiency.Our results indicate that TasselNetV4 emerges to be a vision foundation model for cross-scene, cross-scale, and cross-species plant counting.

  • 11 authors
·
Sep 25, 2025

What indeed can GPT models do in chemistry? A comprehensive benchmark on eight tasks

Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been rapidly applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper,we establish a comprehensive benchmark containing 8 practical chemistry tasks, including 1) name prediction, 2) property prediction, 3) yield prediction, 4) reaction prediction, 5) retrosynthesis (prediction of reactants from products), 6)text-based molecule design, 7) molecule captioning, and 8) reagent selection. Our analysis draws on widely recognized datasets including BBBP, Tox21, PubChem, USPTO, and ChEBI, facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Three GPT models (GPT-4, GPT-3.5,and Davinci-003) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. The key results of our investigation are 1) GPT-4 outperforms the other two models among the three evaluated; 2) GPT models exhibit less competitive performance in tasks demanding precise understanding of molecular SMILES representation, such as reaction prediction and retrosynthesis;3) GPT models demonstrate strong capabilities in text-related explanation tasks such as molecule captioning; and 4) GPT models exhibit comparable or better performance to classical machine learning models when applied to chemical problems that can be transformed into classification or ranking tasks, such as property prediction, and yield prediction.

  • 8 authors
·
May 27, 2023

Zyxin is all you need: machine learning adherent cell mechanics

Cellular form and function emerge from complex mechanochemical systems within the cytoplasm. No systematic strategy currently exists to infer large-scale physical properties of a cell from its many molecular components. This is a significant obstacle to understanding biophysical processes such as cell adhesion and migration. Here, we develop a data-driven biophysical modeling approach to learn the mechanical behavior of adherent cells. We first train neural networks to predict forces generated by adherent cells from images of cytoskeletal proteins. Strikingly, experimental images of a single focal adhesion protein, such as zyxin, are sufficient to predict forces and generalize to unseen biological regimes. This protein field alone contains enough information to yield accurate predictions even if forces themselves are generated by many interacting proteins. We next develop two approaches - one explicitly constrained by physics, the other more agnostic - that help construct data-driven continuum models of cellular forces using this single focal adhesion field. Both strategies consistently reveal that cellular forces are encoded by two different length scales in adhesion protein distributions. Beyond adherent cell mechanics, our work serves as a case study for how to integrate neural networks in the construction of predictive phenomenological models in cell biology, even when little knowledge of the underlying microscopic mechanisms exist.

  • 8 authors
·
Feb 28, 2023

UniRec: A Dual Enhancement of Uniformity and Frequency in Sequential Recommendations

Representation learning in sequential recommendation is critical for accurately modeling user interaction patterns and improving recommendation precision. However, existing approaches predominantly emphasize item-to-item transitions, often neglecting the time intervals between interactions, which are closely related to behavior pattern changes. Additionally, broader interaction attributes, such as item frequency, are frequently overlooked. We found that both sequences with more uniform time intervals and items with higher frequency yield better prediction performance. Conversely, non-uniform sequences exacerbate user interest drift and less-frequent items are difficult to model due to sparse sampling, presenting unique challenges inadequately addressed by current methods. In this paper, we propose UniRec, a novel bidirectional enhancement sequential recommendation method. UniRec leverages sequence uniformity and item frequency to enhance performance, particularly improving the representation of non-uniform sequences and less-frequent items. These two branches mutually reinforce each other, driving comprehensive performance optimization in complex sequential recommendation scenarios. Additionally, we present a multidimensional time module to further enhance adaptability. To the best of our knowledge, UniRec is the first method to utilize the characteristics of uniformity and frequency for feature augmentation. Comparing with eleven advanced models across four datasets, we demonstrate that UniRec outperforms SOTA models significantly. The code is available at https://github.com/Linxi000/UniRec.

  • 3 authors
·
Jun 26, 2024

The Effect of Person-Specific Biometrics in Improving Generic Stress Predictive Models

Because stress is subjective and is expressed differently from one person to another, generic stress prediction models (i.e., models that predict the stress of any person) perform crudely. Only person-specific ones (i.e., models that predict the stress of a preordained person) yield reliable predictions, but they are not adaptable and costly to deploy in real-world environments. For illustration, in an office environment, a stress monitoring system that uses person-specific models would require collecting new data and training a new model for every employee. Moreover, once deployed, the models would deteriorate and need expensive periodic upgrades because stress is dynamic and depends on unforeseeable factors. We propose a simple, yet practical and cost effective calibration technique that derives an accurate and personalized stress prediction model from physiological samples collected from a large population. We validate our approach on two stress datasets. The results show that our technique performs much better than a generic model. For instance, a generic model achieved only a 42.5% accuracy. However, with only 100 calibration samples, we raised its accuracy to 95.2% We also propose a blueprint for a stress monitoring system based on our strategy, and we debate its merits and limitation. Finally, we made public our source code and the relevant datasets to allow other researchers to replicate our findings.

  • 3 authors
·
Oct 3, 2019

The Consensus Game: Language Model Generation via Equilibrium Search

When applied to question answering and other text generation tasks, language models (LMs) may be queried generatively (by sampling answers from their output distribution) or discriminatively (by using them to score or rank a set of candidate outputs). These procedures sometimes yield very different predictions. How do we reconcile mutually incompatible scoring procedures to obtain coherent LM predictions? We introduce a new, a training-free, game-theoretic procedure for language model decoding. Our approach casts language model decoding as a regularized imperfect-information sequential signaling game - which we term the CONSENSUS GAME - in which a GENERATOR seeks to communicate an abstract correctness parameter using natural language sentences to a DISCRIMINATOR. We develop computational procedures for finding approximate equilibria of this game, resulting in a decoding algorithm we call EQUILIBRIUM-RANKING. Applied to a large number of tasks (including reading comprehension, commonsense reasoning, mathematical problem-solving, and dialog), EQUILIBRIUM-RANKING consistently, and sometimes substantially, improves performance over existing LM decoding procedures - on multiple benchmarks, we observe that applying EQUILIBRIUM-RANKING to LLaMA-7B outperforms the much larger LLaMA-65B and PaLM-540B models. These results highlight the promise of game-theoretic tools for addressing fundamental challenges of truthfulness and consistency in LMs.

  • 4 authors
·
Oct 13, 2023 3

Exact Learning of Permutations for Nonzero Binary Inputs with Logarithmic Training Size and Quadratic Ensemble Complexity

The ability of an architecture to realize permutations is quite fundamental. For example, Large Language Models need to be able to correctly copy (and perhaps rearrange) parts of the input prompt into the output. Classical universal approximation theorems guarantee the existence of parameter configurations that solve this task but offer no insights into whether gradient-based algorithms can find them. In this paper, we address this gap by focusing on two-layer fully connected feed-forward neural networks and the task of learning permutations on nonzero binary inputs. We show that in the infinite width Neural Tangent Kernel (NTK) regime, an ensemble of such networks independently trained with gradient descent on only the k standard basis vectors out of 2^k - 1 possible inputs successfully learns any fixed permutation of length k with arbitrarily high probability. By analyzing the exact training dynamics, we prove that the network's output converges to a Gaussian process whose mean captures the ground truth permutation via sign-based features. We then demonstrate how averaging these runs (an "ensemble" method) and applying a simple rounding step yields an arbitrarily accurate prediction on any possible input unseen during training. Notably, the number of models needed to achieve exact learning with high probability (which we refer to as ensemble complexity) exhibits a linearithmic dependence on the input size k for a single test input and a quadratic dependence when considering all test inputs simultaneously.

  • 3 authors
·
Feb 23, 2025

REBORN: Reinforcement-Learned Boundary Segmentation with Iterative Training for Unsupervised ASR

Unsupervised automatic speech recognition (ASR) aims to learn the mapping between the speech signal and its corresponding textual transcription without the supervision of paired speech-text data. A word/phoneme in the speech signal is represented by a segment of speech signal with variable length and unknown boundary, and this segmental structure makes learning the mapping between speech and text challenging, especially without paired data. In this paper, we propose REBORN, Reinforcement-Learned Boundary Segmentation with Iterative Training for Unsupervised ASR. REBORN alternates between (1) training a segmentation model that predicts the boundaries of the segmental structures in speech signals and (2) training the phoneme prediction model, whose input is a segmental structure segmented by the segmentation model, to predict a phoneme transcription. Since supervised data for training the segmentation model is not available, we use reinforcement learning to train the segmentation model to favor segmentations that yield phoneme sequence predictions with a lower perplexity. We conduct extensive experiments and find that under the same setting, REBORN outperforms all prior unsupervised ASR models on LibriSpeech, TIMIT, and five non-English languages in Multilingual LibriSpeech. We comprehensively analyze why the boundaries learned by REBORN improve the unsupervised ASR performance.

  • 7 authors
·
Feb 6, 2024

Disentangle then Parse:Night-time Semantic Segmentation with Illumination Disentanglement

Most prior semantic segmentation methods have been developed for day-time scenes, while typically underperforming in night-time scenes due to insufficient and complicated lighting conditions. In this work, we tackle this challenge by proposing a novel night-time semantic segmentation paradigm, i.e., disentangle then parse (DTP). DTP explicitly disentangles night-time images into light-invariant reflectance and light-specific illumination components and then recognizes semantics based on their adaptive fusion. Concretely, the proposed DTP comprises two key components: 1) Instead of processing lighting-entangled features as in prior works, our Semantic-Oriented Disentanglement (SOD) framework enables the extraction of reflectance component without being impeded by lighting, allowing the network to consistently recognize the semantics under cover of varying and complicated lighting conditions. 2) Based on the observation that the illumination component can serve as a cue for some semantically confused regions, we further introduce an Illumination-Aware Parser (IAParser) to explicitly learn the correlation between semantics and lighting, and aggregate the illumination features to yield more precise predictions. Extensive experiments on the night-time segmentation task with various settings demonstrate that DTP significantly outperforms state-of-the-art methods. Furthermore, with negligible additional parameters, DTP can be directly used to benefit existing day-time methods for night-time segmentation.

  • 6 authors
·
Jul 18, 2023

PointRAFT: 3D deep learning for high-throughput prediction of potato tuber weight from partial point clouds

Potato yield is a key indicator for optimizing cultivation practices in agriculture. Potato yield can be estimated on harvesters using RGB-D cameras, which capture three-dimensional (3D) information of individual tubers moving along the conveyor belt. However, point clouds reconstructed from RGB-D images are incomplete due to self-occlusion, leading to systematic underestimation of tuber weight. To address this, we introduce PointRAFT, a high-throughput point cloud regression network that directly predicts continuous 3D shape properties, such as tuber weight, from partial point clouds. Rather than reconstructing full 3D geometry, PointRAFT infers target values directly from raw 3D data. Its key architectural novelty is an object height embedding that incorporates tuber height as an additional geometric cue, improving weight prediction under practical harvesting conditions. PointRAFT was trained and evaluated on 26,688 partial point clouds collected from 859 potato tubers across four cultivars and three growing seasons on an operational harvester in Japan. On a test set of 5,254 point clouds from 172 tubers, PointRAFT achieved a mean absolute error of 12.0 g and a root mean squared error of 17.2 g, substantially outperforming a linear regression baseline and a standard PointNet++ regression network. With an average inference time of 6.3 ms per point cloud, PointRAFT supports processing rates of up to 150 tubers per second, meeting the high-throughput requirements of commercial potato harvesters. Beyond potato weight estimation, PointRAFT provides a versatile regression network applicable to a wide range of 3D phenotyping and robotic perception tasks. The code, network weights, and a subset of the dataset are publicly available at https://github.com/pieterblok/pointraft.git.

  • 6 authors
·
Dec 30, 2025

Inflationary Attractors Predictions for Static Neutron Stars in the Mass-Gap Region

In this work we study static neutron stars in the context of several inflationary models which are popular in cosmology. These inflationary models are non-minimally coupled scalar theories which yield a viable inflationary phenomenology in both Jordan and Einstein frames. By considering the constraints from inflationary theories, which basically determine the values of the potential strength, usually considered as a free parameter in astrophysical neutron star works, we construct and solve the Tolman-Oppenheimer-Volkoff equations using a solid python-3 LSODA integrator. For our study we consider several popular inflationary models, such as the universal attractors, the R^p attractors (three distinct model values), the induced inflation, the quadratic inflation, the Higgs inflation and the a-attractors (two distinct model values) and for the following popular equations of state the WFF1, the SLy, the APR, the MS1, the AP3, the AP4, the ENG, the MPA1 and the MS1b. We construct the M-R diagram and we confront the resulting theory with theoretical and observational constraints. As we demonstrate, remarkably, all the neutron stars produced by all the inflationary models we considered are compatible with all the constraints for the MPA1 equation of state. It is notable that for this particular equation of state, the maximum masses of the neutron stars are in the mass-gap region with M>2.5M_{odot}, but lower than the 3 solar masses causal limit. We also make the observation that as the NICER constraints are pushed towards larger radii, as for example in the case of the black widow pulsar PSR J0952-0607, it seems that equations of state that produce neutron stars with maximum masses in the mass gap region, with M>2.5M_{odot}, but lower than the 3 solar masses causal limit, are favored and are compatible with the modified NICER constraints.

  • 2 authors
·
May 9, 2023

GeoMAE: Masked Geometric Target Prediction for Self-supervised Point Cloud Pre-Training

This paper tries to address a fundamental question in point cloud self-supervised learning: what is a good signal we should leverage to learn features from point clouds without annotations? To answer that, we introduce a point cloud representation learning framework, based on geometric feature reconstruction. In contrast to recent papers that directly adopt masked autoencoder (MAE) and only predict original coordinates or occupancy from masked point clouds, our method revisits differences between images and point clouds and identifies three self-supervised learning objectives peculiar to point clouds, namely centroid prediction, normal estimation, and curvature prediction. Combined with occupancy prediction, these four objectives yield an nontrivial self-supervised learning task and mutually facilitate models to better reason fine-grained geometry of point clouds. Our pipeline is conceptually simple and it consists of two major steps: first, it randomly masks out groups of points, followed by a Transformer-based point cloud encoder; second, a lightweight Transformer decoder predicts centroid, normal, and curvature for points in each voxel. We transfer the pre-trained Transformer encoder to a downstream peception model. On the nuScene Datset, our model achieves 3.38 mAP improvment for object detection, 2.1 mIoU gain for segmentation, and 1.7 AMOTA gain for multi-object tracking. We also conduct experiments on the Waymo Open Dataset and achieve significant performance improvements over baselines as well.

  • 4 authors
·
May 15, 2023

An Interdisciplinary Comparison of Sequence Modeling Methods for Next-Element Prediction

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

  • 3 authors
·
Oct 31, 2018

AttriLens-Mol: Attribute Guided Reinforcement Learning for Molecular Property Prediction with Large Language Models

Large Language Models (LLMs) have shown promise in assisting molecular property prediction tasks but often rely on human-crafted prompts and chain-of-thought templates. While recent advanced large reasoning models like DeepSeek-R1 employ reinforcement learning for an extended ``thinking'' process, their reasoning can be verbose and lack relevance. We introduce AttriLens-Mol, an attribute-guided reinforcement learning framework for molecular property prediction with LLMs. AttriLens-Mol steers the model's reasoning by using: (1) a format reward encouraging attribute-based structured output, (2) a count reward to avoid enumerating irrelevant attributes, and (3) a rationality reward using advanced LLMs and RDKit to verify the relatedness of the generated attributes. This approach implicitly elicits the model's inherent knowledge of relevant molecular attributes during reasoning, enables making predictions for the molecular property more effectively. Experiments on both in-distribution and out-of-distribution datasets show that, training both 7B-size R1-Distilled-Qwen2.5 and R1-Distilled-LLaMA3.1 models on 4,000 samples with our proposed AttriLens-Mol method significantly boosts the performance, getting comparable or better results than supervised fine-tuning models (Mol-Instructions, ChemDFM, etc.) and advanced models (GPT-3.5, GPT-4o, DeepSeek-V3, DeepSeek-R1, etc.). Further, our extracted attributes for the target property, when used as features for an interpretable decision tree model, yield superior performance compared to attributes generated by prompting LLMs. This shows that AttriLens-Mol effectively elicits more relevant and predictive molecular attributes, leading to enhanced interpretability and performance for property prediction. We release the code in https://github.com/szu-tera/AttriLens-Mol.

  • 3 authors
·
Aug 6, 2025

A Three-Phase Analysis of Synergistic Effects During Co-pyrolysis of Algae and Wood for Biochar Yield Using Machine Learning

Pyrolysis techniques have served to be a groundbreaking technique for effectively utilising natural and man-made biomass products like plastics, wood, crop residue, fruit peels etc. Recent advancements have shown a greater yield of essential products like biochar, bio-oil and other non-condensable gases by blending different biomasses in a certain ratio. This synergy effect of combining two pyrolytic raw materials i.e co-pyrolysis of algae and wood biomass has been systematically studied and grouped into 3 phases in this research paper-kinetic analysis of co-pyrolysis, correlation among proximate and ultimate analysis with bio-char yield and lastly grouping of different weight ratios based on biochar yield up to a certain percentage. Different ML and DL algorithms have been utilized for regression and classification techniques to give a comprehensive overview of the effect of the synergy of two different biomass materials on biochar yield. For the first phase, the best prediction of biochar yield was obtained by using a decision tree regressor with a perfect MSE score of 0.00, followed by a gradient-boosting regressor. The second phase was analyzed using both ML and DL techniques. Within ML, SVR proved to be the most convenient model with an accuracy score of 0.972 with DNN employed for deep learning technique. Finally, for the third phase, binary classification was applied to biochar yield with and without heating rate for biochar yield percentage above and below 40%. The best technique for ML was Support Vector followed by Random forest while ANN was the most suitable Deep Learning Technique.

  • 2 authors
·
May 20, 2024

Total Nitrogen Estimation in Agricultural Soils via Aerial Multispectral Imaging and LIBS

Measuring soil health indicators is an important and challenging task that affects farmers' decisions on timing, placement, and quantity of fertilizers applied in the farms. Most existing methods to measure soil health indicators (SHIs) are in-lab wet chemistry or spectroscopy-based methods, which require significant human input and effort, time-consuming, costly, and are low-throughput in nature. To address this challenge, we develop an artificial intelligence (AI)-driven near real-time unmanned aerial vehicle (UAV)-based multispectral sensing (UMS) solution to estimate total nitrogen (TN) of the soil, an important macro-nutrient or SHI that directly affects the crop health. Accurate prediction of soil TN can significantly increase crop yield through informed decision making on the timing of seed planting, and fertilizer quantity and timing. We train two machine learning models including multi-layer perceptron and support vector machine to predict the soil nitrogen using a suite of data classes including multispectral characteristics of the soil and crops in red, near-infrared, and green spectral bands, computed vegetation indices, and environmental variables including air temperature and relative humidity. To generate the ground-truth data or the training data for the machine learning models, we measure the total nitrogen of the soil samples (collected from a farm) using laser-induced breakdown spectroscopy (LIBS).

  • 3 authors
·
Jul 5, 2021

Senna: Bridging Large Vision-Language Models and End-to-End Autonomous Driving

End-to-end autonomous driving demonstrates strong planning capabilities with large-scale data but still struggles in complex, rare scenarios due to limited commonsense. In contrast, Large Vision-Language Models (LVLMs) excel in scene understanding and reasoning. The path forward lies in merging the strengths of both approaches. Previous methods using LVLMs to predict trajectories or control signals yield suboptimal results, as LVLMs are not well-suited for precise numerical predictions. This paper presents Senna, an autonomous driving system combining an LVLM (Senna-VLM) with an end-to-end model (Senna-E2E). Senna decouples high-level planning from low-level trajectory prediction. Senna-VLM generates planning decisions in natural language, while Senna-E2E predicts precise trajectories. Senna-VLM utilizes a multi-image encoding approach and multi-view prompts for efficient scene understanding. Besides, we introduce planning-oriented QAs alongside a three-stage training strategy, which enhances Senna-VLM's planning performance while preserving commonsense. Extensive experiments on two datasets show that Senna achieves state-of-the-art planning performance. Notably, with pre-training on a large-scale dataset DriveX and fine-tuning on nuScenes, Senna significantly reduces average planning error by 27.12% and collision rate by 33.33% over model without pre-training. We believe Senna's cross-scenario generalization and transferability are essential for achieving fully autonomous driving. Code and models will be released at https://github.com/hustvl/Senna.

  • 9 authors
·
Oct 29, 2024

K-HATERS: A Hate Speech Detection Corpus in Korean with Target-Specific Ratings

Numerous datasets have been proposed to combat the spread of online hate. Despite these efforts, a majority of these resources are English-centric, primarily focusing on overt forms of hate. This research gap calls for developing high-quality corpora in diverse languages that also encapsulate more subtle hate expressions. This study introduces K-HATERS, a new corpus for hate speech detection in Korean, comprising approximately 192K news comments with target-specific offensiveness ratings. This resource is the largest offensive language corpus in Korean and is the first to offer target-specific ratings on a three-point Likert scale, enabling the detection of hate expressions in Korean across varying degrees of offensiveness. We conduct experiments showing the effectiveness of the proposed corpus, including a comparison with existing datasets. Additionally, to address potential noise and bias in human annotations, we explore a novel idea of adopting the Cognitive Reflection Test, which is widely used in social science for assessing an individual's cognitive ability, as a proxy of labeling quality. Findings indicate that annotations from individuals with the lowest test scores tend to yield detection models that make biased predictions toward specific target groups and are less accurate. This study contributes to the NLP research on hate speech detection and resource construction. The code and dataset can be accessed at https://github.com/ssu-humane/K-HATERS.

  • 4 authors
·
Oct 23, 2023

Efficient Global Optimization of Two-layer ReLU Networks: Quadratic-time Algorithms and Adversarial Training

The non-convexity of the artificial neural network (ANN) training landscape brings inherent optimization difficulties. While the traditional back-propagation stochastic gradient descent (SGD) algorithm and its variants are effective in certain cases, they can become stuck at spurious local minima and are sensitive to initializations and hyperparameters. Recent work has shown that the training of an ANN with ReLU activations can be reformulated as a convex program, bringing hope to globally optimizing interpretable ANNs. However, naively solving the convex training formulation has an exponential complexity, and even an approximation heuristic requires cubic time. In this work, we characterize the quality of this approximation and develop two efficient algorithms that train ANNs with global convergence guarantees. The first algorithm is based on the alternating direction method of multiplier (ADMM). It solves both the exact convex formulation and the approximate counterpart. Linear global convergence is achieved, and the initial several iterations often yield a solution with high prediction accuracy. When solving the approximate formulation, the per-iteration time complexity is quadratic. The second algorithm, based on the "sampled convex programs" theory, is simpler to implement. It solves unconstrained convex formulations and converges to an approximately globally optimal classifier. The non-convexity of the ANN training landscape exacerbates when adversarial training is considered. We apply the robust convex optimization theory to convex training and develop convex formulations that train ANNs robust to adversarial inputs. Our analysis explicitly focuses on one-hidden-layer fully connected ANNs, but can extend to more sophisticated architectures.

  • 3 authors
·
Jan 6, 2022

GUI-360: A Comprehensive Dataset and Benchmark for Computer-Using Agents

We introduce GUI-360^circ, a large-scale, comprehensive dataset and benchmark suite designed to advance computer-using agents (CUAs). CUAs present unique challenges and is constrained by three persistent gaps: a scarcity of real-world CUA tasks, the lack of automated collection-and-annotation pipelines for multi-modal trajectories, and the absence of a unified benchmark that jointly evaluates GUI grounding, screen parsing, and action prediction. GUI-360^circ addresses these gaps with an LLM-augmented, largely automated pipeline for query sourcing, environment-template construction, task instantiation, batched execution, and LLM-driven quality filtering. The released corpus contains over 1.2M executed action steps across thousands of trajectories in popular Windows office applications, and includes full-resolution screenshots, accessibility metadata when available, instantiated goals, intermediate reasoning traces, and both successful and failed action trajectories. The dataset supports three canonical tasks, GUI grounding, screen parsing, and action prediction, and a hybrid GUI+API action space that reflects modern agent designs. Benchmarking state-of-the-art vision--language models on GUI-360^circ reveals substantial out-of-the-box shortcomings in grounding and action prediction; supervised fine-tuning and reinforcement learning yield significant gains but do not close the gap to human-level reliability. We release GUI-360^circ and accompanying code to facilitate reproducible research and accelerate progress on robust desktop CUAs. The full dataset has been made public on https://huggingface.co/datasets/vyokky/GUI-360.

microsoft Microsoft
·
Nov 6, 2025 2

Predicting In-game Actions from Interviews of NBA Players

Sports competitions are widely researched in computer and social science, with the goal of understanding how players act under uncertainty. While there is an abundance of computational work on player metrics prediction based on past performance, very few attempts to incorporate out-of-game signals have been made. Specifically, it was previously unclear whether linguistic signals gathered from players' interviews can add information which does not appear in performance metrics. To bridge that gap, we define text classification tasks of predicting deviations from mean in NBA players' in-game actions, which are associated with strategic choices, player behavior and risk, using their choice of language prior to the game. We collected a dataset of transcripts from key NBA players' pre-game interviews and their in-game performance metrics, totalling in 5,226 interview-metric pairs. We design neural models for players' action prediction based on increasingly more complex aspects of the language signals in their open-ended interviews. Our models can make their predictions based on the textual signal alone, or on a combination with signals from past-performance metrics. Our text-based models outperform strong baselines trained on performance metrics only, demonstrating the importance of language usage for action prediction. Moreover, the models that employ both textual input and past-performance metrics produced the best results. Finally, as neural networks are notoriously difficult to interpret, we propose a method for gaining further insight into what our models have learned. Particularly, we present an LDA-based analysis, where we interpret model predictions in terms of correlated topics. We find that our best performing textual model is most associated with topics that are intuitively related to each prediction task and that better models yield higher correlation with more informative topics.

  • 3 authors
·
Oct 24, 2019

Zero-shot 3D-Aware Trajectory-Guided image-to-video generation via Test-Time Training

Trajectory-Guided image-to-video (I2V) generation aims to synthesize videos that adhere to user-specified motion instructions. Existing methods typically rely on computationally expensive fine-tuning on scarce annotated datasets. Although some zero-shot methods attempt to trajectory control in the latent space, they may yield unrealistic motion by neglecting 3D perspective and creating a misalignment between the manipulated latents and the network's noise predictions. To address these challenges, we introduce Zo3T, a novel zero-shot test-time-training framework for trajectory-guided generation with three core innovations: First, we incorporate a 3D-Aware Kinematic Projection, leveraging inferring scene depth to derive perspective-correct affine transformations for target regions. Second, we introduce Trajectory-Guided Test-Time LoRA, a mechanism that dynamically injects and optimizes ephemeral LoRA adapters into the denoising network alongside the latent state. Driven by a regional feature consistency loss, this co-adaptation effectively enforces motion constraints while allowing the pre-trained model to locally adapt its internal representations to the manipulated latent, thereby ensuring generative fidelity and on-manifold adherence. Finally, we develop Guidance Field Rectification, which refines the denoising evolutionary path by optimizing the conditional guidance field through a one-step lookahead strategy, ensuring efficient generative progression towards the target trajectory. Zo3T significantly enhances 3D realism and motion accuracy in trajectory-controlled I2V generation, demonstrating superior performance over existing training-based and zero-shot approaches.

  • 8 authors
·
Sep 8, 2025

Retrospective Reader for Machine Reading Comprehension

Machine reading comprehension (MRC) is an AI challenge that requires machine to determine the correct answers to questions based on a given passage. MRC systems must not only answer question when necessary but also distinguish when no answer is available according to the given passage and then tactfully abstain from answering. When unanswerable questions are involved in the MRC task, an essential verification module called verifier is especially required in addition to the encoder, though the latest practice on MRC modeling still most benefits from adopting well pre-trained language models as the encoder block by only focusing on the "reading". This paper devotes itself to exploring better verifier design for the MRC task with unanswerable questions. Inspired by how humans solve reading comprehension questions, we proposed a retrospective reader (Retro-Reader) that integrates two stages of reading and verification strategies: 1) sketchy reading that briefly investigates the overall interactions of passage and question, and yield an initial judgment; 2) intensive reading that verifies the answer and gives the final prediction. The proposed reader is evaluated on two benchmark MRC challenge datasets SQuAD2.0 and NewsQA, achieving new state-of-the-art results. Significance tests show that our model is significantly better than the strong ELECTRA and ALBERT baselines. A series of analysis is also conducted to interpret the effectiveness of the proposed reader.

  • 3 authors
·
Jan 27, 2020

Category-Level 6D Object Pose and Size Estimation using Self-Supervised Deep Prior Deformation Networks

It is difficult to precisely annotate object instances and their semantics in 3D space, and as such, synthetic data are extensively used for these tasks, e.g., category-level 6D object pose and size estimation. However, the easy annotations in synthetic domains bring the downside effect of synthetic-to-real (Sim2Real) domain gap. In this work, we aim to address this issue in the task setting of Sim2Real, unsupervised domain adaptation for category-level 6D object pose and size estimation. We propose a method that is built upon a novel Deep Prior Deformation Network, shortened as DPDN. DPDN learns to deform features of categorical shape priors to match those of object observations, and is thus able to establish deep correspondence in the feature space for direct regression of object poses and sizes. To reduce the Sim2Real domain gap, we formulate a novel self-supervised objective upon DPDN via consistency learning; more specifically, we apply two rigid transformations to each object observation in parallel, and feed them into DPDN respectively to yield dual sets of predictions; on top of the parallel learning, an inter-consistency term is employed to keep cross consistency between dual predictions for improving the sensitivity of DPDN to pose changes, while individual intra-consistency ones are used to enforce self-adaptation within each learning itself. We train DPDN on both training sets of the synthetic CAMERA25 and real-world REAL275 datasets; our results outperform the existing methods on REAL275 test set under both the unsupervised and supervised settings. Ablation studies also verify the efficacy of our designs. Our code is released publicly at https://github.com/JiehongLin/Self-DPDN.

  • 4 authors
·
Jul 12, 2022

Post-Hoc Split-Point Self-Consistency Verification for Efficient, Unified Quantification of Aleatoric and Epistemic Uncertainty in Deep Learning

Uncertainty quantification (UQ) is vital for trustworthy deep learning, yet existing methods are either computationally intensive, such as Bayesian or ensemble methods, or provide only partial, task-specific estimates, such as single-forward-pass techniques. In this paper, we propose a post-hoc single-forward-pass framework that jointly captures aleatoric and epistemic uncertainty without modifying or retraining pretrained models. Our method applies Split-Point Analysis (SPA) to decompose predictive residuals into upper and lower subsets, computing Mean Absolute Residuals (MARs) on each side. We prove that, under ideal conditions, the total MAR equals the harmonic mean of subset MARs; deviations define a novel Self-consistency Discrepancy Score (SDS) for fine-grained epistemic estimation across regression and classification. For regression, side-specific quantile regression yields prediction intervals with improved empirical coverage, which are further calibrated via SDS. For classification, when calibration data are available, we apply SPA-based calibration identities to adjust the softmax outputs and then compute predictive entropy on these calibrated probabilities. Extensive experiments on diverse regression and classification benchmarks demonstrate that our framework matches or exceeds several state-of-the-art UQ methods while incurring minimal overhead. Our source code is available at https://github.com/zzz0527/SPC-UQ.

  • 2 authors
·
Sep 16, 2025

TabPFN: A Transformer That Solves Small Tabular Classification Problems in a Second

We present TabPFN, a trained Transformer that can do supervised classification for small tabular datasets in less than a second, needs no hyperparameter tuning and is competitive with state-of-the-art classification methods. TabPFN performs in-context learning (ICL), it learns to make predictions using sequences of labeled examples (x, f(x)) given in the input, without requiring further parameter updates. TabPFN is fully entailed in the weights of our network, which accepts training and test samples as a set-valued input and yields predictions for the entire test set in a single forward pass. TabPFN is a Prior-Data Fitted Network (PFN) and is trained offline once, to approximate Bayesian inference on synthetic datasets drawn from our prior. This prior incorporates ideas from causal reasoning: It entails a large space of structural causal models with a preference for simple structures. On the 18 datasets in the OpenML-CC18 suite that contain up to 1 000 training data points, up to 100 purely numerical features without missing values, and up to 10 classes, we show that our method clearly outperforms boosted trees and performs on par with complex state-of-the-art AutoML systems with up to 230times speedup. This increases to a 5 700times speedup when using a GPU. We also validate these results on an additional 67 small numerical datasets from OpenML. We provide all our code, the trained TabPFN, an interactive browser demo and a Colab notebook at https://github.com/automl/TabPFN.

  • 4 authors
·
Jul 5, 2022 1

Provably Robust Conformal Prediction with Improved Efficiency

Conformal prediction is a powerful tool to generate uncertainty sets with guaranteed coverage using any predictive model, under the assumption that the training and test data are i.i.d.. Recently, it has been shown that adversarial examples are able to manipulate conformal methods to construct prediction sets with invalid coverage rates, as the i.i.d. assumption is violated. To address this issue, a recent work, Randomized Smoothed Conformal Prediction (RSCP), was first proposed to certify the robustness of conformal prediction methods to adversarial noise. However, RSCP has two major limitations: (i) its robustness guarantee is flawed when used in practice and (ii) it tends to produce large uncertainty sets. To address these limitations, we first propose a novel framework called RSCP+ to provide provable robustness guarantee in evaluation, which fixes the issues in the original RSCP method. Next, we propose two novel methods, Post-Training Transformation (PTT) and Robust Conformal Training (RCT), to effectively reduce prediction set size with little computation overhead. Experimental results in CIFAR10, CIFAR100, and ImageNet suggest the baseline method only yields trivial predictions including full label set, while our methods could boost the efficiency by up to 4.36times, 5.46times, and 16.9times respectively and provide practical robustness guarantee. Our codes are available at https://github.com/Trustworthy-ML-Lab/Provably-Robust-Conformal-Prediction.

  • 3 authors
·
Apr 30, 2024

Diffusion-based Visual Anagram as Multi-task Learning

Visual anagrams are images that change appearance upon transformation, like flipping or rotation. With the advent of diffusion models, generating such optical illusions can be achieved by averaging noise across multiple views during the reverse denoising process. However, we observe two critical failure modes in this approach: (i) concept segregation, where concepts in different views are independently generated, which can not be considered a true anagram, and (ii) concept domination, where certain concepts overpower others. In this work, we cast the visual anagram generation problem in a multi-task learning setting, where different viewpoint prompts are analogous to different tasks,and derive denoising trajectories that align well across tasks simultaneously. At the core of our designed framework are two newly introduced techniques, where (i) an anti-segregation optimization strategy that promotes overlap in cross-attention maps between different concepts, and (ii) a noise vector balancing method that adaptively adjusts the influence of different tasks. Additionally, we observe that directly averaging noise predictions yields suboptimal performance because statistical properties may not be preserved, prompting us to derive a noise variance rectification method. Extensive qualitative and quantitative experiments demonstrate our method's superior ability to generate visual anagrams spanning diverse concepts.

  • 6 authors
·
Dec 3, 2024

The interstellar flux gap: From dust to kilometer-scale objects

Context. Three kilometer-sized interstellar objects (ISOs) have been detected transiting the Solar System, and spacecraft have directly measured micrometer-scale interstellar dust (ISD). Yet no intermediate-size interstellar meteoroids have been identified in current meteor surveys. Aims. We test whether a power-law flux extrapolation connecting spacecraft ISD and kilometer-scale ISOs is consistent with meteor surveys, and we quantify the expected interstellar impacting flux based on various observational reports. Methods. We compiled differential fluxes and limits from spacecraft ISD, radar and optical meteor surveys, and theoretical estimates. We evaluated the power-law size-frequency fits, computed the 3I-like flux, and compared measured fluxes to predictions. Results. The spacecraft-measured dust flux exceeds extrapolations constrained by meteor surveys and kilometer-scale ISOs by sim2-7 orders of magnitude. An r^{-3.0} fit combining spacecraft ISD detections with kilometer-scale ISOs overpredicts the number of meteors with hyperbolic orbits, whereas slopes of r^{-2.7}-r^{-2.3} (derived from radar and optical meteor upper limits, respectively) instead yield interplanetary-to-interstellar flux ratios of 10^{3}-10^{6}. Conclusions. A simple power-law from ISD to ISOs is inconsistent with meteor survey constraints and yields unrealistic predictions for interstellar meteoroids. The data reveal a gap between submicron dust entrained in the Local Interstellar Cloud (LIC) and macroscopic bodies ejected from planetary systems. This gap may reflect distinct origins and destruction-transport processes rather than a continuous size-frequency distribution. This would imply either the dominance of a small-particle LIC component or the need to reassess spacecraft dust fluxes.

  • 2 authors
·
Nov 3, 2025

Revisiting Modeling and Evaluation Approaches in Speech Emotion Recognition: Considering Subjectivity of Annotators and Ambiguity of Emotions

Over the past two decades, speech emotion recognition (SER) has received growing attention. To train SER systems, researchers collect emotional speech databases annotated by crowdsourced or in-house raters who select emotions from predefined categories. However, disagreements among raters are common. Conventional methods treat these disagreements as noise, aggregating labels into a single consensus target. While this simplifies SER as a single-label task, it ignores the inherent subjectivity of human emotion perception. This dissertation challenges such assumptions and asks: (1) Should minority emotional ratings be discarded? (2) Should SER systems learn from only a few individuals' perceptions? (3) Should SER systems predict only one emotion per sample? Psychological studies show that emotion perception is subjective and ambiguous, with overlapping emotional boundaries. We propose new modeling and evaluation perspectives: (1) Retain all emotional ratings and represent them with soft-label distributions. Models trained on individual annotator ratings and jointly optimized with standard SER systems improve performance on consensus-labeled tests. (2) Redefine SER evaluation by including all emotional data and allowing co-occurring emotions (e.g., sad and angry). We propose an ``all-inclusive rule'' that aggregates all ratings to maximize diversity in label representation. Experiments on four English emotion databases show superior performance over majority and plurality labeling. (3) Construct a penalization matrix to discourage unlikely emotion combinations during training. Integrating it into loss functions further improves performance. Overall, embracing minority ratings, multiple annotators, and multi-emotion predictions yields more robust and human-aligned SER systems.

SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction

Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the SSM-DTA framework, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling (MLM) using paired drug-target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS, and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug-target binding activities, virtual screening experiments, drug feature visualizations, and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes. Our code is available at https://github.com/QizhiPei/SSM-DTA{Github}.

  • 9 authors
·
Jun 20, 2022