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Joseph Lee

Publications and source records attributed to Joseph Lee.

16 recordsLinked to original sources

Knowledge Acquisition During Pre-training? Large Language Models Learn Better With Auxiliary Views

Gaps remain in our understanding of how large language models (LLMs) acquire knowledge during pre-training. We posit that auxiliary views, reformulations of knowledge, are causally helpful for learning. We design controlled experiments to isolate this. First, we confirm that repetition is necessary for acquisition and clarify that paraphrasing helps only at smaller batch sizes. Second, holding the token budget fixed, allocating tokens from document repetition to auxiliary views improves learning, counterintuitively, even for factual recall. Third, the effectiveness of auxiliary views is not contingent on the strength of the teacher model that generates them. Fourth, we identify forms of knowledge, contextual and foundational, that aid learning in the presence of prior knowledge gaps. Finally, we examine how these effects manifest mechanistically via layer-wise biases and compression. Together, our findings suggest that auxiliary representations of knowledge, which arise naturally in large pre-training corpora, are a key factor in the success of pre-training and offer a plausible explanation for why data diversity matters.

cs.CL

BaRA: Budget-constrained and Reliable Web Data Collection Agent

Large language model (LLM)-based web agents automate web navigation and data collection. However, live web data collection demands capabilities beyond task completion: agents must discover site-internal pages and retrieve text, image, and video artifacts in an accessible form within a fixed interaction budget. We formulate this setting as budget-constrained, site-level multimodal web data collection and propose Budget-constrained and Reliable Agent (BaRA). BaRA performs breadth-first search (BFS)-based link discovery with liveness verification to filter hallucinated and dead links, then validates extracted multimodal artifacts using rule-based provenance and accessibility checks. A history-based self-reflection module recovers from execution failures and incomplete outputs. On controlled synthetic and real-world websites, BaRA consistently improves valid-link discovery and download-valid multimodal extraction over existing agents. Our code is available at https://github.com/MLAI-Yonsei/BaRA-Agent.

cs.IR

StochasTok: Improving Fine-Grained Subword Understanding in LLMs

Subword-level understanding is integral to numerous tasks, including understanding multi-digit numbers, spelling mistakes, abbreviations, rhyming, and wordplay. Despite this, current large language models (LLMs) still struggle disproportionally with simple subword-level tasks like 'How many r's in strawberry?'. A key factor behind these failures is tokenization, which obscures the fine-grained structure of words. Current alternatives, such as character-level and dropout tokenization methods, significantly increase computational costs and provide inconsistent improvements. In this paper we revisit tokenization and introduce StochasTok, a simple, efficient stochastic tokenization scheme that randomly splits tokens during training, allowing LLMs to 'see' their internal structure. Our experiments show that pretraining with StochasTok substantially improves LLMs' downstream performance across multiple subword-level language games, including character counting, substring identification, and math tasks. Furthermore, StochasTok's simplicity allows seamless integration at any stage of the training pipeline; and we demonstrate that post-training with StochasTok can instill improved subword understanding into existing pretrained models, thus avoiding costly pretraining from scratch. These dramatic improvements achieved with a minimal change suggest StochasTok holds exciting potential when applied to larger, more capable models. Code open-sourced at: github.com/anyasims/stochastok.

cs.CL

From Promising Capability to Pervasive Bias: Assessing Large Language Models for Emergency Department Triage

Large Language Models (LLMs) have shown promise in clinical decision support, yet their application to triage remains underexplored. We systematically investigate the capabilities of LLMs in emergency department triage through two key dimensions: (1) robustness to distribution shifts and missing data, and (2) counterfactual analysis of intersectional biases across sex and race. We assess multiple LLM-based approaches, ranging from continued pre-training to in-context learning, as well as machine learning approaches. Our results indicate that LLMs exhibit superior robustness, and we investigate the key factors contributing to the promising LLM-based approaches. Furthermore, in this setting, we identify gaps in LLM preferences that emerge in particular intersections of sex and race. LLMs generally exhibit sex-based differences, but they are most pronounced in certain racial groups. These findings suggest that LLMs encode demographic preferences that may emerge in specific clinical contexts or particular combinations of characteristics.

cs.AI

Advances in RNA secondary structure prediction and RNA modifications: Methods, data, and applications

Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic. This review sets out to explore the computational prediction of RNA secondary structure and its connections to RNA modifications, which have emerged as an active domain in recent years. We first examine the progression of RNA secondary structure prediction methodology, focusing on a set of representative works categorized into thermodynamic, comparative, machine learning, and hybrid approaches. Next, we survey the advances in RNA modifications and computational methods for identifying RNA modifications, focusing on the prominent modification types. Subsequently, we highlight the interplay between RNA modifications and secondary structures, emphasizing how modifications such as m6A dynamically affect RNA folding and vice versa. In addition, we also review relevant data sources and provide a discussion of current challenges and opportunities in the field. Ultimately, we hope our review will be able to serve as a cornerstone to aid in the development of innovative methods for this emerging topic and foster therapeutic applications in the future.

q-bio.BM

Navigation under uncertainty: Trajectory prediction and occlusion reasoning with switching dynamical systems

Predicting future trajectories of nearby objects, especially under occlusion, is a crucial task in autonomous driving and safe robot navigation. Prior works typically neglect to maintain uncertainty about occluded objects and only predict trajectories of observed objects using high-capacity models such as Transformers trained on large datasets. While these approaches are effective in standard scenarios, they can struggle to generalize to the long-tail, safety-critical scenarios. In this work, we explore a conceptual framework unifying trajectory prediction and occlusion reasoning under the same class of structured probabilistic generative model, namely, switching dynamical systems. We then present some initial experiments illustrating its capabilities using the Waymo open dataset.

cs.RO

Knowledge-Driven Feature Selection and Engineering for Genotype Data with Large Language Models

Predicting phenotypes with complex genetic bases based on a small, interpretable set of variant features remains a challenging task. Conventionally, data-driven approaches are utilized for this task, yet the high dimensional nature of genotype data makes the analysis and prediction difficult. Motivated by the extensive knowledge encoded in pre-trained LLMs and their success in processing complex biomedical concepts, we set to examine the ability of LLMs in feature selection and engineering for tabular genotype data, with a novel knowledge-driven framework. We develop FREEFORM, Free-flow Reasoning and Ensembling for Enhanced Feature Output and Robust Modeling, designed with chain-of-thought and ensembling principles, to select and engineer features with the intrinsic knowledge of LLMs. Evaluated on two distinct genotype-phenotype datasets, genetic ancestry and hereditary hearing loss, we find this framework outperforms several data-driven methods, particularly on low-shot regimes. FREEFORM is available as open-source framework at GitHub: https://github.com/PennShenLab/FREEFORM.

cs.LG

Pragma driven shared memory parallelism in Zig by supporting OpenMP loop directives

The Zig programming language, which is designed to provide performance and safety as first class concerns, has become popular in recent years. Given that Zig is built upon LLVM, and-so enjoys many of the benefits provided by the ecosystem, including access to a rich set of backends, Zig has significant potential for high performance workloads. However, it is yet to gain acceptance in HPC and one of the reasons for this is that support for the pragma driven shared memory parallelism is missing. In this paper we describe enhancing the Zig compiler to add support for OpenMP loop directives. Then exploring performance using NASA's NAS Parallel Benchmark (NPB) suite. We demonstrate that not only does our integration of OpenMP with Zig scale comparatively to Fortran and C reference implementations of NPB, but furthermore Zig provides up to a 1.25 times performance increase compared to Fortran.

cs.DC

Implementing OpenMP for Zig to enable its use in HPC context

This extended abstract explores supporting OpenMP in the Zig programming language. Whilst, C and Fortran are currently the main languages used to implement HPC applications, Zig provides a similar level of performance complimented with several modern language features, such as enforcing memory safety. However, Zig lacks support for OpenMP which is the de facto threaded programming technology. Leveraging Zig's LLVM compiler tooling, we have added partial support for OpenMP to the Zig compiler and demonstrated that the performance attained by using Zig with OpenMP is comparable to, and in come cases exceeds, that of conventional HPC languages. Consequently we demonstrate that Zig is a viable and important programming technology to use for HPC, and this work paves the way for more HPC features to be added to Zig, ultimately providing HPC developers with the option of using a safer, more modern language for creating high performance applications.

cs.DC

DALK: Dynamic Co-Augmentation of LLMs and KG to answer Alzheimer's Disease Questions with Scientific Literature

Recent advancements in large language models (LLMs) have achieved promising performances across various applications. Nonetheless, the ongoing challenge of integrating long-tail knowledge continues to impede the seamless adoption of LLMs in specialized domains. In this work, we introduce DALK, a.k.a. Dynamic Co-Augmentation of LLMs and KG, to address this limitation and demonstrate its ability on studying Alzheimer's Disease (AD), a specialized sub-field in biomedicine and a global health priority. With a synergized framework of LLM and KG mutually enhancing each other, we first leverage LLM to construct an evolving AD-specific knowledge graph (KG) sourced from AD-related scientific literature, and then we utilize a coarse-to-fine sampling method with a novel self-aware knowledge retrieval approach to select appropriate knowledge from the KG to augment LLM inference capabilities. The experimental results, conducted on our constructed AD question answering (ADQA) benchmark, underscore the efficacy of DALK. Additionally, we perform a series of detailed analyses that can offer valuable insights and guidelines for the emerging topic of mutually enhancing KG and LLM. We will release the code and data at https://github.com/David-Li0406/DALK.

cs.CL

Is RISC-V ready for HPC prime-time: Evaluating the 64-core Sophon SG2042 RISC-V CPU

The Sophon SG2042 is the world's first commodity 64-core RISC-V CPU for high performance workloads and an important question is whether the SG2042 has the potential to encourage the HPC community to embrace RISC-V. In this paper we undertaking a performance exploration of the SG2042 against existing RISC-V hardware and high performance x86 CPUs in use by modern supercomputers. Leveraging the RAJAPerf benchmarking suite, we discover that on average, the SG2042 delivers, per core, between five and ten times the performance compared to the nearest widely available RISC-V hardware. We found that, on average, the x86 high performance CPUs under test outperform the SG2042 by between four and eight times for multi-threaded workloads, although some individual kernels do perform faster on the SG2042. The result of this work is a performance study that not only contrasts this new RISC-V CPU against existing technologies, but furthermore shares performance best practice.

cs.DC

Improved statistical benchmarking of digital pathology models using pairwise frames evaluation

Nested pairwise frames is a method for relative benchmarking of cell or tissue digital pathology models against manual pathologist annotations on a set of sampled patches. At a high level, the method compares agreement between a candidate model and pathologist annotations with agreement among pathologists' annotations. This evaluation framework addresses fundamental issues of data size and annotator variability in using manual pathologist annotations as a source of ground truth for model validation. We implemented nested pairwise frames evaluation for tissue classification, cell classification, and cell count prediction tasks and show results for cell and tissue models deployed on an H&E-stained melanoma dataset.

cs.CV

Cooperation and Cognition in Social Networks

Social networks can sustain cooperation by amplifying the consequences of a single defection through a cascade of relationship losses. Building on Jackson et al. (2012), we introduce a novel robustness notion to characterize low cognitive complexity (LCC) networks - a subset of equilibrium networks that imposes a minimal cognitive burden to calculate and comprehend the consequences of defection. We test our theory in a laboratory experiment and find that cooperation is higher in equilibrium than in non-equilibrium networks. Within equilibrium networks, LCC networks exhibit higher levels of cooperation than non-LCC networks. Learning is essential for the emergence of equilibrium play.

econ.GN

Two-stage stochastic programming approach for path planning problems under travel time and availability uncertainties

Significant advances in sensing, robotics, and wireless networks have enabled the collaborative utilization of autonomous aerial, ground and underwater vehicles for various applications. However, to successfully harness the benefits of these unmanned ground vehicles (UGVs) in homeland security operations, it is critical to efficiently solve UGV path planning problem which lies at the heart of these operations. Furthermore, in the real-world applications of UGVs, these operations encounter uncertainties such as incomplete information about the target sites, travel times, and the availability of vehicles, sensors, and fuel. This research paper focuses on developing algebraic-based-modeling framework to enable the successful deployment of a team of vehicles while addressing uncertainties in the distance traveled and the availability of UGVs for the mission.

math.OC

Tree Search Techniques for Minimizing Detectability and Maximizing Visibility

We introduce and study the problem of planning a trajectory for an agent to carry out a scouting mission while avoiding being detected by an adversarial guard. This introduces an adversarial version of classical visibility-based planning problems such as the Watchman Route Problem. The agent receives a positive reward for increasing its visibility and a negative penalty when it is detected by the guard. The objective is to find a finite-horizon path for the agent that balances the trade-off maximizing visibility and minimizing detectability. We model this problem as a sequential two-player zero-sum discrete game. A minimax tree search can give the optimal policy for the agent but requires an exponential-time computation and space. We propose several pruning techniques to reduce the computational cost while still preserving optimality guarantees. Simulation results show that the proposed strategy prunes approximately three orders of magnitude nodes as compared to the brute-force strategy.

cs.RO

A table-top, repetitive pulsed magnet for nonlinear and ultrafast spectroscopy in high magnetic fields up to 30 T

We have developed a mini-coil pulsed magnet system with direct optical access, ideally suited for nonlinear and ultrafast spectroscopy studies of materials in high magnetic fields up to 30 T. The apparatus consists of a small coil in a liquid nitrogen cryostat coupled with a helium flow cryostat to provide sample temperatures down to below 10 K. Direct optical access to the sample is achieved with the use of easily interchangeable windows separated by a short distance of ~135 mm on either side of the coupled cryostats with numerical apertures of 0.20 and 0.03 for measurements employing the Faraday geometry. As a demonstration, we performed time-resolved and time-integrated photoluminescence measurements as well as transmission measurements on InGaAs quantum wells.

cond-mat.mes-hall