Ivan Garibay

Mohammad Jahid Ibna Basher, Ali Khodabandeh Yalabadi, Ivan Garibay et al.

Template based single step retrosynthesis predicts reactants by selecting and applying an explicit reaction template, making each prediction traceable to a chemical transformation rule. This is useful for synthesis planning, but template based methods are often viewed as less competitive than template free models because template prediction is commonly formulated as global classification over a long tailed rule library. We argue that this weakness is not inherent to templates, but to the learning formulation. We present ConRetroBert, a dual encoder framework that reframes template based retrosynthesis as dense product template retrieval followed by candidate set listwise ranking. Stage 1 uses contrastive pretraining to learn a shared embedding space between products and reaction templates. Stage 2 refines template ranking over mined hard negative candidate sets with a multi positive listwise objective. To enable template side adaptation without destabilizing hard negative mining, ConRetroBert uses a slow moving exponential moving average template encoder for retrieval bank construction while updating the live template encoder through the ranking loss. On the local USPTO-50k benchmark, Stage 2 candidate set ranking improves top-1 reaction accuracy from 50.5% to 61.3%, while EMA stabilized template adaptation further improves it to 62.4%. Fine tuning from a leakage controlled USPTO-Full checkpoint reaches 75.4% top-1 accuracy on USPTO-50k. We also show that retrieval based template prediction is strong in the long tail of rare templates, and that many correct reactant predictions arise from alternative explicit templates rather than only the recorded positive label. Code and data are available at https://github.com/JahidBasher/ConRetroBert.

Elias Hossain, Shubhashis Roy Dipta, Subash Neupane et al.

Neural NLP models are often miscalibrated, assigning high confidence to incorrect predictions, which undermines selective prediction and high-stakes deployment. Post-hoc calibration methods adjust output probabilities but leave internal computation unchanged, while ensemble and Bayesian approaches improve uncertainty at substantial training or storage cost. We propose UAT-LITE, an inference-time framework that makes self-attention uncertainty-aware using approximate Bayesian inference via Monte Carlo dropout in pretrained transformer classifiers. Token-level epistemic uncertainty is estimated from stochastic forward passes and used to modulate self-attention during contextualization, without modifying pretrained weights or training objectives. We additionally introduce a layerwise variance decomposition to diagnose how predictive uncertainty accumulates across transformer depth. Across the SQuAD 2.0 answerability, MNLI, and SST-2, UAT-LITE reduces Expected Calibration Error by approximately 20% on average relative to a fine-tuned BERT-base baseline while preserving task accuracy, and improves selective prediction and robustness under distribution shift.

Mehrdad Shoeibi, Elias Hossain, Ivan Garibay et al.

Learning from weak or proxy supervision is common when ground-truth labels are unavailable, yet robustness under distribution shift remains poorly understood, especially when the supervision mechanism itself changes. We formalize this as supervision drift, defined as changes in P(y | x, c) across contexts, and study it in CRISPR-Cas13d experiments where guide efficacy is inferred indirectly from RNA-seq responses. Using data from two human cell lines and multiple time points, we build a controlled non-IID benchmark with explicit domain and temporal shifts while keeping the weak-label construction fixed. Models achieve strong in-domain performance (ridge R^2 = 0.356, Spearman rho = 0.442) and partial cross-cell-line transfer (rho ~ 0.40). However, temporal transfer fails across all models, with negative R^2 and near-zero correlation (e.g., XGBoost R^2 = -0.155, rho = 0.056). Additional analyses confirm this pattern. Feature-label relationships remain stable across cell lines but change sharply over time, indicating that failures arise from supervision drift rather than model limitations. These findings highlight feature stability as a simple diagnostic for detecting non-transferability before deployment.

Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, AmirArsalan Rajabi et al.

The persistent challenge of bias in machine learning models necessitates robust solutions to ensure parity and equal treatment across diverse groups, particularly in classification tasks. Current methods for mitigating bias often result in information loss and an inadequate balance between accuracy and fairness. To address this, we propose a novel methodology grounded in bilevel optimization principles. Our deep learning-based approach concurrently optimizes for both accuracy and fairness objectives, and under certain assumptions, achieving proven Pareto optimal solutions while mitigating bias in the trained model. Theoretical analysis indicates that the upper bound on the loss incurred by this method is less than or equal to the loss of the Lagrangian approach, which involves adding a regularization term to the loss function. We demonstrate the efficacy of our model primarily on tabular datasets such as UCI Adult and Heritage Health. When benchmarked against state-of-the-art fairness methods, our model exhibits superior performance, advancing fairness-aware machine learning solutions and bridging the accuracy-fairness gap. The implementation of FairBiNN is available on https://github.com/yazdanimehdi/FairBiNN.

Nusrat Jahan Prottasha, Md Kowsher, Hafijur Raman et al.

User profile modeling plays a key role in personalized systems, as it requires building accurate profiles and updating them with new information. In this paper, we present two high-quality open-source user profile datasets: one for profile construction and another for profile updating. These datasets offer a strong basis for evaluating user profile modeling techniques in dynamic settings. We also show a methodology that uses large language models (LLMs) to tackle both profile construction and updating. Our method uses a probabilistic framework to predict user profiles from input text, allowing for precise and context-aware profile generation. Our experiments demonstrate that models like Mistral-7b and Llama2-7b perform strongly in both tasks. LLMs improve the precision and recall of the generated profiles, and high evaluation scores confirm the effectiveness of our approach.

Elias Hossain, Mohammad Jahid Ibna Basher, Ivan Garibay et al.

Offline reinforcement learning (RL) can learn effective policies from fixed datasets, but deployment objectives may change after training, and in many applications the trained actor cannot be retrained because of data, cost, or governance constraints. We study deployment-time adaptation for frozen offline actors using Product-of-Experts (PoE) composition with a goal-conditioned prior. Our main practical finding is graceful degradation rather than universal performance gain: under degraded or random priors, precision-weighted composition remains anchored to the frozen actor, while additive and prior-only adaptation collapse, and a KL-budget selector often recovers a near-oracle operating point. We also make explicit a closed-form identity in the frozen-actor setting: for diagonal-Gaussian actors and priors, PoE with coefficient alpha yields the same deterministic policy as KL-regularized adaptation with beta = alpha / (1 - alpha), with posterior covariances differing only by a global scalar factor. Empirically, across four D4RL environments (3,900 MuJoCo episodes), we observe a 4/5/3 HELP/FROZEN/HURT split. Extending the analysis to six harder cells and two AntMaze diagnostics reveals an actor-competence ceiling: medium-expert remains HURT in all 9 cells at every tested alpha, while AntMaze with a behavior-cloned frozen actor yields zero success for all composition rules. Overall, PoE and KL-regularized adaptation are best viewed as a single actor-anchored safety mechanism for deployment-time steering.

Md Kowsher, Nusrat Jahan Prottasha, Prakash Bhat et al.

This paper argues that generating output tokens is more effective than using pooled representations for prediction tasks because token-level generation retains more mutual information. Since LLMs are trained on massive text corpora using next-token prediction, generation aligns naturally with their learned behavior. Using the Data Processing Inequality (DPI), we provide both theoretical and empirical evidence supporting this claim. However, autoregressive models face two key challenges when used for prediction: (1) exposure bias, where the model sees ground truth tokens during training but relies on its own predictions during inference, leading to errors, and (2) format mismatch, where discrete tokens do not always align with the tasks required output structure. To address these challenges, we introduce PredGen(Predicting Through Generating), an end to end framework that (i) uses scheduled sampling to reduce exposure bias, and (ii) introduces a task adapter to convert the generated tokens into structured outputs. Additionally, we introduce Writer-Director Alignment Loss (WDAL), which ensures consistency between token generation and final task predictions, improving both text coherence and numerical accuracy. We evaluate PredGen on multiple classification and regression benchmarks. Our results show that PredGen consistently outperforms standard baselines, demonstrating its effectiveness in structured prediction tasks.

Elias Hossain, Mehrdad Shoeibi, Ivan Garibay et al.

We propose CITE V.1, an agentic, evidence-grounded framework that leverages Large Language Models (LLMs) to provide transparent and reproducible interpretations of RNA-seq clusters. Unlike existing enrichment-based approaches that reduce results to broad statistical associations and LLM-only models that risk unsupported claims or fabricated citations, CITE V.1 transforms cluster interpretation by producing biologically coherent explanations explicitly anchored in the biomedical literature. The framework orchestrates three specialized agents: a Retriever that gathers domain knowledge from PubMed and UniProt, an Interpreter that formulates functional hypotheses, and Critics that evaluate claims, enforce evidence grounding, and qualify uncertainty through confidence and reliability indicators. Applied to Salmonella enterica RNA-seq data, CITE V.1 generated biologically meaningful insights supported by the literature, while an LLM-only Gemini baseline frequently produced speculative results with false citations. By moving RNA-seq analysis from surface-level enrichment to auditable, interpretable, and evidence-based hypothesis generation, CITE V.1 advances the transparency and reliability of AI in biomedicine.

Sina Abdidizaji, Md Kowsher, Niloofar Yousefi et al.

In the era of digitalization, as individuals increasingly rely on digital platforms for communication and news consumption, various actors employ linguistic strategies to influence public perception. While models have become proficient at detecting explicit patterns, which typically appear in texts as single remarks referred to as utterances, such as social media posts, malicious actors have shifted toward utilizing implicit influential verbal patterns embedded within conversations. These verbal patterns aim to mentally penetrate the victim's mind in order to influence them, enabling the actor to obtain the desired information through implicit means. This paper presents an improved approach for detecting such implicit influential patterns. Furthermore, the proposed model is capable of identifying the specific locations of these influential elements within a conversation. To achieve this, the existing dataset was augmented using the reasoning capabilities of state-of-the-art language models. Our designed framework resulted in a 6% improvement in the detection of implicit influential patterns in conversations. Moreover, this approach improved the multi-label classification tasks related to both the techniques used for influence and the vulnerability of victims by 33% and 43%, respectively.

Toktam A. Oghaz, Ivan Garibay

Recent advances in natural language processing (NLP) in online social media are evidently owed to large-scale datasets. However, labeling, storing, and processing a large number of textual data points, e.g., tweets, has remained challenging. On top of that, in applications such as hate speech detection, labeling a sufficiently large dataset containing offensive content can be mentally and emotionally taxing for human annotators. Thus, NLP methods that can make the best use of significantly less labeled data points are of great interest. In this paper, we present a novel pool-based active learning method that can be used for the training of large unlabeled corpus with minimum annotation cost. For that, we propose to find the dominant sets of local clusters in the feature space. These sets represent maximally cohesive structures in the data. Then, the samples that do not belong to any of the dominant sets are selected to be used to train the model, as they represent the boundaries of the local clusters and are more challenging to classify. Our proposed method does not have any parameters to be tuned, making it dataset-independent, and it can approximately achieve the same classification accuracy as full training data, with significantly fewer data points. Additionally, our method achieves a higher performance in comparison to the state-of-the-art active learning strategies. Furthermore, our proposed algorithm is able to incorporate conventional active learning scores, such as uncertainty-based scores, into its selection criteria. We show the effectiveness of our method on different datasets and using different neural network architectures.

Jasser Jasser, Ivan Garibay

Traditional deep learning networks (DNN) exhibit intriguing vulnerabilities that allow an attacker to force them to fail at their task. Notorious attacks such as the Fast Gradient Sign Method (FGSM) and the more powerful Projected Gradient Descent (PGD) generate adversarial samples by adding a magnitude of perturbation $ε$ to the input's computed gradient, resulting in a deterioration of the effectiveness of the model's classification. This work introduces a model that is resilient to adversarial attacks. Our model leverages an established mechanism of defense which utilizes randomness and a population of DNNs. More precisely, our model consists of a population of $n$ diverse submodels, each one of them trained to individually obtain a high accuracy for the task at hand, while forced to maintain meaningful differences in their weights. Each time our model receives a classification query, it selects a submodel from its population at random to answer the query. To counter the attack transferability, diversity is introduced and maintained in the population of submodels. Thus introducing the concept of counter linking weights. A Counter-Linked Model (CLM) consists of a population of DNNs of the same architecture where a periodic random similarity examination is conducted during the simultaneous training to guarantee diversity while maintaining accuracy. Though the randomization technique proved to be resilient against adversarial attacks, we show that by retraining the DNNs ensemble or training them from the start with counter linking would enhance the robustness by around 20\% when tested on the MNIST dataset and at least 15\% when tested on the CIFAR-10 dataset. When CLM is coupled with adversarial training, this defense mechanism achieves state-of-the-art robustness.

Ramya Akula, Ivan Garibay

The concept of AI for Social Good(AI4SG) is gaining momentum in both information societies and the AI community. Through all the advancement of AI-based solutions, it can solve societal issues effectively. To date, however, there is only a rudimentary grasp of what constitutes AI socially beneficial in principle, what constitutes AI4SG in reality, and what are the policies and regulations needed to ensure it. This paper fills the vacuum by addressing the ethical aspects that are critical for future AI4SG efforts. Some of these characteristics are new to AI, while others have greater importance due to its usage.

Ramya Akula, Ivan Garibay

Sarcasm is a linguistic expression often used to communicate the opposite of what is said, usually something that is very unpleasant with an intention to insult or ridicule. Inherent ambiguity in sarcastic expressions, make sarcasm detection very difficult. In this work, we focus on detecting sarcasm in textual conversations from various social networking platforms and online media. To this end, we develop an interpretable deep learning model using multi-head self-attention and gated recurrent units. Multi-head self-attention module aids in identifying crucial sarcastic cue-words from the input, and the recurrent units learn long-range dependencies between these cue-words to better classify the input text. We show the effectiveness of our approach by achieving state-of-the-art results on multiple datasets from social networking platforms and online media. Models trained using our proposed approach are easily interpretable and enable identifying sarcastic cues in the input text which contribute to the final classification score. We visualize the learned attention weights on few sample input texts to showcase the effectiveness and interpretability of our model.

Ece Çiğdem Mutlu, Toktam A. Oghaz, Jasser Jasser et al.

At the time of this study, the SARS-CoV-2 virus that caused the COVID-19 pandemic has spread significantly across the world. Considering the uncertainty about policies, health risks, financial difficulties, etc. the online media, specially the Twitter platform, is experiencing a high volume of activity related to this pandemic. Among the hot topics, the polarized debates about unconfirmed medicines for the treatment and prevention of the disease have attracted significant attention from online media users. In this work, we present a stance data set, COVID-CQ, of user-generated content on Twitter in the context of COVID-19. We investigated more than 14 thousand tweets and manually annotated the opinions of the tweet initiators regarding the use of "chloroquine" and "hydroxychloroquine" for the treatment or prevention of COVID-19. To the best of our knowledge, COVID-CQ is the first data set of Twitter users' stances in the context of the COVID-19 pandemic, and the largest Twitter data set on users' stances towards a claim, in any domain. We have made this data set available to the research community via GitHub. We expect this data set to be useful for many research purposes, including stance detection, evolution and dynamics of opinions regarding this outbreak, and changes in opinions in response to the exogenous shocks such as policy decisions and events.

Toktam A. Oghaz, Ece C. Mutlu, Jasser Jasser et al.

Online social media platforms are turning into the prime source of news and narratives about worldwide events. However,a systematic summarization-based narrative extraction that can facilitate communicating the main underlying events is lacking. To address this issue, we propose a novel event-based narrative summary extraction framework. Our proposed framework is designed as a probabilistic topic model, with categorical time distribution, followed by extractive text summarization. Our topic model identifies topics' recurrence over time with a varying time resolution. This framework not only captures the topic distributions from the data, but also approximates the user activity fluctuations over time. Furthermore, we define significance-dispersity trade-off (SDT) as a comparison measure to identify the topic with the highest lifetime attractiveness in a timestamped corpus. We evaluate our model on a large corpus of Twitter data, including more than one million tweets in the domain of the disinformation campaigns conducted against the White Helmets of Syria. Our results indicate that the proposed framework is effective in identifying topical trends, as well as extracting narrative summaries from text corpus with timestamped data.

Marie Alaghband, Niloofar Yousefi, Ivan Garibay

Facial expressions are important parts of both gesture and sign language recognition systems. Despite the recent advances in both fields, annotated facial expression datasets in the context of sign language are still scarce resources. In this manuscript, we introduce an annotated sequenced facial expression dataset in the context of sign language, comprising over $3000$ facial images extracted from the daily news and weather forecast of the public tv-station PHOENIX. Unlike the majority of currently existing facial expression datasets, FePh provides sequenced semi-blurry facial images with different head poses, orientations, and movements. In addition, in the majority of images, identities are mouthing the words, which makes the data more challenging. To annotate this dataset we consider primary, secondary, and tertiary dyads of seven basic emotions of "sad", "surprise", "fear", "angry", "neutral", "disgust", and "happy". We also considered the "None" class if the image's facial expression could not be described by any of the aforementioned emotions. Although we provide FePh as a facial expression dataset of signers in sign language, it has a wider application in gesture recognition and Human Computer Interaction (HCI) systems.

Niloofar Yousefi, Marie Alaghband, Ivan Garibay

With the increase of credit card usage, the volume of credit card misuse also has significantly increased. As a result, financial organizations are working hard on developing and deploying credit card fraud detection methods, in order to adapt to ever-evolving, increasingly sophisticated defrauding strategies and identifying illicit transactions as quickly as possible to protect themselves and their customers. Compounding on the complex nature of such adverse strategies, credit card fraudulent activities are rare events compared to the number of legitimate transactions. Hence, the challenge to develop fraud detection that are accurate and efficient is substantially intensified and, as a consequence, credit card fraud detection has lately become a very active area of research. In this work, we provide a survey of current techniques most relevant to the problem of credit card fraud detection. We carry out our survey in two main parts. In the first part,we focus on studies utilizing classical machine learning models, which mostly employ traditional transnational features to make fraud predictions. These models typically rely on some static physical characteristics, such as what the user knows (knowledge-based method), or what he/she has access to (object-based method). In the second part of our survey, we review more advanced techniques of user authentication, which use behavioral biometrics to identify an individual based on his/her unique behavior while he/she is interacting with his/her electronic devices. These approaches rely on how people behave (instead of what they do), which cannot be easily forged. By providing an overview of current approaches and the results reported in the literature, this survey aims to drive the future research agenda for the community in order to develop more accurate, reliable and scalable models of credit card fraud detection.

Ramya Akula, Zachary Wieselthier, Laura Martin et al.

Television is an ever-evolving multi billion dollar industry. The success of a television show in an increasingly technological society is a vast multi-variable formula. The art of success is not just something that happens, but is studied, replicated, and applied. Hollywood can be unpredictable regarding success, as many movies and sitcoms that are hyped up and promise to be a hit end up being box office failures and complete disappointments. In current studies, linguistic exploration is being performed on the relationship between Television series and target community of viewers. Having a decision support system that can display sound and predictable results would be needed to build confidence in the investment of a new TV series. The models presented in this study use data to study and determine what makes a sitcom successful. In this paper, we use descriptive and predictive modeling techniques to assess the continuing success of television comedies: The Office, Big Bang Theory, Arrested Development, Scrubs, and South Park. The factors that are tested for statistical significance on episode ratings are character presence, director, and writer. These statistics show that while characters are indeed crucial to the shows themselves, the creation and direction of the shows pose implication upon the ratings and therefore the success of the shows. We use machine learning based forecasting models to accurately predict the success of shows. The models represent a baseline to understanding the success of a television show and how producers can increase the success of current television shows or utilize this data in the creation of future shows. Due to the many factors that go into a series, the empirical analysis in this work shows that there is no one-fits-all model to forecast the rating or success of a television show.

Ramya Akula, Ni Nguyen, Ivan Garibay

According to the American Diabetes Association(ADA), 30.3 million people in the United States have diabetes, but only 7.2 million may be undiagnosed and unaware of their condition. Type 2 diabetes is usually diagnosed for most patients later on in life whereas the less common Type 1 diabetes is diagnosed early on in life. People can live healthy and happy lives while living with diabetes, but early detection produces a better overall outcome on most patient's health. Thus, to test the accurate prediction of Type 2 diabetes, we use the patients' information from an electronic health records company called Practice Fusion, which has about 10,000 patient records from 2009 to 2012. This data contains individual key biometrics, including age, diastolic and systolic blood pressure, gender, height, and weight. We use this data on popular machine learning algorithms and for each algorithm, we evaluate the performance of every model based on their classification accuracy, precision, sensitivity, specificity/recall, negative predictive value, and F1 score. In our study, we find that all algorithms other than Naive Bayes suffered from very low precision. Hence, we take a step further and incorporate all the algorithms into a weighted average or soft voting ensemble model where each algorithm will count towards a majority vote towards the decision outcome of whether a patient has diabetes or not. The accuracy of the Ensemble model on Practice Fusion is 85\%, by far our ensemble approach is new in this space. We firmly believe that the weighted average ensemble model not only performed well in overall metrics but also helped to recover wrong predictions and aid in accurate prediction of Type 2 diabetes. Our accurate novel model can be used as an alert for the patients to seek medical evaluation in time.

Ramya Akula, Niloofar Yousefi, Ivan Garibay

Information spreads on complex social networks extremely fast, in other words, a piece of information can go viral within no time. Often it is hard to barricade this diffusion prior to the significant occurrence of chaos, be it a social media or an online coding platform. GitHub is one such trending online focal point for any business to reach their potential contributors and customers, simultaneously. By exploiting such software development paradigm, millions of free software emerged lately in diverse communities. To understand human influence, information spread and evolution of transmitted information among assorted users in GitHub, we developed a deep neural network model: DeepFork, a supervised machine learning based approach that aims to predict information diffusion in complex social networks; considering node as well as topological features. In our empirical studies, we observed that information diffusion can be detected by link prediction using supervised learning. DeepFork outperforms other machine learning models as it better learns the discriminative patterns from the input features. DeepFork aids in understanding information spread and evolution through a bipartite network of users and repositories i.e., information flow from a user to repository to user.