Saeed Khaki

Saeed Khaki, Akhouri Abhinav Aditya, Zohar Karnin et al.

Drift in machine learning refers to the phenomenon where the statistical properties of data or context, in which the model operates, change over time leading to a decrease in its performance. Therefore, maintaining a constant monitoring process for machine learning model performance is crucial in order to proactively prevent any potential performance regression. However, supervised drift detection methods require human annotation and consequently lead to a longer time to detect and mitigate the drift. In our proposed unsupervised drift detection method, we follow a two step process. Our first step involves encoding a sample of production data as the target distribution, and the model training data as the reference distribution. In the second step, we employ a kernel-based statistical test that utilizes the maximum mean discrepancy (MMD) distance metric to compare the reference and target distributions and estimate any potential drift. Our method also identifies the subset of production data that is the root cause of the drift. The models retrained using these identified high drift samples show improved performance on online customer experience quality metrics.

Zahra Khalilzadeh, Motahareh Kashanian, Saeed Khaki et al.

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.

Saeed Khaki, JinJin Li, Lan Ma et al.

Reinforcement learning from human feedback (RLHF) has been extensively employed to align large language models with user intent. However, proximal policy optimization (PPO) based RLHF is occasionally unstable requiring significant hyperparameter finetuning, and computationally expensive to maximize the estimated reward during alignment. Recently, direct preference optimization (DPO) is proposed to address those challenges. However, DPO relies on contrastive responses generated from human annotator and alternative LLM, instead of the policy model, limiting the effectiveness of the RLHF. In this paper, we addresses both challenges by systematically combining rejection sampling (RS) and DPO. Our proposed method, RS-DPO, initiates with the development of a supervised fine-tuned policy model (SFT). A varied set of k responses per prompt are sampled directly from the SFT model. RS-DPO identifies pairs of contrastive samples based on their reward distribution. Finally, we apply DPO with the contrastive samples to align the model to human preference. Our experiments indicate that our proposed method effectively fine-tunes LLMs with limited resource environments, leading to improved alignment with user intent. Furthermore, it outperforms existing methods, including RS, PPO, and DPO.

Saeed Khaki, Nima Safaei, Kamal Ginotra

Transformer-based vision-language models (VLMs) contain substantial depth redundancy, yet the effect of removing specific decoder layers remains poorly understood, especially for domains that require tight coupling between perception and multi-step reasoning. We study structured decoder layer pruning through the lens of domain-aware activation similarity, measuring how strongly each layer transforms representations for math versus non-math inputs. This yields simple math-aware, non-math-aware, and mixed ranking criteria that identify layers whose input-output activations change least within a target domain. Across two state-of-the-art VLMs and a broad suite of math and general multimodal benchmarks, we uncover a consistent three-regime structure: at low pruning budgets, performance is highly sensitive to which layers are removed; at moderate budgets, methods converge as structural damage accumulates; and at high budgets, structural continuity dominates, favoring spacing-aware strategies. Our domain-aware rankings achieve the strongest stability in the ranking-sensitive regime, while matching or exceeding structure-aware baselines at larger budgets. These results provide a clearer picture of how depth contributes to domain-specific behavior in VLMs and offer a practical, interpretable approach to reducing model depth without sacrificing essential mathematical or general vision-language capabilities.

Saeed Khaki, Ashudeep Singh, Nima Safaei et al.

Vision-language models (VLMs) lag behind text-only language models on mathematical reasoning when the same problems are presented as images rather than text. We empirically characterize this as a modality gap: the same question in text form yields markedly higher accuracy than its visually typeset counterpart, due to compounded failures in reading dense formulas, layout, and mixed symbolic-diagrammatic context. First, we introduce VisTIRA (Vision and Tool-Integrated Reasoning Agent), a tool-integrated reasoning framework that enables structured problem solving by iteratively decomposing a given math problem (as an image) into natural language rationales and executable Python steps to determine the final answer. Second, we build a framework to measure and improve visual math reasoning: a LaTeX-based pipeline that converts chain-of-thought math corpora (e.g., NuminaMath) into challenging image counterparts, and a large set of synthetic tool-use trajectories derived from a real-world, homework-style image dataset (called SnapAsk) for fine-tuning VLMs. Our experiments show that tool-integrated supervision improves image-based reasoning, and OCR grounding can further narrow the gap for smaller models, although its benefit diminishes at scale. These findings highlight that modality gap severity inversely correlates with model size, and that structured reasoning and OCR-based grounding are complementary strategies for advancing visual mathematical reasoning.

Mohsen Shahhosseini, Guiping Hu, Saeed Khaki et al.

We investigate the predictive performance of two novel CNN-DNN machine learning ensemble models in predicting county-level corn yields across the US Corn Belt (12 states). The developed data set is a combination of management, environment, and historical corn yields from 1980-2019. Two scenarios for ensemble creation are considered: homogenous and heterogeneous ensembles. In homogenous ensembles, the base CNN-DNN models are all the same, but they are generated with a bagging procedure to ensure they exhibit a certain level of diversity. Heterogenous ensembles are created from different base CNN-DNN models which share the same architecture but have different levels of depth. Three types of ensemble creation methods were used to create several ensembles for either of the scenarios: Basic Ensemble Method (BEM), Generalized Ensemble Method (GEM), and stacked generalized ensembles. Results indicated that both designed ensemble types (heterogenous and homogenous) outperform the ensembles created from five individual ML models (linear regression, LASSO, random forest, XGBoost, and LightGBM). Furthermore, by introducing improvements over the heterogeneous ensembles, the homogenous ensembles provide the most accurate yield predictions across US Corn Belt states. This model could make 2019 yield predictions with a root mean square error of 866 kg/ha, equivalent to 8.5% relative root mean square, and could successfully explain about 77% of the spatio-temporal variation in the corn grain yields. The significant predictive power of this model can be leveraged for designing a reliable tool for corn yield prediction which will, in turn, assist agronomic decision-makers.

Amit Kumar Srivastava, Nima Safaei, Saeed Khaki et al.

Crop yield forecasting depends on many interactive factors, including crop genotype, weather, soil, and management practices. This study analyzes the performance of machine learning and deep learning methods for winter wheat yield prediction using an extensive dataset of weather, soil, and crop phenology variables in 271 counties across Germany from 1999 to 2019. We proposed a Convolutional Neural Network (CNN) model, which uses a 1-dimensional convolution operation to capture the time dependencies of environmental variables. We used eight supervised machine learning models as baselines and evaluated their predictive performance using RMSE, MAE, and correlation coefficient metrics to benchmark the yield prediction results. Our findings suggested that nonlinear models such as the proposed CNN, Deep Neural Network (DNN), and XGBoost were more effective in understanding the relationship between the crop yield and input data compared to the linear models. Our proposed CNN model outperformed all other baseline models used for winter wheat yield prediction (7 to 14% lower RMSE, 3 to 15% lower MAE, and 4 to 50% higher correlation coefficient than the best performing baseline across test data). We aggregated soil moisture and meteorological features at the weekly resolution to address the seasonality of the data. We also moved beyond prediction and interpreted the outputs of our proposed CNN model using SHAP and force plots which provided key insights in explaining the yield prediction results (importance of variables by time). We found DUL, wind speed at week ten, and radiation amount at week seven as the most critical features in winter wheat yield prediction.

Saeed Khaki, Nima Safaei, Hieu Pham et al.

For a globally recognized planting breeding organization, manually-recorded field observation data is crucial for plant breeding decision making. However, certain phenotypic traits such as plant color, height, kernel counts, etc. can only be collected during a specific time-window of a crop's growth cycle. Due to labor-intensive requirements, only a small subset of possible field observations are recorded each season. To help mitigate this data collection bottleneck in wheat breeding, we propose a novel deep learning framework to accurately and efficiently count wheat heads to aid in the gathering of real-time data for decision making. We call our model WheatNet and show that our approach is robust and accurate for a wide range of environmental conditions of the wheat field. WheatNet uses a truncated MobileNetV2 as a lightweight backbone feature extractor which merges feature maps with different scales to counter image scale variations. Then, extracted multi-scale features go to two parallel sub-networks for simultaneous density-based counting and localization tasks. Our proposed method achieves an MAE and RMSE of 3.85 and 5.19 in our wheat head counting task, respectively, while having significantly fewer parameters when compared to other state-of-the-art methods. Our experiments and comparisons with other state-of-the-art methods demonstrate the superiority and effectiveness of our proposed method.

Saeed Khaki, Hieu Pham, Lizhi Wang

Large-scale crop yield estimation is, in part, made possible due to the availability of remote sensing data allowing for the continuous monitoring of crops throughout their growth cycle. Having this information allows stakeholders the ability to make real-time decisions to maximize yield potential. Although various models exist that predict yield from remote sensing data, there currently does not exist an approach that can estimate yield for multiple crops simultaneously, and thus leads to more accurate predictions. A model that predicts the yield of multiple crops and concurrently considers the interaction between multiple crop yields. We propose a new convolutional neural network model called YieldNet which utilizes a novel deep learning framework that uses transfer learning between corn and soybean yield predictions by sharing the weights of the backbone feature extractor. Additionally, to consider the multi-target response variable, we propose a new loss function. We conduct our experiment using data from 1,132 counties for corn and 1,076 counties for soybean across the United States. Numerical results demonstrate that our proposed method accurately predicts corn and soybean yield from one to four months before the harvest with a MAE being 8.74% and 8.70% of the average yield, respectively, and is competitive to other state-of-the-art approaches.

Saeed Khaki, Hieu Pham, Ye Han et al.

The future landscape of modern farming and plant breeding is rapidly changing due to the complex needs of our society. The explosion of collectable data has started a revolution in agriculture to the point where innovation must occur. To a commercial organization, the accurate and efficient collection of information is necessary to ensure that optimal decisions are made at key points of the breeding cycle. However, due to the shear size of a breeding program and current resource limitations, the ability to collect precise data on individual plants is not possible. In particular, efficient phenotyping of crops to record its color, shape, chemical properties, disease susceptibility, etc. is severely limited due to labor requirements and, oftentimes, expert domain knowledge. In this paper, we propose a deep learning based approach, named DeepStand, for image-based corn stand counting at early phenological stages. The proposed method adopts a truncated VGG-16 network as a backbone feature extractor and merges multiple feature maps with different scales to make the network robust against scale variation. Our extensive computational experiments suggest that our proposed method can successfully count corn stands and out-perform other state-of-the-art methods. It is the goal of our work to be used by the larger agricultural community as a way to enable high-throughput phenotyping without the use of extensive time and labor requirements.

Saeed Khaki, Hieu Pham, Ye Han et al.

The success of modern farming and plant breeding relies on accurate and efficient collection of data. For a commercial organization that manages large amounts of crops, collecting accurate and consistent data is a bottleneck. Due to limited time and labor, accurately phenotyping crops to record color, head count, height, weight, etc. is severely limited. However, this information, combined with other genetic and environmental factors, is vital for developing new superior crop species that help feed the world's growing population. Recent advances in machine learning, in particular deep learning, have shown promise in mitigating this bottleneck. In this paper, we propose a novel deep learning method for counting on-ear corn kernels in-field to aid in the gathering of real-time data and, ultimately, to improve decision making to maximize yield. We name this approach DeepCorn, and show that this framework is robust under various conditions. DeepCorn estimates the density of corn kernels in an image of corn ears and predicts the number of kernels based on the estimated density map. DeepCorn uses a truncated VGG-16 as a backbone for feature extraction and merges feature maps from multiple scales of the network to make it robust against image scale variations. We also adopt a semi-supervised learning approach to further improve the performance of our proposed method. Our proposed method achieves the MAE and RMSE of 41.36 and 60.27 in the corn kernel counting task, respectively. Our experimental results demonstrate the superiority and effectiveness of our proposed method compared to other state-of-the-art methods.

Saeed Khaki, Dan Nettleton

Neural networks are among the most powerful nonlinear models used to address supervised learning problems. Similar to most machine learning algorithms, neural networks produce point predictions and do not provide any prediction interval which includes an unobserved response value with a specified probability. In this paper, we proposed the $k$-fold prediction interval method to construct prediction intervals for neural networks based on $k$-fold cross validation. Simulation studies and analysis of 10 real datasets are used to compare the finite-sample properties of the prediction intervals produced by the proposed method and the split conformal (SC) method. The results suggest that the proposed method tends to produce narrower prediction intervals compared to the SC method while maintaining the same coverage probability. Our experimental results also reveal that the proposed $k$-fold prediction interval method produces effective prediction intervals and is especially advantageous relative to competing approaches when the number of training observations is limited.

Saeed Khaki, Hieu Pham, Ye Han et al.

Precise in-season corn grain yield estimates enable farmers to make real-time accurate harvest and grain marketing decisions minimizing possible losses of profitability. A well developed corn ear can have up to 800 kernels, but manually counting the kernels on an ear of corn is labor-intensive, time consuming and prone to human error. From an algorithmic perspective, the detection of the kernels from a single corn ear image is challenging due to the large number of kernels at different angles and very small distance among the kernels. In this paper, we propose a kernel detection and counting method based on a sliding window approach. The proposed method detect and counts all corn kernels in a single corn ear image taken in uncontrolled lighting conditions. The sliding window approach uses a convolutional neural network (CNN) for kernel detection. Then, a non-maximum suppression (NMS) is applied to remove overlapping detections. Finally, windows that are classified as kernel are passed to another CNN regression model for finding the (x,y) coordinates of the center of kernel image patches. Our experiments indicate that the proposed method can successfully detect the corn kernels with a low detection error and is also able to detect kernels on a batch of corn ears positioned at different angles.

Saeed Khaki, Zahra Khalilzadeh, Lizhi Wang

Experimental corn hybrids are created in plant breeding programs by crossing two parents, so-called inbred and tester, together. Identification of best parent combinations for crossing is challenging since the total number of possible cross combinations of parents is large and it is impractical to test all possible cross combinations due to limited resources of time and budget. In the 2020 Syngenta Crop Challenge, Syngenta released several large datasets that recorded the historical yield performances of around 4% of total cross combinations of 593 inbreds with 496 testers which were planted in 280 locations between 2016 and 2018 and asked participants to predict the yield performance of cross combinations of inbreds and testers that have not been planted based on the historical yield data collected from crossing other inbreds and testers. In this paper, we present a collaborative filtering method which is an ensemble of matrix factorization method and neural networks to solve this problem. Our computational results suggested that the proposed model significantly outperformed other models such as LASSO, random forest (RF), and neural networks. Presented method and results were produced within the 2020 Syngenta Crop Challenge.

Saeed Khaki, Lizhi Wang, Sotirios V. Archontoulis

Crop yield prediction is extremely challenging due to its dependence on multiple factors such as crop genotype, environmental factors, management practices, and their interactions. This paper presents a deep learning framework using convolutional neural networks (CNN) and recurrent neural networks (RNN) for crop yield prediction based on environmental data and management practices. The proposed CNN-RNN model, along with other popular methods such as random forest (RF), deep fully-connected neural networks (DFNN), and LASSO, was used to forecast corn and soybean yield across the entire Corn Belt (including 13 states) in the United States for years 2016, 2017, and 2018 using historical data. The new model achieved a root-mean-square-error (RMSE) 9% and 8% of their respective average yields, substantially outperforming all other methods that were tested. The CNN-RNN have three salient features that make it a potentially useful method for other crop yield prediction studies. (1) The CNN-RNN model was designed to capture the time dependencies of environmental factors and the genetic improvement of seeds over time without having their genotype information. (2) The model demonstrated the capability to generalize the yield prediction to untested environments without significant drop in the prediction accuracy. (3) Coupled with the backpropagation method, the model could reveal the extent to which weather conditions, accuracy of weather predictions, soil conditions, and management practices were able to explain the variation in the crop yields.

Saeed Khaki, Zahra Khalilzadeh, Lizhi Wang

Environmental stresses such as drought and heat can cause substantial yield loss in agriculture. As such, hybrid crops that are tolerant to drought and heat stress would produce more consistent yields compared to the hybrids that are not tolerant to these stresses. In the 2019 Syngenta Crop Challenge, Syngenta released several large datasets that recorded the yield performances of 2,452 corn hybrids planted in 1,560 locations between 2008 and 2017 and asked participants to classify the corn hybrids as either tolerant or susceptible to drought stress, heat stress, and combined drought and heat stress. However, no data was provided that classified any set of hybrids as tolerant or susceptible to any type of stress. In this paper, we present an unsupervised approach to solving this problem, which was recognized as one of the winners in the 2019 Syngenta Crop Challenge. Our results labeled 121 hybrids as drought tolerant, 193 as heat tolerant, and 29 as tolerant to both stresses.

Saeed Khaki, Lizhi Wang

Crop yield is a highly complex trait determined by multiple factors such as genotype, environment, and their interactions. Accurate yield prediction requires fundamental understanding of the functional relationship between yield and these interactive factors, and to reveal such relationship requires both comprehensive datasets and powerful algorithms. In the 2018 Syngenta Crop Challenge, Syngenta released several large datasets that recorded the genotype and yield performances of 2,267 maize hybrids planted in 2,247 locations between 2008 and 2016 and asked participants to predict the yield performance in 2017. As one of the winning teams, we designed a deep neural network (DNN) approach that took advantage of state-of-the-art modeling and solution techniques. Our model was found to have a superior prediction accuracy, with a root-mean-square-error (RMSE) being 12% of the average yield and 50% of the standard deviation for the validation dataset using predicted weather data. With perfect weather data, the RMSE would be reduced to 11% of the average yield and 46% of the standard deviation. We also performed feature selection based on the trained DNN model, which successfully decreased the dimension of the input space without significant drop in the prediction accuracy. Our computational results suggested that this model significantly outperformed other popular methods such as Lasso, shallow neural networks (SNN), and regression tree (RT). The results also revealed that environmental factors had a greater effect on the crop yield than genotype.