arXiv subjects

Rongjie Liu

Publications and source records attributed to Rongjie Liu.

7 recordsLinked to original sources

arXiv2026

Complex Problem Solving in Large Language Models: A Statistical Control Survey and Diagnostic Framework

Complex problem solving (CPS) with large language models (LLMs) is often framed as a matter of stronger reasoning or longer generation. Yet early-step error amplification, prompt brittleness, and failures to revise incorrect commitments are difficult to explain by missing knowledge or expressive capacity alone. This survey interprets CPS as a sequential estimation-and-decision problem over a latent solution state. A controller maintains a belief about an unobserved solution trajectory, updates it as noisy intermediate evidence arrives, and decides whether to commit, verify, branch, roll back, or abstain to minimize expected loss. Reasoning supplies candidate transitions and interpretations, whereas process control shapes and evaluates those proposals and regulates subsequent transitions and observations. Within this framework, we organize existing methods around five components: explicit state representation, transition structuring, validation and constraint enforcement, search and rollback, and uncertainty management. We also interpret evaluation metrics according to the statistical quantities they estimate. The framework further yields a diagnostic hypothesis: interventions should be most effective when they target the error or uncertainty component implicated by an observed failure. We distinguish systematic, stochastic, and irreducible error together with epistemic and aleatoric uncertainty, and call this alignment problem-control fit and its failure control mismatch. For example, additional sampling may reduce sampling variability while leaving a shared systematic error unchanged. This perspective clarifies what current methods estimate and control, what remains uncontrolled, and why reliable validation, targeted recovery, calibrated uncertainty, and matched-budget evaluation are central open problems.

stat.ML↗

arXiv2025

GP-GPT: Large Language Model for Gene-Phenotype Mapping

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose significant challenges when adapting these models to the bioinformatics and biomedical field. To address these challenges, we present GP-GPT, the first specialized large language model for genetic-phenotype knowledge representation and genomics relation analysis. Our model is fine-tuned in two stages on a comprehensive corpus composed of over 3,000,000 terms in genomics, proteomics, and medical genetics, derived from multiple large-scale validated datasets and scientific publications. GP-GPT demonstrates proficiency in accurately retrieving medical genetics information and performing common genomics analysis tasks, such as genomics information retrieval and relationship determination. Comparative experiments across domain-specific tasks reveal that GP-GPT outperforms state-of-the-art LLMs, including Llama2, Llama3 and GPT-4. These results highlight GP-GPT's potential to enhance genetic disease relation research and facilitate accurate and efficient analysis in the fields of genomics and medical genetics. Our investigation demonstrated the subtle changes of bio-factor entities' representations in the GP-GPT, which suggested the opportunities for the application of LLMs to advancing gene-phenotype research.

cs.CL↗

arXiv2025

Alignment and Safety in Large Language Models: Safety Mechanisms, Training Paradigms, and Emerging Challenges

Due to the remarkable capabilities and growing impact of large language models (LLMs), they have been deeply integrated into many aspects of society. Thus, ensuring their alignment with human values and intentions has emerged as a critical challenge. This survey provides a comprehensive overview of practical alignment techniques, training protocols, and empirical findings in LLM alignment. We analyze the development of alignment methods across diverse paradigms, characterizing the fundamental trade-offs between core alignment objectives. Our analysis shows that while supervised fine-tuning enables basic instruction-following, preference-based methods offer more flexibility for aligning with nuanced human intent. We discuss state-of-the-art techniques, including Direct Preference Optimization (DPO), Constitutional AI, brain-inspired methods, and alignment uncertainty quantification (AUQ), highlighting their approaches to balancing quality and efficiency. We review existing evaluation frameworks and benchmarking datasets, emphasizing limitations such as reward misspecification, distributional robustness, and scalable oversight. We summarize strategies adopted by leading AI labs to illustrate the current state of practice. We conclude by outlining open problems in oversight, value pluralism, robustness, and continuous alignment. This survey aims to inform both researchers and practitioners navigating the evolving landscape of LLM alignment.

cs.AI↗

arXiv2025

AD-GPT: Large Language Models in Alzheimer's Disease

Large language models (LLMs) have emerged as powerful tools for medical information retrieval, yet their accuracy and depth remain limited in specialized domains such as Alzheimer's disease (AD), a growing global health challenge. To address this gap, we introduce AD-GPT, a domain-specific generative pre-trained transformer designed to enhance the retrieval and analysis of AD-related genetic and neurobiological information. AD-GPT integrates diverse biomedical data sources, including potential AD-associated genes, molecular genetic information, and key gene variants linked to brain regions. We develop a stacked LLM architecture combining Llama3 and BERT, optimized for four critical tasks in AD research: (1) genetic information retrieval, (2) gene-brain region relationship assessment, (3) gene-AD relationship analysis, and (4) brain region-AD relationship mapping. Comparative evaluations against state-of-the-art LLMs demonstrate AD-GPT's superior precision and reliability across these tasks, underscoring its potential as a robust and specialized AI tool for advancing AD research and biomarker discovery.

cs.CL↗

arXiv2025

Large Language Models for Bioinformatics

With the rapid advancements in large language model (LLM) technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.

q-bio.QM↗

arXiv2022

PPA: Principal Parcellation Analysis for Brain Connectomes and Multiple Traits

Our understanding of the structure of the brain and its relationships with human traits is largely determined by how we represent the structural connectome. Standard practice divides the brain into regions of interest (ROIs) and represents the connectome as an adjacency matrix having cells measuring connectivity between pairs of ROIs. Statistical analyses are then heavily driven by the (largely arbitrary) choice of ROIs. In this article, we propose a novel tractography-based representation of brain connectomes, which clusters fiber endpoints to define a data adaptive parcellation targeted to explain variation among individuals and predict human traits. This representation leads to Principal Parcellation Analysis (PPA), representing individual brain connectomes by compositional vectors building on a basis system of fiber bundles that captures the connectivity at the population level. PPA reduces subjectivity and facilitates statistical analyses. We illustrate the proposed approach through applications to data from the Human Connectome Project (HCP) and show that PPA connectomes improve power in predicting human traits over state-of-the-art methods based on classical connectomes, while dramatically improving parsimony and maintaining interpretability. Our PPA package is publicly available on GitHub, and can be implemented routinely for diffusion image data.

stat.AP↗

arXiv2020

Efficient in-situ image and video compression through probabilistic image representation

Fast and effective image compression for multi-dimensional images has become increasingly important for efficient storage and transfer of massive amounts of high-resolution images and videos. Desirable properties in compression methods include (1) high reconstruction quality at a wide range of compression rates while preserving key local details, (2) computational scalability, (3) applicability to a variety of different image/video types and of different dimensions, (4) progressive transmission, and (5) ease of tuning. We present such a method for multi-dimensional image compression called Compression via Adaptive Recursive Partitioning (CARP). CARP uses an optimal permutation of the image pixels inferred from a Bayesian probabilistic model on recursive partitions of the image to reduce its effective dimensionality, achieving a parsimonious representation that preserves information. CARP uses a multi-layer Bayesian hierarchical model to achieve in-situ compression along with self-tuning and regularization, with just one single parameter to be specified by the user to achieve the desired compression rate. Extensive numerical experiments using a variety of datasets including 2D still images, real-life YouTube videos, and surveillance videos show that CARP dominates the state-of-the-art image/video compression approaches---including JPEG, JPEG2000, BPG, MPEG4, HEVC and a neural network-based method---for all of these different image types and on nearly all of the individual images and videos over some methods.

eess.IV↗