arXiv subjects

Laks V. S. Lakshmanan

Publications and source records attributed to Laks V. S. Lakshmanan.

At least 19 recordsLinked to original sources

arXiv2026

GyroNovo: Error-Guided Fragment Imputation with Mass-Aware Attention for De Novo Peptide Sequencing

De novo peptide sequencing from tandem mass spectra is essential for identifying peptides without relying on reference databases. Despite advances in deep learning, accurate sequencing remains challenging because experimental spectra are often sparse, noisy, and incomplete, leaving informative b- and y-ion fragments unobserved. Existing methods attempt to recover this missing evidence via latent-space imputation before autoregressive decoding. However, they typically treat imputation as a fixed reconstruction task, without considering which missing fragments are most relevant to decoder errors. Moreover, existing peak representations do not explicitly model mass differences between peaks, despite their fundamental importance. We introduce GyroNovo, a framework with two main contributions. First, we use decoder errors observed during training to adapt the imputation objective, prioritizing fragments associated with frequent decoding errors. We further use the decoder error distribution to construct easy and hard augmented views of each spectrum, enabling the decoder to learn under varying degrees of spectral corruption and missing-fragment severity. Second, we introduce a mass-aware inductive bias into self-attention by using rotary embeddings to encode pairwise mass differences between spectral peaks. Together, these components align missing-fragment recovery with decoder behavior while explicitly incorporating the mass relationships that underlie peptide fragmentation. At inference time, GyroNovo retains a standard encoder-imputer-decoder architecture and requires neither additional inputs nor auxiliary search procedures. Experiments on NovoBench show gains of about 9 percentage points in peptide-level precision and 7 percentage points in amino-acid-level precision over the state-of-the-art baseline. Code: https://github.com/UBC-NLP/gyronovo.

cs.LG↗

arXiv2026

A Survey of Densest Subgraph Discovery on Large Graphs

With the prevalence of graphs for modeling complex relationships among objects, the topic of graph mining has attracted a great deal of attention from both academic and industrial communities in recent years. As one of the most fundamental problems in graph mining, the densest subgraph discovery (DSD) problem has found a wide spectrum of real applications, such as discovery of filter bubbles in social media, finding groups of actors propagating misinformation in social media, social network community detection, graph index construction, regulatory motif discovery in DNA, fake follower detection, and so on. Theoretically, DSD closely relates to other fundamental graph problems, such as network flow and bipartite matching. Triggered by these applications and connections, DSD has garnered much attention from the database, data mining, theory, and network communities. In this survey, we first highlight the importance of DSD in various real-world applications and the unique challenges that need to be addressed. Subsequently, we classify existing DSD solutions into several groups, which cover around 50 research papers published in many well-known venues (e.g., SIGMOD, PVLDB, TODS, WWW), and conduct a thorough review of these solutions in each group. Afterwards, we analyze and compare the models and solutions in these works. Finally, we point out a list of promising future research directions. It is our hope that this survey not only helps researchers have a better understanding of existing densest subgraph models and solutions, but also provides insights and identifies directions for future study.

cs.SI↗

arXiv2026

Parameterized Fair Resource Allocation under Diversity Constraints

Resource allocation across multiple agent groups arises in many applications including e-commerce recommendation systems, housing assignment, and course allocation, and is commonly formulated as an optimization problem with diversity constraints to ensure group fairness. Existing approaches typically enforce these constraints as hard conditions, which overly restrict the feasible solution space and often lead to suboptimal allocations. In this paper, we propose PRA, a parameterized framework for fair resource allocation under diversity constraints. Inspired by the use of risk-aversion parameters in economic models, PRA introduces a set of controllable inequality-aversion parameters to softly regulate group-level diversity, thereby enabling flexible trade-offs between fairness and allocation efficiency. With appropriately calibrated parameters, PRA yields fairness-optimal assignments that comply with the specified diversity constraints. To accommodate additional application-specific constraints, we further extend the framework to an adaptive variant, APRA. We establish that the optimality of both PRA and APRA holds regardless of the chosen fairness metric and the nature of the additional constraints, underscoring the generality and robustness of our approach. Extensive experiments on three real-world applications demonstrate that our proposed framework consistently outperforms existing baselines in both effectiveness and robustness.

cs.SI↗

arXiv2026

WISERouter: LLM Routing with Workload Budget Constraint

Large language models (LLMs) achieve impressive performance across multiple domains, but using the most capable model for every query is prohibitive at scale. LLM routing exploits diversity in model capability and cost by assigning each query to a suitable model to balance utility and budget. Current methods have two limitations: (i) they either use heuristics that do not always enforce the budget constraint or impose a fixed per-query budget that cannot adapt across the workload and leads to suboptimal performance; (ii) they require supervised learning on a dense dataset with statistics for every query-model pair, which is expensive to collect. To address these challenges, we formulate LLM routing as a constrained contextual multi-armed bandit problem and introduce WISERouter (WR for short), a framework that supports offline learning from historical interactions as well as online learning with exploration. We further prove that WR-Online achieves a sublinear regret bound of $O(\sqrt{T})$ over a time horizon $T$. Empirical results on RouterBench and SWE-Bench demonstrate that (i) WR-Offline surpasses existing baselines in performance under a fixed budget and adheres more closely to budget constraints, and (ii) WR-Online achieves comparable performance to the baselines, while using substantially less exploration data.

cs.LG↗

arXiv2026

DRFLOW: A Deep Research Benchmark for Personalized Workflow Prediction

Deep research (DR) systems are increasingly used for complex information-seeking tasks, but existing works mainly focus on generating reports and summaries. In contrast, many enterprise tasks instead require an agent to identify concrete workflows which is a sequence of action-steps. For example, rather than summarizing budgeting policies, an agent should be able to determine the steps needed to answer a question such as: "How do I request new headcount given a fixed budget?". Therefore, we introduce DRFLOW, a benchmark for evaluating personalized workflows predicted by agents from heterogeneous sources. Each task requires the agent to identify relevant evidence from scattered sources, then use that evidence to predict the correct action-step sequence for the user's task. DRFLOW contains 100 tasks across five domains, with 1,246 reference workflow steps grounded in more than 3,900 sources. We define seven diagnostic metrics covering factual grounding, step recovery, structural ordering, condition resolution, and personalization. We further present DRFLOW-Agent (DRFA), a workflow-oriented reference agent to predict personalized workflow. We show that although DRFA improves over strong baseline agents (upto 10.02% average F1 score), there is substantial room for improvement remains across these workflow metrics, indicating that predicting complete and correct personalized workflows remains a challenging frontier for deep research.

cs.AI↗

arXiv2026

Topology-Aware LLM-Driven Social Simulation: A Unified Framework for Efficient and Realistic Agent Dynamics

Social simulation is essential for understanding collective human behavior by modeling how individual interactions give rise to large-scale social dynamics. Recent advances in large language models (LLMs) have enabled multi-agent frameworks with human-like reasoning and communication capabilities. However, existing LLM-based simulations treat social networks as fixed communication scaffolds, failing to leverage the structural signals that shape behavioral convergence and heterogeneous influence in real-world systems, which often leads to inefficient and unrealistic dynamics. To address this challenge, we propose TopoSim, a unified topology-aware social simulation framework that explicitly integrates structural reasoning into agent interactions along two complementary dimensions. First, TopoSim aligns agents with similar structural roles and interaction contexts into shared backbone units, enabling coordinated updates that reduce redundant computation while preserving emergent social dynamics. Second, TopoSim models social influence as a structure-induced signal, introducing heterogeneous interaction patterns grounded in network topology rather than uniform influence assumptions. Extensive experiments across three social simulation frameworks and diverse datasets demonstrate that TopoSim achieves comparable or improved simulation fidelity while reducing token consumption by 50 - 90%. Moreover, our approach more accurately reproduces key structural phenomena observed in real-world social systems and exhibits strong generalization and scalability.

cs.SI↗

arXiv2026

Chinese Short-Form Creative Content Generation via Explanation-Oriented Multi-Objective Optimization

Chinese demonstrates high semantic compactness and rich metaphorical expressiveness, enabling limited text to convey dense meanings while increasing the difficulty of generation and verification, particularly in short-form creative natural language generation (CNLG). In the real world, users often require personalized, fine-grained creative constraints, making reliable verification critical to guiding optimization. According to Brunswik's Lens Model from psychology, constraints' achievement can be inferred from sufficient observable cues. Existing studies are mainly outcome-oriented, implicitly assuming that the outcome itself provides adequate cues for verification. However, this assumption breaks down in Chinese short-form CNLG (e.g., naming or advertising) with diverse personalized constraints, where extremely brief outcomes inherently offer limited information. Explanations can naturally serve as extra cues. Nevertheless, under complex constraints, LLMs' explanations may suffer from hallucination, incompleteness, or ambiguity. To address these, we novelly formalize the Chinese short-form CNLG task as a heterogeneous multi-objective optimization (HMO) issue that needs to jointly optimize multiple personalized constraints and explanation reliability. We further propose MAGIC-HMO, a training-free multi-agent framework that optimizes these objectives through iterative generation and verification under an explanation-oriented multi-objective strategy. Experiments on \emph{Chinese Baby Naming}, a challenging benchmark, demonstrate that MAGIC-HMO significantly outperforms six strong baselines across various LLM backbones. Relevant data and codes are available at https://github.com/foolfun/MAGIC_HMO.

cs.CL↗

arXiv2026

A Multi-Agent Approach for Claim Verification from Tabular Data Documents

We present a novel approach for claim verification from tabular data documents. Recent LLM-based approaches either employ complex pretraining/fine-tuning or decompose verification into subtasks, often lacking comprehensive explanations and generalizability. To address these limitations, we propose a Multi-Agentic framework for Claim verification (MACE) consisting of three specialized agents: Planner, Executor, and Verifier. Instead of elaborate finetuning, each agent employs a zero-shot Chain-of-Thought setup to perform its tasks. MACE produces interpretable verification traces, with the Planner generating explicit reasoning strategies, the Executor providing detailed computation steps, and the Verifier validating the logic. Experiments demonstrate that MACE achieves state-of-the-art (SOTA) performance on two datasets and performs on par with the best models on two others, while achieving 80--100\% of best performance with substantially smaller models: 27--92B parameters versus 235B. This combination of competitive performance, memory efficiency, and transparent reasoning highlights our framework's effectiveness.

cs.CL↗

arXiv2026

A Community-Based Approach for Stance Distribution and Argument Organization

The proliferation of online debate platforms and social media has led to an unprecedented volume of argumentative content on controversial topics from multiple perspectives. While this wealth of perspectives offers opportunities for developing critical thinking and breaking filter bubbles (Pariser 2011), the sheer volume and complexity of arguments make it challenging for readers to synthesize and comprehend diverse viewpoints effectively. We present an unsupervised graph-based approach for community-based argument organization that helps users navigate and understand complex argumentative landscapes. Our system analyzes collections of topic-focused articles and constructs a rich interaction graph by capturing multiple relationship types between arguments: topic similarity, semantic coherence, shared keywords, and common entities. We then employ community detection to identify argument communities that reveal homogeneous and heterogeneous viewpoint distributions. The detected communities are simplified through strategic graph operations to present users with digestible, yet comprehensive summaries of key argumentative patterns. Our approach requires no training data and can effectively process hundreds of articles while preserving nuanced relationships between arguments. Experimental results demonstrate our system's ability to identify meaningful argument communities and present them in an interpretable manner, facilitating users' understanding of complex socio-political debates.

cs.CL↗

arXiv2026

On Efficient Approximate Aggregate Nearest Neighbor Queries over Learned Representations

We study Aggregation Queries over Nearest Neighbors (AQNN), which compute aggregates over the learned representations of the neighborhood of a designated query object. For example, a medical professional may be interested in the average heart rate of patients whose representations are similar to that of an insomnia patient. Answering AQNNs accurately and efficiently is challenging due to the high cost of generating high-quality representations (e.g., via a deep learning model trained on human expert annotations) and the different sensitivities of different aggregation functions to neighbor selection errors. We address these challenges by combining high-quality and low-cost representations to approximate the aggregate. We characterize value- and count-sensitive AQNNs and propose the Sampler with Precision-Recall in Target (SPRinT), a query answering framework that works in three steps: (1) sampling, (2) nearest neighbor selection, and (3) aggregation. We further establish theoretical bounds on sample sizes and aggregation errors. Extensive experiments on five datasets from three domains (medical, social media, and e-commerce) demonstrate that SPRinT achieves the lowest aggregation error with minimal computation cost in most cases compared to existing solutions. SPRinT's performance remains stable as dataset size grows, confirming its scalability for large-scale applications requiring both accuracy and efficiency.

cs.DS↗

arXiv2025

Reflection Pretraining Enables Token-Level Self-Correction in Biological Sequence Models

Chain-of-Thought (CoT) prompting has significantly advanced task-solving capabilities in natural language processing with large language models. Unlike standard prompting, CoT encourages the model to generate intermediate reasoning steps, non-answer tokens, that help guide the model toward more accurate final outputs. These intermediate steps enable more complex reasoning processes such as error correction, memory management, future planning, and self-reflection. However, applying CoT to non-natural language domains, such as protein and RNA language models, is not yet possible, primarily due to the limited expressiveness of their token spaces (e.g., amino acid tokens). In this work, we propose and define the concept of language expressiveness: the ability of a given language, using its tokens and grammar, to encode information. We show that the limited expressiveness of protein language severely restricts the applicability of CoT-style reasoning. To overcome this, we introduce reflection pretraining, for the first time in a biological sequence model, which enables the model to engage in intermediate reasoning through the generation of auxiliary "thinking tokens" beyond simple answer tokens. Theoretically, we demonstrate that our augmented token set significantly enhances biological language expressiveness, thereby improving the overall reasoning capacity of the model. Experimentally, our pretraining approach teaches protein models to self-correct and leads to substantial performance gains compared to standard pretraining.

cs.CL↗

arXiv2025

Unifying Tree Search Algorithm and Reward Design for LLM Reasoning: A Survey

Deliberative tree search is a cornerstone of modern Large Language Model (LLM) research, driving the pivot from brute-force scaling toward algorithmic efficiency. This single paradigm unifies two critical frontiers: \textbf{Test-Time Scaling (TTS)}, which deploys on-demand computation to solve hard problems, and \textbf{Self-Improvement}, which uses search-generated data to durably enhance model parameters. However, this burgeoning field is fragmented and lacks a common formalism, particularly concerning the ambiguous role of the reward signal -- is it a transient heuristic or a durable learning target? This paper resolves this ambiguity by introducing a unified framework that deconstructs search algorithms into three core components: the \emph{Search Mechanism}, \emph{Reward Formulation}, and \emph{Transition Function}. We establish a formal distinction between transient \textbf{Search Guidance} for TTS and durable \textbf{Parametric Reward Modeling} for Self-Improvement. Building on this formalism, we introduce a component-centric taxonomy, synthesize the state-of-the-art, and chart a research roadmap toward more systematic progress in creating autonomous, self-improving agents.

cs.CL↗

arXiv2025

KRAFT: A Knowledge Graph-Based Framework for Automated Map Conflation

Digital maps play a crucial role in various applications such as navigation, fleet management, and ride-sharing, necessitating their accuracy and currency, which require timely updates. While the majority of geospatial databases (GDBs) provide high-quality information, their data is (i) limited to specific regions and/or (ii) missing some entities, even in their covered areas. Map conflation is the process of augmentation of a GDB using another GDB to conflate missing spatial features. Existing map conflation methods suffer from two main limitations: (1) They are designed for the conflation of linear objects (e.g., road networks) and cannot simply be extended to non-linear objects, thus missing information about most entities in the map. (2) They are heuristic algorithmic approaches that are based on pre-defined rules, unable to learn entities matching in a data-driven manner. To address these limitations, we design KRAFT, a learning based approach consisting of three parts: (1) Knowledge Graph Construction - where each GDB is represented by a knowledge graph, (2) Map Matching - where we use a knowledge graph alignment method as well as a geospatial feature encoder to match entities in obtained knowledge graphs, and (3) Map Merging - where we merge matched entities in the previous modules in a consistent manner, using a mixed integer linear programming formulation that fully merges the GDBs without adding any inconsistencies. Our experimental evaluation shows that not only does KRAFT achieve outstanding performance compared to state-of-the-art and baseline methods in map conflation tasks, but each of its modules (e.g., Map Matching and Map Merging) also separately outperforms traditional matching and merging methods.

cs.LG↗

arXiv2025

A Comprehensive Benchmark on Spectral GNNs: The Impact on Efficiency, Memory, and Effectiveness

With recent advancements in graph neural networks (GNNs), spectral GNNs have received increasing popularity by virtue of their ability to retrieve graph signals in the spectral domain. These models feature uniqueness in efficient computation as well as rich expressiveness, which stems from advanced management and profound understanding of graph data. However, few systematic studies have been conducted to assess spectral GNNs, particularly in benchmarking their efficiency, memory consumption, and effectiveness in a unified and fair manner. There is also a pressing need to select spectral models suitable for learning specific graph data and deploying them to massive web-scale graphs, which is currently constrained by the varied model designs and training settings. In this work, we extensively benchmark spectral GNNs with a focus on the spectral perspective, demystifying them as spectral graph filters. We analyze and categorize 35 GNNs with 27 corresponding filters, spanning diverse formulations and utilizations of the graph data. Then, we implement the filters within a unified spectral-oriented framework with dedicated graph computations and efficient training schemes. In particular, our implementation enables the deployment of spectral GNNs over million-scale graphs and various tasks with comparable performance and less overhead. Thorough experiments are conducted on the graph filters with comprehensive metrics on effectiveness and efficiency, offering novel observations and practical guidelines that are only available from our evaluations across graph scales. Different from the prevailing belief, our benchmark reveals an intricate landscape regarding the effectiveness and efficiency of spectral graph filters, demonstrating the potential to achieve desirable performance through tailored spectral manipulation of graph data.

cs.LG↗

arXiv2025

BEST-Route: Adaptive LLM Routing with Test-Time Optimal Compute

Large language models (LLMs) are powerful tools but are often expensive to deploy at scale. LLM query routing mitigates this by dynamically assigning queries to models of varying cost and quality to obtain a desired trade-off. Prior query routing approaches generate only one response from the selected model and a single response from a small (inexpensive) model was often not good enough to beat a response from a large (expensive) model due to which they end up overusing the large model and missing out on potential cost savings. However, it is well known that for small models, generating multiple responses and selecting the best can enhance quality while remaining cheaper than a single large-model response. We leverage this idea to propose BEST-Route, a novel routing framework that chooses a model and the number of responses to sample from it based on query difficulty and the quality thresholds. Experiments on real-world datasets demonstrate that our method reduces costs by up to 60% with less than 1% performance drop.

cs.LG↗

arXiv2025

Finding Locally Densest Subgraphs: Convex Programming with Edge and Triangle Density

Finding the densest subgraph (DS) from a graph is a fundamental problem in graph databases. The DS obtained, which reveals closely related entities, has been found to be useful in various application domains such as e-commerce, social science, and biology. However, in a big graph that contains billions of edges, it is desirable to find more than one subgraph cluster that is not necessarily the densest, yet they reveal closely related vertices. In this paper, we study the locally densest subgraph (LDS), a recently proposed variant of DS. An LDS is a subgraph which is the densest among the ``local neighbors''. Given a graph $G$, a number of LDSs can be returned, which reflect different dense regions of $G$ and thus give more information than DS. The existing LDS solution suffers from low efficiency. We thus develop a convex-programming-based solution that enables powerful pruning. We also extend our algorithm to triangle-based density to solve LTDS problem. Based on current algorithms, we propose a unified framework for the LDS and LTDS problems. Extensive experiments on thirteen real large graph datasets show that our proposed algorithm is up to four orders of magnitude faster than the state-of-the-art.

cs.DB↗

arXiv2025

BEACON: A Benchmark for Efficient and Accurate Counting of Subgraphs

Subgraph counting the task of determining the number of instances of a query pattern within a large graph lies at the heart of many critical applications, from analyzing financial networks and transportation systems to understanding biological interactions. Despite decades of work yielding efficient algorithmic (AL) solutions and, more recently, machine learning (ML) approaches, a clear comparative understanding is elusive. This gap stems from the absence of a unified evaluation framework, standardized datasets, and accessible ground truths, all of which hinder systematic analysis and fair benchmarking. To overcome these barriers, we introduce BEACON: a comprehensive benchmark designed to rigorously evaluate both AL and ML-based subgraph counting methods. BEACON provides a standardized dataset with verified ground truths, an integrated evaluation environment, and a public leaderboard, enabling reproducible and transparent comparisons across diverse approaches. Our extensive experiments reveal that while AL methods excel in efficiently counting subgraphs on very large graphs, they struggle with complex patterns (e.g., those exceeding six nodes). In contrast, ML methods are capable of handling larger patterns but demand massive graph data inputs and often yield suboptimal accuracy on small, dense graphs. These insights not only highlight the unique strengths and limitations of each approach but also pave the way for future advancements in subgraph counting techniques. Overall, BEACON represents a significant step towards unifying and accelerating research in subgraph counting, encouraging innovative solutions and fostering a deeper understanding of the trade-offs between algorithmic and machine learning paradigms.

cs.DS↗

arXiv2025

TRACE: Intra-visit Clinical Event Nowcasting via Effective Patient Trajectory Encoding

Electronic Health Records (EHR) have become a valuable resource for a wide range of predictive tasks in healthcare. However, existing approaches have largely focused on inter-visit event predictions, overlooking the importance of intra-visit nowcasting, which provides prompt clinical insights during an ongoing patient visit. To address this gap, we introduce the task of laboratory measurement prediction within a hospital visit. We study the laboratory data that, however, remained underexplored in previous work. We propose TRACE, a Transformer-based model designed for clinical event nowcasting by encoding patient trajectories. TRACE effectively handles long sequences and captures temporal dependencies through a novel timestamp embedding that integrates decay properties and periodic patterns of data. Additionally, we introduce a smoothed mask for denoising, improving the robustness of the model. Experiments on two large-scale electronic health record datasets demonstrate that the proposed model significantly outperforms previous methods, highlighting its potential for improving patient care through more accurate laboratory measurement nowcasting. The code is available at https://github.com/Amehi/TRACE.

cs.LG↗