arXiv subjects

Mayur Naik

Publications and source records attributed to Mayur Naik.

At least 19 recordsLinked to original sources

arXiv2026

The Output-Space Hypothesis: Enumerative Equivalence Checking for Tensor Programs

Tensor programs, as used in deep learning models, are a prime target for optimization, as small performance improvements can have a large impact across training or inference workloads. However, such optimizations are complicated and can produce subtle bugs. Traditionally, correctness is assumed when differential testing against a reference on random inputs fails to reveal bugs. However, the inputs to these programs are massive tensors, and finding bugs can require generating extremely low likelihood inputs with precise relationships among their values. We propose a novel way to find bugs more consistently by flipping the quantifiers. Rather than generating a single input and checking all output tensor locations for equivalence, what if you could check a single output tensor location's equivalence for all inputs? We implement this idea in a system, \dirigo, by using a novel symbolic execution strategy. We demonstrate that \dirigo can find bugs effectively in a public dataset of 6,988 AI-written CUDA kernels that are all marked correct by differential testing. Of these, \dirigo finds 600 kernels that are actually buggy, and finds 97.3\% of those bugs within two minutes.

cs.PL↗

arXiv2026

QLCoder: A Query Synthesizer For Static Analysis of Security Vulnerabilities

Static analysis tools provide a powerful means to detect security vulnerabilities by specifying queries that encode vulnerable code patterns. However, writing such queries is challenging and requires diverse expertise in security and program analysis. To address this challenge, we present QLCoder - an agentic framework that automatically synthesizes queries in CodeQL, a powerful static analysis engine, directly from a given CVE metadata. QLCode embeds an LLM in a synthesis loop with execution feedback, while constraining its reasoning using a custom MCP interface that allows structured interaction with a Language Server Protocol (for syntax guidance) and a RAG database (for semantic retrieval of queries and documentation). This approach allows QLCoder to generate syntactically and semantically valid security queries. We evaluate QLCode on 176 existing CVEs across 111 Java projects. Building upon the Claude Code agent framework, QLCoder synthesizes correct queries that detect the CVE in the vulnerable but not in the patched versions for 53.4% of CVEs. In comparison, using only Claude Code synthesizes 10% correct queries. QLCoder code is available publicly at https://github.com/neuralprogram/QLCoder.

cs.CR↗

arXiv2026

MathDuels: A Self-Play Benchmark That Grows

As frontier language models attain near-ceiling performance on static mathematical benchmarks, existing evaluations are increasingly unable to differentiate model capabilities, largely because they cast models solely as solvers of fixed problem sets. We introduce MathDuels, a self-play benchmark in which models occupy dual roles: each authors math problems under adversarial prompting and solves problems authored by every other participant. Problems are produced through a three-stage generation pipeline (meta-prompting, problem generation, and difficulty amplification), and validated by an independent verifier that excludes ill-posed questions. A Rasch model (Rasch, 1993) jointly estimates solver abilities and problem difficulties; author quality is derived from the difficulties of each model's authored problems. Experiments across 19 frontier models reveal that authoring and solving capabilities are partially decoupled, and that dual-role evaluation reveals capability separations invisible in single-role benchmarks. As newer models enter the arena, they produce problems that defeat previously dominant solvers, so the benchmark's difficulty co-evolves with participant strength rather than saturating at a fixed ceiling. We host a public leaderboard that updates as new models are released.

cs.CL↗

arXiv2026

Detecting Safety Violations Across Many Agent Traces

To identify safety violations, auditors often search over large sets of agent traces. This search is difficult because failures are often rare, complex, and sometimes even adversarially hidden and only detectable when multiple traces are analyzed together. These challenges arise in diverse settings such as misuse campaigns, covert sabotage, reward hacking, and prompt injection. Existing approaches struggle here for several reasons. Per-trace judges miss failures that only become visible across traces, naive agentic auditing does not scale to large trace collections, and fixed monitors are brittle to unanticipated behaviors. We introduce Meerkat, which combines clustering with agentic search to uncover violations specified in natural language. Through structured search and adaptive investigation of promising regions, Meerkat finds sparse failures without relying on seed scenarios, fixed workflows, or exhaustive enumeration. Across misuse, misalignment, and task gaming settings, Meerkat significantly improves detection of safety violations over baseline monitors, discovers widespread developer cheating on a top agent benchmark, and finds nearly 4x more examples of reward hacking on CyBench than previous audits.

cs.AI↗

arXiv2026

Do We Need Frontier Models to Verify Mathematical Proofs?

Advances in training, post-training, and inference-time methods have enabled frontier reasoning models to win gold medals in math competitions and settle challenging open problems. Gaining trust in the responses of these models requires that natural language proofs be checked for errors. LLM judges are increasingly being adopted to meet the growing demand for evaluating such proofs. While verification is considered easier than generation, what model capability does reliable verification actually require? We systematically evaluate four open-source and two frontier LLMs on datasets of human-graded natural language proofs of competition-level problems. We consider two key metrics: verifier accuracy and self-consistency (the rate of agreement across repeated judgments on the same proof). We observe that smaller open-source models are only up to ~10% behind frontier models in accuracy but they are up to ~25% more inconsistent. Furthermore, we see that verifier accuracy is sensitive to prompt choice across all models. We then demonstrate that the smaller models, in fact, do possess the mathematical capabilities to verify proofs at the level of frontier models, but they struggle to reliably elicit these capabilities with general judging prompts. Through an LLM-guided prompt search, we synthesize an ensemble of specialized prompts that overcome the specific failure modes of smaller models, boosting their performance by up to 9.1% in accuracy and 15.9% in self-consistency. These gains are realized across models and datasets, allowing models like Qwen3.5-35B to perform on par with frontier models such as Gemini 3.1 Pro for proof verification.

cs.LG↗

arXiv2026

CAMEL: An ECG Language Model for Forecasting Cardiac Events

Electrocardiograms (ECG) are electrical recordings of the heart that are critical for diagnosing cardiovascular conditions. ECG language models (ELMs) have recently emerged as a promising framework for ECG classification accompanied by report generation. However, current models cannot forecast future cardiac events despite the immense clinical value for planning earlier intervention. To address this gap, we propose CAMEL, the first ELM that is capable of inference over longer signal durations which enables its forecasting capability. Our key insight is a specialized ECG encoder which enables cross-understanding of ECG signals with text. We train CAMEL using established LLM training procedures, combining LoRA adaptation with a curriculum learning pipeline. Our curriculum includes ECG classification, metrics calculations, and multi-turn conversations to elicit reasoning. CAMEL demonstrates strong zero-shot performance across 6 tasks and 9 datasets, including ECGForecastBench, a new benchmark that we introduce for forecasting arrhythmias. CAMEL is on par with or surpasses ELMs and fully supervised baselines both in- and out-of-distribution, achieving SOTA results on ECGBench (+7.0% absolute average gain) as well as ECGForecastBench (+12.4% over fully supervised models and +21.1% over zero-shot ELMs).

cs.LG↗

arXiv2026

On Improving Neurosymbolic Learning by Exploiting the Representation Space

We study the problem of learning neural classifiers in a neurosymbolic setting where the hidden gold labels of input instances must satisfy a logical formula. Learning in this setting proceeds by first computing (a subset of) the possible combinations of labels that satisfy the formula and then computing a loss using those combinations and the classifiers' scores. One challenge is that the space of label combinations can grow exponentially, making learning difficult. We propose a technique that prunes this space by exploiting the intuition that instances with similar latent representations are likely to share the same label. While this intuition has been widely used in weakly supervised learning, its application in our setting is challenging due to label dependencies imposed by logical constraints. We formulate the pruning process as an integer linear program that discards inconsistent label combinations while respecting logical structure. Our approach, CLIPPER, is orthogonal to existing training algorithms and can be seamlessly integrated with them. Across 16 benchmarks over complex neurosymbolic tasks, we demonstrate that CLIPPER boosts the performance of state-of-the-art neurosymbolic engines like Scallop, Dolphin, and ISED by up to 48%, 53%, and 8%, leading to state-of-the-art accuracies.

cs.LG↗

arXiv2025

Dolphin: A Programmable Framework for Scalable Neurosymbolic Learning

Neurosymbolic learning enables the integration of symbolic reasoning with deep learning but faces significant challenges in scaling to complex symbolic programs, large datasets, or both. We introduce DOLPHIN, a framework that tackles these challenges by supporting neurosymbolic programs in Python, executing complex symbolic reasoning on the CPU while vectorizing probabilistic computations and gradient propagation on the GPU. Across 13 benchmarks spanning tasks over text, image, and video data, with symbolic reasoning features like recursion and black-box functions, DOLPHIN converges to state-of-the-art accuracies on the more complex benchmarks while existing frameworks such as Scallop, ISED, and IndeCateR+ fail to converge within the time limit. On simpler benchmarks, DOLPHIN matches their performance, while achieving these results 1.71x to 62x faster than the baselines. Overall, DOLPHIN advances the scalability of neurosymbolic frameworks, achieving state-of-the-art efficiency and convergence on difficult benchmarks where existing frameworks struggle. The code is published at https://github.com/Dolphin-NeSy/Dolphin.

cs.LG↗

arXiv2025

LASER: A Neuro-Symbolic Framework for Learning Spatial-Temporal Scene Graphs with Weak Supervision

Supervised approaches for learning spatio-temporal scene graphs (STSG) from video are greatly hindered due to their reliance on STSG-annotated videos, which are labor-intensive to construct at scale. Is it feasible to instead use readily available video captions as weak supervision? To address this question, we propose LASER, a neuro-symbolic framework to enable training STSG generators using only video captions. LASER employs large language models to first extract logical specifications with rich spatio-temporal semantic information from video captions. LASER then trains the underlying STSG generator to align the predicted STSG with the specification. The alignment algorithm overcomes the challenges of weak supervision by leveraging a differentiable symbolic reasoner and using a combination of contrastive, temporal, and semantics losses. The overall approach efficiently trains low-level perception models to extract a fine-grained STSG that conforms to the video caption. In doing so, it enables a novel methodology for learning STSGs without tedious annotations. We evaluate our method on three video datasets: OpenPVSG, 20BN, and MUGEN. Our approach demonstrates substantial improvements over fully-supervised baselines, achieving a unary predicate prediction accuracy of 27.78% (+12.65%) and a binary recall@5 of 0.42 (+0.22) on OpenPVSG. Additionally, LASER exceeds baselines by 7% on 20BN and 5.2% on MUGEN in terms of overall predicate prediction accuracy.

cs.CV↗

arXiv2025

ESCA: Contextualizing Embodied Agents via Scene-Graph Generation

Multi-modal large language models (MLLMs) are making rapid progress toward general-purpose embodied agents. However, existing MLLMs do not reliably capture fine-grained links between low-level visual features and high-level textual semantics, leading to weak grounding and inaccurate perception. To overcome this challenge, we propose ESCA, a framework that contextualizes embodied agents by grounding their perception in spatial-temporal scene graphs. At its core is SGCLIP, a novel, open-domain, promptable foundation model for generating scene graphs that is based on CLIP. SGCLIP is trained on 87K+ open-domain videos using a neurosymbolic pipeline that aligns automatically generated captions with scene graphs produced by the model itself, eliminating the need for human-labeled annotations. We demonstrate that SGCLIP excels in both prompt-based inference and task-specific fine-tuning, achieving state-of-the-art results on scene graph generation and action localization benchmarks. ESCA with SGCLIP improves perception for embodied agents based on both open-source and commercial MLLMs, achieving state of-the-art performance across two embodied environments. Notably, ESCA significantly reduces agent perception errors and enables open-source models to surpass proprietary baselines. We release the source code for SGCLIP model training at https://github.com/video-fm/LASER and for the embodied agent at https://github.com/video-fm/ESCA.

cs.CV↗

arXiv2025

Once Upon an Input: Reasoning via Per-Instance Program Synthesis

Large language models (LLMs) excel at zero-shot inference but continue to struggle with complex, multi-step reasoning. Recent methods that augment LLMs with intermediate reasoning steps such as Chain of Thought (CoT) and Program of Thought (PoT) improve performance but often produce undesirable solutions, especially in algorithmic domains. We introduce Per-Instance Program Synthesis (PIPS), a method that generates and refines programs at the instance-level using structural feedback without relying on task-specific guidance or explicit test cases. To further improve performance, PIPS incorporates a confidence metric that dynamically chooses between direct inference and program synthesis on a per-instance basis. Experiments across three frontier LLMs and 30 benchmarks including all tasks of Big Bench Extra Hard (BBEH), visual question answering tasks, relational reasoning tasks, and mathematical reasoning tasks show that PIPS improves the absolute harmonic mean accuracy by up to 8.6% and 9.4% compared to PoT and CoT respectively, and reduces undesirable program generations by 65.1% on the algorithmic tasks compared to PoT with Gemini-2.0-Flash.

cs.CL↗

arXiv2025

Stable Prediction of Adverse Events in Medical Time-Series Data

Early event prediction (EEP) systems continuously estimate a patient's imminent risk to support clinical decision-making. For bedside trust, risk trajectories must be accurate and temporally stable, shifting only with new, relevant evidence. However, current benchmarks (a) ignore stability of risk scores and (b) evaluate mainly on tabular inputs, leaving trajectory behavior untested. To address this gap, we introduce CAREBench, an EEP benchmark that evaluates deployability using multi-modal inputs-tabular EHR, ECG waveforms, and clinical text-and assesses temporal stability alongside predictive accuracy. We propose a stability metric that quantifies short-term variability in per-patient risk and penalizes abrupt oscillations based on local-Lipschitz constants. CAREBench spans six prediction tasks such as sepsis onset and compares classical learners, deep sequence models, and zero-shot LLMs. Across tasks, existing methods, especially LLMs, struggle to jointly optimize accuracy and stability, with notably poor recall at high-precision operating points. These results highlight the need for models that produce evidence-aligned, stable trajectories to earn clinician trust in continuous monitoring settings. (Code: https://github.com/SeewonChoi/CAREBench.)

cs.LG↗

arXiv2025

Lobster: A GPU-Accelerated Framework for Neurosymbolic Programming

Neurosymbolic programs combine deep learning with symbolic reasoning to achieve better data efficiency, interpretability, and generalizability compared to standalone deep learning approaches. However, existing neurosymbolic learning frameworks implement an uneasy marriage between a highly scalable, GPU-accelerated neural component and a slower symbolic component that runs on CPUs. We propose Lobster, a unified framework for harnessing GPUs in an end-to-end manner for neurosymbolic learning. Lobster maps a general neurosymbolic language based on Datalog to the GPU programming paradigm. This mapping is implemented via compilation to a new intermediate language called APM. The extra abstraction provided by apm allows Lobster to be both flexible, supporting discrete, probabilistic, and differentiable modes of reasoning on GPU hardware with a library of provenance semirings, and performant, implementing new optimization passes. We demonstrate that Lobster programs can solve interesting problems spanning the domains of natural language processing, image processing, program reasoning, bioinformatics, and planning. On a suite of 9 applications, Lobster achieves an average speedup of 3.9x over Scallop, a state-of-the-art neurosymbolic framework, and enables scaling of neurosymbolic solutions to previously infeasible tasks.

cs.PL↗

arXiv2025

Delta Activations: A Representation for Finetuned Large Language Models

The success of powerful open source Large Language Models (LLMs) has enabled the community to create a vast collection of post-trained models adapted to specific tasks and domains. However, navigating and understanding these models remains challenging due to inconsistent metadata and unstructured repositories. We introduce Delta Activations, a method to represent finetuned models as vector embeddings by measuring shifts in their internal activations relative to a base model. This representation allows for effective clustering by domain and task, revealing structure in the model landscape. Delta Activations also demonstrate desirable properties: it is robust across finetuning settings and exhibits an additive property when finetuning datasets are mixed. In addition, we show that Delta Activations can embed tasks via few-shot finetuning, and further explore its use for model selection and merging. We hope Delta Activations can facilitate the practice of reusing publicly available models. Code is available at https://github.com/OscarXZQ/delta_activations.

cs.LG↗

arXiv2025

The Road to Generalizable Neuro-Symbolic Learning Should be Paved with Foundation Models

Neuro-symbolic learning was proposed to address challenges with training neural networks for complex reasoning tasks with the added benefits of interpretability, reliability, and efficiency. Neuro-symbolic learning methods traditionally train neural models in conjunction with symbolic programs, but they face significant challenges that limit them to simplistic problems. On the other hand, purely-neural foundation models now reach state-of-the-art performance through prompting rather than training, but they are often unreliable and lack interpretability. Supplementing foundation models with symbolic programs, which we call neuro-symbolic prompting, provides a way to use these models for complex reasoning tasks. Doing so raises the question: What role does specialized model training as part of neuro-symbolic learning have in the age of foundation models? To explore this question, we highlight three pitfalls of traditional neuro-symbolic learning with respect to the compute, data, and programs leading to generalization problems. This position paper argues that foundation models enable generalizable neuro-symbolic solutions, offering a path towards achieving the original goals of neuro-symbolic learning without the downsides of training from scratch.

cs.LG↗

arXiv2025

IRIS: LLM-Assisted Static Analysis for Detecting Security Vulnerabilities

Software is prone to security vulnerabilities. Program analysis tools to detect them have limited effectiveness in practice due to their reliance on human labeled specifications. Large language models (or LLMs) have shown impressive code generation capabilities but they cannot do complex reasoning over code to detect such vulnerabilities especially since this task requires whole-repository analysis. We propose IRIS, a neuro-symbolic approach that systematically combines LLMs with static analysis to perform whole-repository reasoning for security vulnerability detection. Specifically, IRIS leverages LLMs to infer taint specifications and perform contextual analysis, alleviating needs for human specifications and inspection. For evaluation, we curate a new dataset, CWE-Bench-Java, comprising 120 manually validated security vulnerabilities in real-world Java projects. A state-of-the-art static analysis tool CodeQL detects only 27 of these vulnerabilities whereas IRIS with GPT-4 detects 55 (+28) and improves upon CodeQL's average false discovery rate by 5% points. Furthermore, IRIS identifies 4 previously unknown vulnerabilities which cannot be found by existing tools. IRIS is available publicly at https://github.com/iris-sast/iris.

cs.CR↗

arXiv2025

Where's the Bug? Attention Probing for Scalable Fault Localization

Ensuring code correctness remains a challenging problem even as large language models (LLMs) become increasingly capable at code-related tasks. While LLM-based program repair systems can propose bug fixes using only a user's bug report, their effectiveness is fundamentally limited by their ability to perform fault localization (FL), a challenging problem for both humans and LLMs. Existing FL approaches rely on executable test cases, require training on costly and often noisy line-level annotations, or demand resource-intensive LLMs. In this paper, we present Bug Attention Probe (BAP), a method which learns state-of-the-art fault localization without any direct localization labels, outperforming traditional FL baselines and prompting of large-scale LLMs. We evaluate our approach across a variety of code settings, including real-world Java bugs from the standard Defects4J dataset as well as seven other datasets which span a diverse set of bug types and languages. Averaged across all eight datasets, BAP improves by 34.6% top-1 accuracy compared to the strongest baseline and 93.4% over zero-shot prompting GPT-4o. BAP is also significantly more efficient than prompting, outperforming large open-weight models at a small fraction of the computational cost.

cs.SE↗

arXiv2025

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↗