arXiv subjects

Mayur Naik

Publications and source records attributed to Mayur Naik.

At least 37 records · Page 2Linked to original sources

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↗

arXiv2024

Relational Programming with Foundation Models

Foundation models have vast potential to enable diverse AI applications. The powerful yet incomplete nature of these models has spurred a wide range of mechanisms to augment them with capabilities such as in-context learning, information retrieval, and code interpreting. We propose Vieira, a declarative framework that unifies these mechanisms in a general solution for programming with foundation models. Vieira follows a probabilistic relational paradigm and treats foundation models as stateless functions with relational inputs and outputs. It supports neuro-symbolic applications by enabling the seamless combination of such models with logic programs, as well as complex, multi-modal applications by streamlining the composition of diverse sub-models. We implement Vieira by extending the Scallop compiler with a foreign interface that supports foundation models as plugins. We implement plugins for 12 foundation models including GPT, CLIP, and SAM. We evaluate Vieira on 9 challenging tasks that span language, vision, and structured and vector databases. Our evaluation shows that programs in Vieira are concise, can incorporate modern foundation models, and have comparable or better accuracy than competitive baselines.

cs.AI↗

arXiv2024

Data-Efficient Learning with Neural Programs

Many computational tasks can be naturally expressed as a composition of a DNN followed by a program written in a traditional programming language or an API call to an LLM. We call such composites "neural programs" and focus on the problem of learning the DNN parameters when the training data consist of end-to-end input-output labels for the composite. When the program is written in a differentiable logic programming language, techniques from neurosymbolic learning are applicable, but in general, the learning for neural programs requires estimating the gradients of black-box components. We present an algorithm for learning neural programs, called ISED, that only relies on input-output samples of black-box components. For evaluation, we introduce new benchmarks that involve calls to modern LLMs such as GPT-4 and also consider benchmarks from the neurosymbolic learning literature. Our evaluation shows that for the latter benchmarks, ISED has comparable performance to state-of-the-art neurosymbolic frameworks. For the former, we use adaptations of prior work on gradient approximations of black-box components as a baseline, and show that ISED achieves comparable accuracy but in a more data- and sample-efficient manner.

cs.LG↗

arXiv2024

Understanding the Effectiveness of Large Language Models in Detecting Security Vulnerabilities

While automated vulnerability detection techniques have made promising progress in detecting security vulnerabilities, their scalability and applicability remain challenging. The remarkable performance of Large Language Models (LLMs), such as GPT-4 and CodeLlama, on code-related tasks has prompted recent works to explore if LLMs can be used to detect vulnerabilities. In this paper, we perform a more comprehensive study by concurrently examining a higher number of datasets, languages and LLMs, and qualitatively evaluating performance across prompts and vulnerability classes while addressing the shortcomings of existing tools. Concretely, we evaluate the effectiveness of 16 pre-trained LLMs on 5,000 code samples from five diverse security datasets. These balanced datasets encompass both synthetic and real-world projects in Java and C/C++ and cover 25 distinct vulnerability classes. Overall, LLMs across all scales and families show modest effectiveness in detecting vulnerabilities, obtaining an average accuracy of 62.8% and F1 score of 0.71 across datasets. They are significantly better at detecting vulnerabilities only requiring intra-procedural analysis, such as OS Command Injection and NULL Pointer Dereference. Moreover, they report higher accuracies on these vulnerabilities than popular static analysis tools, such as CodeQL. We find that advanced prompting strategies that involve step-by-step analysis significantly improve performance of LLMs on real-world datasets in terms of F1 score (by upto 0.18 on average). Interestingly, we observe that LLMs show promising abilities at performing parts of the analysis correctly, such as identifying vulnerability-related specifications and leveraging natural language information to understand code behavior (e.g., to check if code is sanitized). We expect our insights to guide future work on LLM-augmented vulnerability detection systems.

cs.CR↗

arXiv2024

TorchQL: A Programming Framework for Integrity Constraints in Machine Learning

Finding errors in machine learning applications requires a thorough exploration of their behavior over data. Existing approaches used by practitioners are often ad-hoc and lack the abstractions needed to scale this process. We present TorchQL, a programming framework to evaluate and improve the correctness of machine learning applications. TorchQL allows users to write queries to specify and check integrity constraints over machine learning models and datasets. It seamlessly integrates relational algebra with functional programming to allow for highly expressive queries using only eight intuitive operators. We evaluate TorchQL on diverse use-cases including finding critical temporal inconsistencies in objects detected across video frames in autonomous driving, finding data imputation errors in time-series medical records, finding data labeling errors in real-world images, and evaluating biases and constraining outputs of language models. Our experiments show that TorchQL enables up to 13x faster query executions than baselines like Pandas and MongoDB, and up to 40% shorter queries than native Python. We also conduct a user study and find that TorchQL is natural enough for developers familiar with Python to specify complex integrity constraints.

cs.DB↗

arXiv2024

Program Structure Aware Precondition Generation

We introduce a novel approach for inferring natural preconditions from code. Our technique produces preconditions of high quality in terms of both correctness (modulo a test generator) and naturalness. Prior works generate preconditions from scratch through combinations of boolean predicates, but fall short in readability and ease of comprehension. Our innovation lies in, instead, leveraging the structure of a target method as a seed to infer a precondition through program transformations. Our evaluation shows that humans can more easily reason over preconditions inferred using our approach. Lastly, we instantiate our technique into a framework which can be applied at scale. We present a dataset of ~18k Java (method, precondition) pairs obtained by applying our framework to 87 real-world projects. We use this dataset to both evaluate our approach and draw useful insights for future research in precondition inference.

cs.SE↗

arXiv2024

Towards Compositionality in Concept Learning

Concept-based interpretability methods offer a lens into the internals of foundation models by decomposing their embeddings into high-level concepts. These concept representations are most useful when they are compositional, meaning that the individual concepts compose to explain the full sample. We show that existing unsupervised concept extraction methods find concepts which are not compositional. To automatically discover compositional concept representations, we identify two salient properties of such representations, and propose Compositional Concept Extraction (CCE) for finding concepts which obey these properties. We evaluate CCE on five different datasets over image and text data. Our evaluation shows that CCE finds more compositional concept representations than baselines and yields better accuracy on four downstream classification tasks. Code and data are available at https://github.com/adaminsky/compositional_concepts .

cs.CL↗

arXiv2024

DISCRET: Synthesizing Faithful Explanations For Treatment Effect Estimation

Designing faithful yet accurate AI models is challenging, particularly in the field of individual treatment effect estimation (ITE). ITE prediction models deployed in critical settings such as healthcare should ideally be (i) accurate, and (ii) provide faithful explanations. However, current solutions are inadequate: state-of-the-art black-box models do not supply explanations, post-hoc explainers for black-box models lack faithfulness guarantees, and self-interpretable models greatly compromise accuracy. To address these issues, we propose DISCRET, a self-interpretable ITE framework that synthesizes faithful, rule-based explanations for each sample. A key insight behind DISCRET is that explanations can serve dually as database queries to identify similar subgroups of samples. We provide a novel RL algorithm to efficiently synthesize these explanations from a large search space. We evaluate DISCRET on diverse tasks involving tabular, image, and text data. DISCRET outperforms the best self-interpretable models and has accuracy comparable to the best black-box models while providing faithful explanations. DISCRET is available at https://github.com/wuyinjun-1993/DISCRET-ICML2024.

cs.LG↗

arXiv2023

Do Machine Learning Models Learn Statistical Rules Inferred from Data?

Machine learning models can make critical errors that are easily hidden within vast amounts of data. Such errors often run counter to rules based on human intuition. However, rules based on human knowledge are challenging to scale or to even formalize. We thereby seek to infer statistical rules from the data and quantify the extent to which a model has learned them. We propose a framework SQRL that integrates logic-based methods with statistical inference to derive these rules from a model's training data without supervision. We further show how to adapt models at test time to reduce rule violations and produce more coherent predictions. SQRL generates up to 300K rules over datasets from vision, tabular, and language settings. We uncover up to 158K violations of those rules by state-of-the-art models for classification, object detection, and data imputation. Test-time adaptation reduces these violations by up to 68.7% with relative performance improvement up to 32%. SQRL is available at https://github.com/DebugML/sqrl.

cs.LG↗

arXiv2023

Rectifying Group Irregularities in Explanations for Distribution Shift

It is well-known that real-world changes constituting distribution shift adversely affect model performance. How to characterize those changes in an interpretable manner is poorly understood. Existing techniques to address this problem take the form of shift explanations that elucidate how to map samples from the original distribution toward the shifted one by reducing the disparity between these two distributions. However, these methods can introduce group irregularities, leading to explanations that are less feasible and robust. To address these issues, we propose Group-aware Shift Explanations (GSE), a method that produces interpretable explanations by leveraging worst-group optimization to rectify group irregularities. We demonstrate how GSE not only maintains group structures, such as demographic and hierarchical subpopulations, but also enhances feasibility and robustness in the resulting explanations in a wide range of tabular, language, and image settings.

cs.LG↗

arXiv2023

Improved Logical Reasoning of Language Models via Differentiable Symbolic Programming

Pre-trained large language models (LMs) struggle to perform logical reasoning reliably despite advances in scale and compositionality. In this work, we tackle this challenge through the lens of symbolic programming. We propose DSR-LM, a Differentiable Symbolic Reasoning framework where pre-trained LMs govern the perception of factual knowledge, and a symbolic module performs deductive reasoning. In contrast to works that rely on hand-crafted logic rules, our differentiable symbolic reasoning framework efficiently learns weighted rules and applies semantic loss to further improve LMs. DSR-LM is scalable, interpretable, and allows easy integration of prior knowledge, thereby supporting extensive symbolic programming to robustly derive a logical conclusion. The results of our experiments suggest that DSR-LM improves the logical reasoning abilities of pre-trained language models, resulting in a significant increase in accuracy of over 20% on deductive reasoning benchmarks. Furthermore, DSR-LM outperforms a variety of competitive baselines when faced with systematic changes in sequence length.

cs.AI↗

arXiv2023

Scallop: A Language for Neurosymbolic Programming

We present Scallop, a language which combines the benefits of deep learning and logical reasoning. Scallop enables users to write a wide range of neurosymbolic applications and train them in a data- and compute-efficient manner. It achieves these goals through three key features: 1) a flexible symbolic representation that is based on the relational data model; 2) a declarative logic programming language that is based on Datalog and supports recursion, aggregation, and negation; and 3) a framework for automatic and efficient differentiable reasoning that is based on the theory of provenance semirings. We evaluate Scallop on a suite of eight neurosymbolic applications from the literature. Our evaluation demonstrates that Scallop is capable of expressing algorithmic reasoning in diverse and challenging AI tasks, provides a succinct interface for machine learning programmers to integrate logical domain knowledge, and yields solutions that are comparable or superior to state-of-the-art models in terms of accuracy. Furthermore, Scallop's solutions outperform these models in aspects such as runtime and data efficiency, interpretability, and generalizability.

cs.PL↗

arXiv2023

Learning to Select Pivotal Samples for Meta Re-weighting

Sample re-weighting strategies provide a promising mechanism to deal with imperfect training data in machine learning, such as noisily labeled or class-imbalanced data. One such strategy involves formulating a bi-level optimization problem called the meta re-weighting problem, whose goal is to optimize performance on a small set of perfect pivotal samples, called meta samples. Many approaches have been proposed to efficiently solve this problem. However, all of them assume that a perfect meta sample set is already provided while we observe that the selections of meta sample set is performance critical. In this paper, we study how to learn to identify such a meta sample set from a large, imperfect training set, that is subsequently cleaned and used to optimize performance in the meta re-weighting setting. We propose a learning framework which reduces the meta samples selection problem to a weighted K-means clustering problem through rigorously theoretical analysis. We propose two clustering methods within our learning framework, Representation-based clustering method (RBC) and Gradient-based clustering method (GBC), for balancing performance and computational efficiency. Empirical studies demonstrate the performance advantage of our methods over various baseline methods.

cs.LG↗

arXiv2021

DeepMerge: Learning to Merge Programs

In collaborative software development, program merging is the mechanism to integrate changes from multiple programmers. Merge algorithms in modern version control systems report a conflict when changes interfere textually. Merge conflicts require manual intervention and frequently stall modern continuous integration pipelines. Prior work found that, although costly, a large majority of resolutions involve re-arranging text without writing any new code. Inspired by this observation we propose the first data-driven approach to resolve merge conflicts with a machine learning model. We realize our approach in a tool DeepMerge that uses a novel combination of (i) an edit-aware embedding of merge inputs and (ii) a variation of pointer networks, to construct resolutions from input segments. We also propose an algorithm to localize manual resolutions in a resolved file and employ it to curate a ground-truth dataset comprising 8,719 non-trivial resolutions in JavaScript programs. Our evaluation shows that, on a held out test set, DeepMerge can predict correct resolutions for 37% of non-trivial merges, compared to only 4% by a state-of-the-art semistructured merge technique. Furthermore, on the subset of merges with upto 3 lines (comprising 24% of the total dataset), DeepMerge can predict correct resolutions with 78% accuracy.

cs.SE↗

arXiv2019

Synthesizing Datalog Programs Using Numerical Relaxation

The problem of learning logical rules from examples arises in diverse fields, including program synthesis, logic programming, and machine learning. Existing approaches either involve solving computationally difficult combinatorial problems, or performing parameter estimation in complex statistical models. In this paper, we present Difflog, a technique to extend the logic programming language Datalog to the continuous setting. By attaching real-valued weights to individual rules of a Datalog program, we naturally associate numerical values with individual conclusions of the program. Analogous to the strategy of numerical relaxation in optimization problems, we can now first determine the rule weights which cause the best agreement between the training labels and the induced values of output tuples, and subsequently recover the classical discrete-valued target program from the continuous optimum. We evaluate Difflog on a suite of 34 benchmark problems from recent literature in knowledge discovery, formal verification, and database query-by-example, and demonstrate significant improvements in learning complex programs with recursive rules, invented predicates, and relations of arbitrary arity.

cs.AI↗

arXiv2019

PolyDroid: Learning-Driven Specialization of Mobile Applications

The increasing prevalence of mobile apps has led to a proliferation of resource usage scenarios in which they are deployed. This motivates the need to specialize mobile apps based on diverse and varying preferences of users. We propose a system, called PolyDroid, for automatically specializing mobile apps based on user preferences. The app developer provides a number of candidate configurations, called reductions, that limit the resource usage of the original app. The key challenge underlying PolyDroid concerns learning the quality of user experience under different reductions. We propose an active learning technique that requires few user experiments to determine the optimal reduction for a given resource usage specification. On a benchmark suite comprising 20 diverse, open-source Android apps, we demonstrate that on average, PolyDroid obtains more than 85% of the optimal performance using just two user experiments.

cs.SE↗

arXiv2019

Learning Neurosymbolic Generative Models via Program Synthesis

Significant strides have been made toward designing better generative models in recent years. Despite this progress, however, state-of-the-art approaches are still largely unable to capture complex global structure in data. For example, images of buildings typically contain spatial patterns such as windows repeating at regular intervals; state-of-the-art generative methods can't easily reproduce these structures. We propose to address this problem by incorporating programs representing global structure into the generative model---e.g., a 2D for-loop may represent a configuration of windows. Furthermore, we propose a framework for learning these models by leveraging program synthesis to generate training data. On both synthetic and real-world data, we demonstrate that our approach is substantially better than the state-of-the-art at both generating and completing images that contain global structure.

cs.LG↗

arXiv2010

Mantis: Predicting System Performance through Program Analysis and Modeling

We present Mantis, a new framework that automatically predicts program performance with high accuracy. Mantis integrates techniques from programming language and machine learning for performance modeling, and is a radical departure from traditional approaches. Mantis extracts program features, which are information about program execution runs, through program instrumentation. It uses machine learning techniques to select features relevant to performance and creates prediction models as a function of the selected features. Through program analysis, it then generates compact code slices that compute these feature values for prediction. Our evaluation shows that Mantis can achieve more than 93% accuracy with less than 10% training data set, which is a significant improvement over models that are oblivious to program features. The system generates code slices that are cheap to compute feature values.

cs.PF↗