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Ananth Grama

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14 published item(s)

preprint2026arXiv

Addressing Performance Saturation for LLM RL via Precise Entropy Curve Control

Reinforcement learning (RL) has enabled complex reasoning abilities in large language models (LLMs). However, most RL algorithms suffer from performance saturation, preventing continued gains as RL training scales. This problem can be characterized by the collapse of entropy, a key diagnostic for exploration in RL. Existing attempts focus on preventing entropy collapse through regularization or clipping. However, their resulting entropy curves often exhibit instability in the long term, which hinders performance gains. In this paper, we introduce Entrocraft, a simple rejection-sampling approach that realizes user-customized entropy schedule by biasing the advantage distributions. Entrocraft requires no objective regularization and is advantage-estimator-agnostic. Theoretically, we relate per-step entropy change to the advantage distribution under minimal assumptions. This explains the behavior of existing RL and entropy-preserving methods. Entrocraft also enables a systematic study of entropy schedules, which reveals that linear annealing, which starts high and decays to a slightly lower target, performs best. Empirically, Entrocraft addresses performance saturation, significantly improving generalization, output diversity, and long-term training. It enables a 4B model to outperform an 8B baseline, sustains improvement for up to 4x longer before plateauing, and raises pass@K by 50% over the baseline.

preprint2022arXiv

CKH: Causal Knowledge Hierarchy for Estimating Structural Causal Models from Data and Priors

Structural causal models (SCMs) provide a principled approach to identifying causation from observational and experimental data in disciplines ranging from economics to medicine. However, SCMs, which is typically represented as graphical models, cannot rely only on data, rather require support of domain knowledge. A key challenge in this context is the absence of a methodological framework for encoding priors (background knowledge) into causal models in a systematic manner. We propose an abstraction called causal knowledge hierarchy (CKH) for encoding priors into causal models. Our approach is based on the foundation of "levels of evidence" in medicine, with a focus on confidence in causal information. Using CKH, we present a methodological framework for encoding causal priors from various information sources and combining them to derive an SCM. We evaluate our approach on a simulated dataset and demonstrate overall performance compared to the ground truth causal model with sensitivity analysis.

preprint2020arXiv

Collaborative Cloud Computing Framework for Health Data with Open Source Technologies

The proliferation of sensor technologies and advancements in data collection methods have enabled the accumulation of very large amounts of data. Increasingly, these datasets are considered for scientific research. However, the design of the system architecture to achieve high performance in terms of parallelization, query processing time, aggregation of heterogeneous data types (e.g., time series, images, structured data, among others), and difficulty in reproducing scientific research remain a major challenge. This is specifically true for health sciences research, where the systems must be i) easy to use with the flexibility to manipulate data at the most granular level, ii) agnostic of programming language kernel, iii) scalable, and iv) compliant with the HIPAA privacy law. In this paper, we review the existing literature for such big data systems for scientific research in health sciences and identify the gaps of the current system landscape. We propose a novel architecture for software-hardware-data ecosystem using open source technologies such as Apache Hadoop, Kubernetes and JupyterHub in a distributed environment. We also evaluate the system using a large clinical data set of 69M patients.

preprint2020arXiv

Newton-ADMM: A Distributed GPU-Accelerated Optimizer for Multiclass Classification Problems

First-order optimization methods, such as stochastic gradient descent (SGD) and its variants, are widely used in machine learning applications due to their simplicity and low per-iteration costs. However, they often require larger numbers of iterations, with associated communication costs in distributed environments. In contrast, Newton-type methods, while having higher per-iteration costs, typically require a significantly smaller number of iterations, which directly translates to reduced communication costs. In this paper, we present a novel distributed optimizer for classification problems, which integrates a GPU-accelerated Newton-type solver with the global consensus formulation of Alternating Direction of Method Multipliers (ADMM). By leveraging the communication efficiency of ADMM, GPU-accelerated inexact-Newton solver, and an effective spectral penalty parameter selection strategy, we show that our proposed method (i) yields better generalization performance on several classification problems; (ii) significantly outperforms state-of-the-art methods in distributed time to solution; and (iii) offers better scaling on large distributed platforms.

preprint2020arXiv

Randomized Linear Algebra Approaches to Estimate the Von Neumann Entropy of Density Matrices

Thevon Neumann entropy, named after John von Neumann, is an extension of the classical concept of entropy to the field of quantum mechanics. From a numerical perspective, von Neumann entropy can be computed simply by computing all eigenvalues of a density matrix, an operation that could be prohibitively expensive for large-scale density matrices. We present and analyze three randomized algorithms to approximate von Neumann entropy of {real} density matrices: our algorithms leverage recent developments in the Randomized Numerical Linear Algebra (RandNLA) literature, such as randomized trace estimators, provable bounds for the power method, and the use of random projections to approximate the eigenvalues of a matrix. All three algorithms come with provable accuracy guarantees and our experimental evaluations support our theoretical findings showing considerable speedup with small loss in accuracy.

preprint2016arXiv

Combining Density and Overlap (CoDO): A New Method for Assessing the Significance of Overlap Among Subgraphs

Algorithms for detecting clusters (including overlapping clusters) in graphs have received significant attention in the research community. A closely related important aspect of the problem -- quantification of statistical significance of overlap of clusters, remains relatively unexplored. This paper presents the first theoretical and practical results on quantifying statistically significant interactions between clusters in networks. Such problems commonly arise in diverse applications, ranging from social network analysis to systems biology. The paper addresses the problem of quantifying the statistical significance of the observed overlap of the two clusters in an Erdős-Rényi graph model. The analytical framework presented in the paper assigns a $p$-value to overlapping subgraphs by combining information about both the sizes of the subgraphs and their edge densities in comparison to the corresponding values for their overlapping component. This $p$-value is demonstrated to have excellent discrimination properties in real applications and is shown to be robust across broad parameter ranges. Our results are comprehensively validated on synthetic, social, and biological networks. We show that our framework: (i) derives insight from both the density and the size of overlap among communities (circles/pathways), (ii) consistently outperforms state-of-the-art methods over all tested datasets, and (iii) when compared to other measures, has much broader application scope. In the context of social networks, we identify highly interdependent (social) circles and show that our predictions are highly co-enriched with known user features. In networks of biomolecular interactions, we show that our method identifies novel cross-talk between pathways, sheds light on their mechanisms of interaction, and provides new opportunities for investigations of biomolecular interactions.

preprint2016arXiv

Fundamental Bounds and Approaches to Sequence Reconstruction from Nanopore Sequencers

Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic analysis of the impact of insertion-deletion (indel) errors in nanopore sequencers. In particular, we consider the following problems: (i) for given indel error characteristics and rate, what is the probability of accurate reconstruction as a function of sequence length; (ii) what is the number of `typical' sequences within the distortion bound induced by indel errors; (iii) using replicated extrusion (the process of passing a DNA strand through the nanopore), what is the number of replicas needed to reduce the distortion bound so that only one typical sequence exists within the distortion bound. Our results provide a number of important insights: (i) the maximum length of a sequence that can be accurately reconstructed in the presence of indel and substitution errors is relatively small; (ii) the number of typical sequences within the distortion bound is large; and (iii) replicated extrusion is an effective technique for unique reconstruction. In particular, we show that the number of replicas is a slow function (logarithmic) of sequence length -- implying that through replicated extrusion, we can sequence large reads using nanopore sequencers. Our model considers indel and substitution errors separately. In this sense, it can be viewed as providing (tight) bounds on reconstruction lengths and repetitions for accurate reconstruction when the two error modes are considered in a single model.

preprint2015arXiv

A Critical Survey of Deconvolution Methods for Separating cell-types in Complex Tissues

Identifying concentrations of components from an observed mixture is a fundamental problem in signal processing. It has diverse applications in fields ranging from hyperspectral imaging to denoising biomedical sensors. This paper focuses on in-silico deconvolution of signals associated with complex tissues into their constitutive cell-type specific components, along with a quantitative characterization of the cell-types. Deconvolving mixed tissues/cell-types is useful in the removal of contaminants (e.g., surrounding cells) from tumor biopsies, as well as in monitoring changes in the cell population in response to treatment or infection. In these contexts, the observed signal from the mixture of cell-types is assumed to be a linear combination of the expression levels of genes in constitutive cell-types. The goal is to use known signals corresponding to individual cell-types along with a model of the mixing process to cast the deconvolution problem as a suitable optimization problem. In this paper, we present a survey of models, methods, and assumptions underlying deconvolution techniques. We investigate the choice of the different loss functions for evaluating estimation error, constraints on solutions, preprocessing and data filtering, feature selection, and regularization to enhance the quality of solutions, along with the impact of these choices on the performance of regression-based methods for deconvolution. We assess different combinations of these factors and use detailed statistical measures to evaluate their effectiveness. We identify shortcomings of current methods and avenues for further investigation. For many of the identified shortcomings, such as normalization issues and data filtering, we provide new solutions. We summarize our findings in a prescriptive step-by-step process, which can be applied to a wide range of deconvolution problems.

preprint2014arXiv

Erasure coding for fault oblivious linear system solvers

Dealing with hardware and software faults is an important problem as parallel and distributed systems scale to millions of processing cores and wide area networks. Traditional methods for dealing with faults include checkpoint-restart, active replicas, and deterministic replay. Each of these techniques has associated resource overheads and constraints. In this paper, we propose an alternate approach to dealing with faults, based on input augmentation. This approach, which is an algorithmic analog of erasure coded storage, applies a minimally modified algorithm on the augmented input to produce an augmented output. The execution of such an algorithm proceeds completely oblivious to faults in the system. In the event of one or more faults, the real solution is recovered using a rapid reconstruction method from the augmented output. We demonstrate this approach on the problem of solving sparse linear systems using a conjugate gradient solver. We present input augmentation and output recovery techniques. Through detailed experiments, we show that our approach can be made oblivious to a large number of faults with low computational overhead. Specifically, we demonstrate cases where a single fault can be corrected with less than 10% overhead in time, and even in extreme cases (fault rates of 20%), our approach is able to compute a solution with reasonable overhead. These results represent a significant improvement over the state of the art.

preprint2014arXiv

Multiple Network Alignment on Quantum Computers

Comparative analyses of graph structured datasets underly diverse problems. Examples of these problems include identification of conserved functional components (biochemical interactions) across species, structural similarity of large biomolecules, and recurring patterns of interactions in social networks. A large class of such analyses methods quantify the topological similarity of nodes across networks. The resulting correspondence of nodes across networks, also called node alignment, can be used to identify invariant subgraphs across the input graphs. Given $k$ graphs as input, alignment algorithms use topological information to assign a similarity score to each $k$-tuple of nodes, with elements (nodes) drawn from each of the input graphs. Nodes are considered similar if their neighbors are also similar. An alternate, equivalent view of these network alignment algorithms is to consider the Kronecker product of the input graphs, and to identify high-ranked nodes in the Kronecker product graph. Conventional methods such as PageRank and HITS (Hypertext Induced Topic Selection) can be used for this purpose. These methods typically require computation of the principal eigenvector of a suitably modified Kronecker product matrix of the input graphs. We adopt this alternate view of the problem to address the problem of multiple network alignment. Using the phase estimation algorithm, we show that the multiple network alignment problem can be efficiently solved on quantum computers. We characterize the accuracy and performance of our method, and show that it can deliver exponential speedups over conventional (non-quantum) methods.

preprint2014arXiv

Quantum Random State Generation with Predefined Entanglement Constraint

Entanglement plays an important role in quantum communication, algorithms, and error correction. Schmidt coefficients are correlated to the eigenvalues of the reduced density matrix. These eigenvalues are used in Von Neumann entropy to quantify the amount of the bipartite entanglement. In this paper, we map the Schmidt basis and the associated coefficients to quantum circuits to generate random quantum states. We also show that it is possible to adjust the entanglement between subsystems by changing the quantum gates corresponding to the Schmidt coefficients. In this manner, random quantum states with predefined bipartite entanglement amounts can be generated using random Schmidt basis. This provides a technique for generating equivalent quantum states for given weighted graph states, which are very useful in the study of entanglement, quantum computing, and quantum error correction.

preprint2012arXiv

Designing Efficient Programmable Quantum Circuits

Constructing general programmable circuits to be able to run any given unitary operator efficiently on a quantum processor is of fundamental importance. We present a new quantum circuit design technique resulting two general programmable circuit schemes. The circuit schemes can be used to simulate any given operator by setting the angle values in the circuit. This provides a fixed circuit design whose angles are determined from the elements of the given matrix, which can be non-unitary, in an efficient way. We also give both classical and quantum complexity analysis for these circuits and show that the circuits require a few classical computations, and the quantum complexities of them are almost the same as non-general circuits.

preprint2012arXiv

Universal Programmable Quantum Circuit Schemes to Emulate an Operator

Unlike fixed designs, programmable circuit designs support an infinite number of operators. The functionality of a programmable circuit can be altered by simply changing the angle values of the rotation gates in the circuit. Here, we present a new quantum circuit design technique resulting in two general programmable circuit schemes. The circuit schemes can be used to simulate any given operator by setting the angle values in the circuit. This provides a fixed circuit design whose angles are determined from the elements of the given matrix-which can be non-unitary-in an efficient way. We also give both the classical and quantum complexity analysis for these circuits and show that the circuits require a few classical computations. They have almost the same quantum complexities as non-general circuits. Since the presented circuit designs are independent from the matrix decomposition techniques and the global optimization processes used to find quantum circuits for a given operator, high accuracy simulations can be done for the unitary propagators of molecular Hamiltonians on quantum computers. As an example, we show how to build the circuit design for the hydrogen molecule.