111 citations · 359 across the 19 of their papers we have counts for
22 papers
Autonomous Learning of Generative Models with Chemical Reaction Network Ensembles
William Poole, Thomas E. Ouldridge, Manoj Gopalkrishnan
Can a micron sized sack of interacting molecules autonomously learn an internal model of a complex and fluctuating environment? We draw insights from control theory, machine learni…
Detailed Balanced Chemical Reaction Networks as Generalized Boltzmann Machines
William Poole, Thomas Ouldridge, Manoj Gopalkrishnan +1
Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but th…
Active Inference for Stochastic Control
Aswin Paul, Noor Sajid, Manoj Gopalkrishnan +1
Active inference has emerged as an alternative approach to control problems given its intuitive (probabilistic) formalism. However, despite its theoretical utility, computational i…
A Compressed Sensing Approach to Pooled RT-PCR Testing for COVID-19 Detection
Sabyasachi Ghosh, Rishi Agarwal, Mohammad Ali Rehan +9
We propose `Tapestry', a novel approach to pooled testing with application to COVID-19 testing with quantitative Reverse Transcription Polymerase Chain Reaction (RT-PCR) that can r…
A reaction network scheme which implements inference and learning for Hidden Markov Models
Abhinav Singh, Carsten Wiuf, Abhishek Behera +1
With a view towards molecular communication systems and molecular multi-agent systems, we propose the Chemical Baum-Welch Algorithm, a novel reaction network scheme that learns par…
A reaction network scheme which implements the EM algorithm
Muppirala Viswa Virinchi, Abhishek Behera, Manoj Gopalkrishnan
A detailed algorithmic explanation is required for how a network of chemical reactions can generate the sophisticated behavior displayed by living cells. Though several previous wo…
Chemical Boltzmann Machines
William Poole, Andrés Ortiz-Muñoz, Abhishek Behera +4
How smart can a micron-sized bag of chemicals be? How can an artificial or real cell make inferences about its environment? From which kinds of probability distributions can chemic…
A stochastic molecular scheme for an artificial cell to infer its environment from partial observations
Muppirala Viswa Virinchi, Abhishek Behera, Manoj Gopalkrishnan
The notion of entropy is shared between statistics and thermodynamics, and is fundamental to both disciplines. This makes statistical problems particularly suitable for reaction ne…
Designing the Optimal Bit: Balancing Energetic Cost, Speed and Reliability
Abhishek Deshpande, Manoj Gopalkrishnan, Thomas E. Ouldridge +1
We consider the technologically relevant costs of operating a reliable bit that can be erased rapidly. We find that both erasing and reliability times are non-monotonic in the unde…
A Bayesian view of Single-Qubit Clocks, and an Energy versus Accuracy tradeoff
Manoj Gopalkrishnan, Varshith Kandula, Praveen Sriram +2
We bring a Bayesian approach to the analysis of clocks. Using exponential distributions as priors for clocks, we analyze how well one can keep time with a single qubit freely prece…
A Scheme for Molecular Computation of Maximum Likelihood Estimators for Log-Linear Models
Manoj Gopalkrishnan
We propose a novel molecular computing scheme for statistical inference. We focus on the much-studied statistical inference problem of computing maximum likelihood estimators for l…
Lyapunov functions, stationary distributions, and non-equilibrium potential for chemical reaction networks
David F. Anderson, Gheorghe Craciun, Manoj Gopalkrishnan +1
We consider the relationship between stationary distributions for stochastic models of reaction systems and Lyapunov functions for their deterministic counterparts. Specifically, w…
A Cost / Speed / Reliability Trade-off to Erasing
Manoj Gopalkrishnan
We present a KL-control treatment of the fundamental problem of erasing a bit. We introduce notions of "reliability" of information storage via a reliability timescale , and "…
Playing games in an uncertain world
Manoj Gopalkrishnan, Girish Varma
Traditional game theory assumes that the players in the game are aware of the rules of the game. However, in practice, often the players are unaware or have only partial knowledge…
On the Lyapunov function for complex-balanced mass-action systems
Manoj Gopalkrishnan
We present a new proof, using the log-sum inequality, that the pseudo-Helmholtz free energy function is a Lyapunov function for complex-balanced mass-action systems. This proof is…
The Hot Bit I: The Szilard-Landauer Correspondence
Manoj Gopalkrishnan
We present a precise formulation of a correspondence between information and thermodynamics that was first observed by Szilard, and later studied by Landauer. The correspondence id…
Autocatalysis in Reaction Networks
Abhishek Deshpande, Manoj Gopalkrishnan
The persistence conjecture is a long-standing open problem in chemical reaction network theory. It concerns the behavior of solutions to coupled ODE systems that arise from applyin…
A coercion-resistant protocol for conducting elections by telephone
Manoj Gopalkrishnan
We present a protocol that allows voters to phone in their votes. Our protocol makes it expensive for a candidate and a voter to cooperate to prove to the candidate who the voter v…
A geometric approach to the Global Attractor Conjecture
Manoj Gopalkrishnan, Ezra Miller, Anne Shiu
This paper introduces the class of "strongly endotactic networks", a subclass of the endotactic networks introduced by G. Craciun, F. Nazarov, and C. Pantea. The main result states…
A Projection Argument for Differential Inclusions, with Applications to Persistence of Mass-Action Kinetics
Manoj Gopalkrishnan, Ezra Miller, Anne Shiu
Motivated by questions in mass-action kinetics, we introduce the notion of vertexical family of differential inclusions. Defined on open hypercubes, these families are characterize…
Catalysis in Reaction Networks
Manoj Gopalkrishnan
We define catalytic networks as chemical reaction networks with an essentially catalytic reaction pathway: one which is on in the presence of certain catalysts and off in their abs…
On the Mathematics of the Law of Mass Action
Leonard Adleman, Manoj Gopalkrishnan, Ming-Deh Huang +2
In 1864,Waage and Guldberg formulated the "law of mass action." Since that time, chemists, chemical engineers, physicists and mathematicians have amassed a great deal of knowledge…