arXiv subjects

George Karypis

Publications and source records attributed to George Karypis.

At least 37 records · Page 2Linked to original sources

arXiv2025

BYOKG-RAG: Multi-Strategy Graph Retrieval for Knowledge Graph Question Answering

Knowledge graph question answering (KGQA) presents significant challenges due to the structural and semantic variations across input graphs. Existing works rely on Large Language Model (LLM) agents for graph traversal and retrieval; an approach that is sensitive to traversal initialization, as it is prone to entity linking errors and may not generalize well to custom ("bring-your-own") KGs. We introduce BYOKG-RAG, a framework that enhances KGQA by synergistically combining LLMs with specialized graph retrieval tools. In BYOKG-RAG, LLMs generate critical graph artifacts (question entities, candidate answers, reasoning paths, and OpenCypher queries), and graph tools link these artifacts to the KG and retrieve relevant graph context. The retrieved context enables the LLM to iteratively refine its graph linking and retrieval, before final answer generation. By retrieving context from different graph tools, BYOKG-RAG offers a more general and robust solution for QA over custom KGs. Through experiments on five benchmarks spanning diverse KG types, we demonstrate that BYOKG-RAG outperforms the second-best graph retrieval method by 4.5% points while showing better generalization to custom KGs. BYOKG-RAG framework is open-sourced at https://github.com/awslabs/graphrag-toolkit.

cs.CL↗

arXiv2025

ProxSparse: Regularized Learning of Semi-Structured Sparsity Masks for Pretrained LLMs

Large Language Models (LLMs) have demonstrated exceptional performance in natural language processing tasks, yet their massive size makes serving them inefficient and costly. Semi-structured pruning has emerged as an effective method for model acceleration, but existing approaches are suboptimal because they focus on local, layer-wise optimizations using heuristic rules, failing to leverage global feedback. We present ProxSparse, a learning-based framework for mask selection enabled by regularized optimization. ProxSparse transforms the rigid, non-differentiable mask selection process into a smoother optimization procedure, allowing gradual mask exploration with flexibility. ProxSparse does not involve additional weight updates once the mask is determined. Our extensive evaluations on 7 widely used models show that ProxSparse consistently outperforms previously proposed semi-structured mask selection methods with significant improvement, demonstrating the effectiveness of our learned approach towards semi-structured pruning.

cs.LG↗

arXiv2025

Beyond instruction-conditioning, MoTE: Mixture of Task Experts for Multi-task Embedding Models

Dense embeddings are fundamental to modern machine learning systems, powering Retrieval-Augmented Generation (RAG), information retrieval, and representation learning. While instruction-conditioning has become the dominant approach for embedding specialization, its direct application to low-capacity models imposes fundamental representational constraints that limit the performance gains derived from specialization. In this paper, we analyze these limitations and introduce the Mixture of Task Experts (MoTE) transformer block, which leverages task-specialized parameters trained with Task-Aware Contrastive Learning (\tacl) to enhance the model ability to generate specialized embeddings. Empirical results show that MoTE achieves $64\%$ higher performance gains in retrieval datasets ($+3.27 \rightarrow +5.21$) and $43\%$ higher performance gains across all datasets ($+1.81 \rightarrow +2.60$). Critically, these gains are achieved without altering instructions, training data, inference time, or number of active parameters.

cs.LG↗

arXiv2025

AgentOccam: A Simple Yet Strong Baseline for LLM-Based Web Agents

Autonomy via agents using large language models (LLMs) for personalized, standardized tasks boosts human efficiency. Automating web tasks (like booking hotels within a budget) is increasingly sought after. Fulfilling practical needs, the web agent also serves as an important proof-of-concept example for various agent grounding scenarios, with its success promising advancements in many future applications. Prior research often handcrafts web agent strategies (e.g., prompting templates, multi-agent systems, search methods, etc.) and the corresponding in-context examples, which may not generalize well across all real-world scenarios. On the other hand, there has been limited study on the misalignment between a web agent's observation/action representation and the pre-training data of the LLM it's based on. This discrepancy is especially notable when LLMs are primarily trained for language completion rather than tasks involving embodied navigation actions and symbolic web elements. Our study enhances an LLM-based web agent by simply refining its observation and action space to better align with the LLM's capabilities. This approach enables our base agent to significantly outperform previous methods on a wide variety of web tasks. Specifically, on WebArena, a benchmark featuring general-purpose web interaction tasks, our agent AgentOccam surpasses the previous state-of-the-art and concurrent work by 9.8 (+29.4%) and 5.9 (+15.8%) absolute points respectively, and boosts the success rate by 26.6 points (+161%) over similar plain web agents with its observation and action space alignment. We achieve this without using in-context examples, new agent roles, online feedback or search strategies. AgentOccam's simple design highlights LLMs' impressive zero-shot performance on web tasks, and underlines the critical role of carefully tuning observation and action spaces for LLM-based agents.

cs.AI↗

arXiv2025

MLZero: A Multi-Agent System for End-to-end Machine Learning Automation

Existing AutoML systems have advanced the automation of machine learning (ML); however, they still require substantial manual configuration and expert input, particularly when handling multimodal data. We introduce MLZero, a novel multi-agent framework powered by Large Language Models (LLMs) that enables end-to-end ML automation across diverse data modalities with minimal human intervention. A cognitive perception module is first employed, transforming raw multimodal inputs into perceptual context that effectively guides the subsequent workflow. To address key limitations of LLMs, such as hallucinated code generation and outdated API knowledge, we enhance the iterative code generation process with semantic and episodic memory. MLZero demonstrates superior performance on MLE-Bench Lite, outperforming all competitors in both success rate and solution quality, securing six gold medals. Additionally, when evaluated on our Multimodal AutoML Agent Benchmark, which includes 25 more challenging tasks spanning diverse data modalities, MLZero outperforms the competing methods by a large margin with a success rate of 0.92 (+263.6\%) and an average rank of 2.28. Our approach maintains its robust effectiveness even with a compact 8B LLM, outperforming full-size systems from existing solutions.

cs.MA↗

arXiv2025

Long-context Protein Language Modeling Using Bidirectional Mamba with Shared Projection Layers

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built upon selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and up to 30% and 16% improvements on protein downstream tasks compared to Transformer-based ESM-2 when trained with 100B and 1T tokens, respectively. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g., structured state space models) in learning universal protein representations and incorporating molecular interaction contexts contained in biological graphs.

q-bio.BM↗

arXiv2025

From Demonstrations to Rewards: Alignment Without Explicit Human Preferences

One of the challenges of aligning large models with human preferences lies in both the data requirements and the technical complexities of current approaches. Predominant methods, such as RLHF, involve multiple steps, each demanding distinct types of data, including demonstration data and preference data. In RLHF, human preferences are typically modeled through a reward model, which serves as a proxy to guide policy learning during the reinforcement learning stage, ultimately producing a policy aligned with human preferences. However, in this paper, we propose a fresh perspective on learning alignment based on inverse reinforcement learning principles, where the optimal policy is still derived from reward maximization. However, instead of relying on preference data, we directly learn the reward model from demonstration data. This new formulation offers the flexibility to be applied even when only demonstration data is available, a capability that current RLHF methods lack, and it also shows that demonstration data offers more utility than what conventional wisdom suggests. Our extensive evaluation, based on public reward benchmark, HuggingFace Open LLM Leaderboard and MT-Bench, demonstrates that our approach compares favorably to state-of-the-art methods that rely solely on demonstration data.

cs.LG↗

arXiv2025

Understanding Silent Data Corruption in LLM Training

As the scale of training large language models (LLMs) increases, one emergent failure is silent data corruption (SDC), where hardware produces incorrect computations without explicit failure signals. In this work, we are the first to investigate the impact of real-world SDCs on LLM training by comparing model training between healthy production nodes and unhealthy nodes exhibiting SDCs. With the help from a cloud computing platform, we access the unhealthy nodes that were swept out from production by automated fleet management. Using deterministic execution via XLA compiler and our proposed synchronization mechanisms, we isolate and analyze the impact of SDC errors on these nodes at three levels: at each submodule computation, at a single optimizer step, and at a training period. Our results reveal that the impact of SDCs on computation varies on different unhealthy nodes. Although in most cases the perturbations from SDCs on submodule computation and gradients are relatively small, SDCs can lead models to converge to different optima with different weights and even cause spikes in the training loss. Our analysis sheds light on further understanding and mitigating the impact of SDCs.

cs.LG↗

arXiv2025

Variational Causal Inference

Estimating an individual's potential outcomes under counterfactual treatments is a challenging task for traditional causal inference and supervised learning approaches when the outcome is high-dimensional (e.g. gene expressions, impulse responses, human faces) and covariates are relatively limited. In this case, to construct one's outcome under a counterfactual treatment, it is crucial to leverage individual information contained in its observed factual outcome on top of the covariates. We propose a deep variational Bayesian framework that rigorously integrates two main sources of information for outcome construction under a counterfactual treatment: one source is the individual features embedded in the high-dimensional factual outcome; the other source is the response distribution of similar subjects (subjects with the same covariates) that factually received this treatment of interest.

stat.ML↗

arXiv2025

Predicting Cellular Responses with Variational Causal Inference and Refined Relational Information

Predicting the responses of a cell under perturbations may bring important benefits to drug discovery and personalized therapeutics. In this work, we propose a novel graph variational Bayesian causal inference framework to predict a cell's gene expressions under counterfactual perturbations (perturbations that this cell did not factually receive), leveraging information representing biological knowledge in the form of gene regulatory networks (GRNs) to aid individualized cellular response predictions. Aiming at a data-adaptive GRN, we also developed an adjacency matrix updating technique for graph convolutional networks and used it to refine GRNs during pre-training, which generated more insights on gene relations and enhanced model performance. Additionally, we propose a robust estimator within our framework for the asymptotically efficient estimation of marginal perturbation effect, which is yet to be carried out in previous works. With extensive experiments, we exhibited the advantage of our approach over state-of-the-art deep learning models for individual response prediction.

cs.LG↗

arXiv2025

CoddLLM: Empowering Large Language Models for Data Analytics

Large Language Models (LLMs) have the potential to revolutionize data analytics by simplifying tasks such as data discovery and SQL query synthesis through natural language interactions. This work serves as a pivotal first step toward the development of foundation models explicitly designed for data analytics applications. To propel this vision forward, we unveil a new data recipe for post-training LLMs, enhancing their comprehension of data management and empowering them to tackle complex real-world analytics tasks. Specifically, our innovative approach includes a scalable synthetic data generation method that enables the creation of a broad spectrum of topics centered on data representation and manipulation. Furthermore, we introduce two new tasks that seamlessly bridge tables and text. We show that such tasks can enhance models' understanding of schema creation and the nuanced translation between natural language and tabular data. Leveraging this data recipe, we post-train a new foundation model, named CoddLLM, based on Mistral-NeMo-12B. To assess the language understanding and reasoning capabilities of LLMs in the realm of data analytics, we contribute AnalyticsMMLU, a benchmark containing thousands of multiple-choice questions on databases, data analysis, and machine learning. Our focus on data discovery, has resulted in the contribution of three comprehensive benchmarks that address both database and data lake scenarios. CoddLLM not only excels in performance but also sets a new standard, achieving the highest average accuracy across eight datasets. It outperforms GPT-3.5-Turbo on AnalyticsMMLU, exceeding GPT-4o by 12.1% in table selection and showing an average improvement of 24.9% in Text-to-SQL compared to the base model.

cs.DB↗

arXiv2025

A Proximal Operator for Inducing 2:4-Sparsity

Recent hardware advancements in AI Accelerators and GPUs allow to efficiently compute sparse matrix multiplications, especially when 2 out of 4 consecutive weights are set to zero. However, this so-called 2:4 sparsity usually comes at a decreased accuracy of the model. We derive a regularizer that exploits the local correlation of features to find better sparsity masks in trained models. We minimize the regularizer jointly with a local squared loss by deriving the proximal operator for which we show that it has an efficient solution in the 2:4-sparse case. After optimizing the mask, we use maskedgradient updates to further minimize the local squared loss. We illustrate our method on toy problems and apply it to pruning entire large language models up to 70B parameters. On models up to 13B we improve over previous state of the art algorithms, whilst on 70B models we match their performance.

cs.LG↗

arXiv2025

Bridging the Training-Inference Gap in LLMs by Leveraging Self-Generated Tokens

Language models are often trained to maximize the likelihood of the next token given past tokens in the training dataset. However, during inference time, they are utilized differently, generating text sequentially and auto-regressively by using previously generated tokens as input to predict the next one. Marginal differences in predictions at each step can cascade over successive steps, resulting in different distributions from what the models were trained for and potentially leading to unpredictable behavior. This paper proposes two simple approaches based on model own generation to address this discrepancy between the training and inference time. Our first approach is Batch-Scheduled Sampling, where, during training, we stochastically choose between the ground-truth token from the dataset and the model's own generated token as input to predict the next token. This is done in an offline manner, modifying the context window by interleaving ground-truth tokens with those generated by the model. Our second approach is Reference-Answer-based Correction, where we explicitly incorporate a self-correction capability into the model during training. This enables the model to effectively self-correct the gaps between the generated sequences and the ground truth data without relying on an external oracle model. By incorporating our proposed strategies during training, we have observed an overall improvement in performance compared to baseline methods, as demonstrated by our extensive experiments using summarization, general question-answering, and math question-answering tasks.

cs.LG↗

arXiv2024

Pre-training Differentially Private Models with Limited Public Data

The superior performance of large foundation models relies on the use of massive amounts of high-quality data, which often contain sensitive, private and copyrighted material that requires formal protection. While differential privacy (DP) is a prominent method to gauge the degree of security provided to the models, its application is commonly limited to the model fine-tuning stage, due to the performance degradation when applying DP during the pre-training stage. Consequently, DP is yet not capable of protecting a substantial portion of the data used during the initial pre-training process. In this work, we first provide a theoretical understanding of the efficacy of DP training by analyzing the per-iteration loss improvement. We make a key observation that DP optimizers' performance degradation can be significantly mitigated by the use of limited public data, which leads to a novel DP continual pre-training strategy. Empirically, using only 10\% of public data, our strategy can achieve DP accuracy of 41.5\% on ImageNet-21k (with $ε=8$), as well as non-DP accuracy of 55.7\% and and 60.0\% on downstream tasks Places365 and iNaturalist-2021, respectively, on par with state-of-the-art standard pre-training and substantially outperforming existing DP pre-trained models. Our DP pre-trained models are released in fastDP library (https://github.com/awslabs/fast-differential-privacy/releases/tag/v2.1)

cs.LG↗

arXiv2024

Fine-Tuning Language Models on Multiple Datasets for Citation Intention Classification

Citation intention Classification (CIC) tools classify citations by their intention (e.g., background, motivation) and assist readers in evaluating the contribution of scientific literature. Prior research has shown that pretrained language models (PLMs) such as SciBERT can achieve state-of-the-art performance on CIC benchmarks. PLMs are trained via self-supervision tasks on a large corpus of general text and can quickly adapt to CIC tasks via moderate fine-tuning on the corresponding dataset. Despite their advantages, PLMs can easily overfit small datasets during fine-tuning. In this paper, we propose a multi-task learning (MTL) framework that jointly fine-tunes PLMs on a dataset of primary interest together with multiple auxiliary CIC datasets to take advantage of additional supervision signals. We develop a data-driven task relation learning (TRL) method that controls the contribution of auxiliary datasets to avoid negative transfer and expensive hyper-parameter tuning. We conduct experiments on three CIC datasets and show that fine-tuning with additional datasets can improve the PLMs' generalization performance on the primary dataset. PLMs fine-tuned with our proposed framework outperform the current state-of-the-art models by 7% to 11% on small datasets while aligning with the best-performing model on a large dataset.

cs.CL↗

arXiv2024

Extreme Miscalibration and the Illusion of Adversarial Robustness

Deep learning-based Natural Language Processing (NLP) models are vulnerable to adversarial attacks, where small perturbations can cause a model to misclassify. Adversarial Training (AT) is often used to increase model robustness. However, we have discovered an intriguing phenomenon: deliberately or accidentally miscalibrating models masks gradients in a way that interferes with adversarial attack search methods, giving rise to an apparent increase in robustness. We show that this observed gain in robustness is an illusion of robustness (IOR), and demonstrate how an adversary can perform various forms of test-time temperature calibration to nullify the aforementioned interference and allow the adversarial attack to find adversarial examples. Hence, we urge the NLP community to incorporate test-time temperature scaling into their robustness evaluations to ensure that any observed gains are genuine. Finally, we show how the temperature can be scaled during \textit{training} to improve genuine robustness.

cs.CL↗

arXiv2024

Inference Optimization of Foundation Models on AI Accelerators

Powerful foundation models, including large language models (LLMs), with Transformer architectures have ushered in a new era of Generative AI across various industries. Industry and research community have witnessed a large number of new applications, based on those foundation models. Such applications include question and answer, customer services, image and video generation, and code completions, among others. However, as the number of model parameters reaches to hundreds of billions, their deployment incurs prohibitive inference costs and high latency in real-world scenarios. As a result, the demand for cost-effective and fast inference using AI accelerators is ever more higher. To this end, our tutorial offers a comprehensive discussion on complementary inference optimization techniques using AI accelerators. Beginning with an overview of basic Transformer architectures and deep learning system frameworks, we deep dive into system optimization techniques for fast and memory-efficient attention computations and discuss how they can be implemented efficiently on AI accelerators. Next, we describe architectural elements that are key for fast transformer inference. Finally, we examine various model compression and fast decoding strategies in the same context.

cs.AI↗

arXiv2024

Revisiting SMoE Language Models by Evaluating Inefficiencies with Task Specific Expert Pruning

Sparse Mixture of Expert (SMoE) models have emerged as a scalable alternative to dense models in language modeling. These models use conditionally activated feedforward subnetworks in transformer blocks, allowing for a separation between total model parameters and per-example computation. However, large token-routed SMoE models face a significant challenge: during inference, the entire model must be used for a sequence or a batch, resulting in high latencies in a distributed setting that offsets the advantages of per-token sparse activation. Our research explores task-specific model pruning to inform decisions about designing SMoE architectures, mainly modulating the choice of expert counts in pretraining. We investigate whether such pruned models offer advantages over smaller SMoE models trained from scratch, when evaluating and comparing them individually on tasks. To that end, we introduce an adaptive task-aware pruning technique UNCURL to reduce the number of experts per MoE layer in an offline manner post-training. Our findings reveal a threshold pruning factor for the reduction that depends on the number of experts used in pretraining, above which, the reduction starts to degrade model performance. These insights contribute to our understanding of model design choices when pretraining with SMoE architectures, particularly useful when considering task-specific inference optimization for later stages.

cs.LG↗