arXiv subjects

Jeyashree Krishnan

Publications and source records attributed to Jeyashree Krishnan.

6 recordsLinked to original sources

arXiv2026

Machine Learning Research Has Outpaced Its Communication Norms and NeurIPS Should Act

Machine learning research has grown exponentially while its communication norms have not. We argue NeurIPS should adopt explicit, measurable writing standards. We analyze 2.8 million arXiv papers (1991-2025), 24,772 NeurIPS papers (1987-2024), and 24.5 million PubMed papers (1990-2025), applying classical readability scores, the Hohmann writing style suite (including sensational language), acronym density and reuse, an LLM as judge readability protocol, and citations from OpenAlex and Semantic Scholar. Four patterns emerge. First, NeurIPS abstracts score harder to read on every classical readability metric: Flesch Reading Ease falls from about 24 in 1987 to 13 in 2024, and sensational language rises by about 50 percent in NeurIPS abstracts between 2015 and 2024. Second, acronym density in NeurIPS titles has grown from 0.33 per 100 words in 1987 to 3.21 in 2024, and about 89 percent of NeurIPS acronyms are used fewer than ten times, ten points above the science-wide baseline. Third, more readable NeurIPS papers tend to receive more citations, suggesting readability and impact are correlated and that less readable papers risk remaining fragmented. LLM as judge scores rate NeurIPS abstracts as roughly stable from 1987 to 2022, with early signs of improvement thereafter, a pattern that disagrees with every classical readability metric and raises a design question for enforcement: is the target reader a human or an LLM? Lastly, NeurIPS volume has grown roughly 50-fold between 1987 and 2024. Assuming the goal is to optimise for human readers, we propose seven standards NeurIPS could pilot at NeurIPS 2027: an acronym budget with a venue-approved term list, a human readability threshold, stricter citation standards, standalone visual elements, a plain language summary, a pre-registered acronym glossary, and open source audit tooling.

cs.LG↗

arXiv2023

Tree-Based Learning on Amperometric Time Series Data Demonstrates High Accuracy for Classification

Elucidating exocytosis processes provide insights into cellular neurotransmission mechanisms, and may have potential in neurodegenerative diseases research. Amperometry is an established electrochemical method for the detection of neurotransmitters released from and stored inside cells. An important aspect of the amperometry method is the sub-millisecond temporal resolution of the current recordings which leads to several hundreds of gigabytes of high-quality data. In this study, we present a universal method for the classification with respect to diverse amperometric datasets using data-driven approaches in computational science. We demonstrate a very high prediction accuracy (greater than or equal to 95%). This includes an end-to-end systematic machine learning workflow for amperometric time series datasets consisting of pre-processing; feature extraction; model identification; training and testing; followed by feature importance evaluation - all implemented. We tested the method on heterogeneous amperometric time series datasets generated using different experimental approaches, chemical stimulations, electrode types, and varying recording times. We identified a certain overarching set of common features across these datasets which enables accurate predictions. Further, we showed that information relevant for the classification of amperometric traces are neither in the spiky segments alone, nor can it be retrieved from just the temporal structure of spikes. In fact, the transients between spikes and the trace baselines carry essential information for a successful classification, thereby strongly demonstrating that an effective feature representation of amperometric time series requires the full time series. To our knowledge, this is one of the first studies that propose a scheme for machine learning, and in particular, supervised learning on full amperometry time series data.

q-bio.SC↗

arXiv2023

Spike-by-Spike Frequency Analysis of Amperometry Traces Provides Statistical Validation of Observations in the Time Domain

Amperometry is a commonly used electrochemical method for studying the process of exocytosis in real-time. Given the high precision of recording that amperometry procedures offer, the volume of data generated can span over several hundreds of megabytes to a few gigabytes and therefore necessitates systematic and reproducible methods for analysis. Though the spike characteristics of amperometry traces in the time domain hold information about the dynamics of exocytosis, these biochemical signals are, more often than not, characterized by time-varying signal properties. Such signals with time-variant properties may occur at different frequencies and therefore analyzing them in the frequency domain may provide statistical validation for observations already established in the time domain. This necessitates the use of time-variant, frequency-selective signal processing methods as well, which can adeptly quantify the dominant or mean frequencies in the signal. The Fast Fourier Transform (FFT) is a well-established computational tool that is commonly used to find the frequency components of a signal buried in noise. In this work, we outline a method for spike-based frequency analysis of amperometry traces using FFT that also provides statistical validation of observations on spike characteristics in the time domain. We demonstrate the method by utilizing simulated signals and by subsequently testing it on diverse amperometry datasets generated from different experiments with various chemical stimulations. To our knowledge, this is the first fully automated open-source tool available dedicated to the analysis of spikes extracted from amperometry signals in the frequency domain.

q-bio.SC↗

arXiv2020

A Long-Range Ising Model of a Barabási-Albert Network

Networks that have power-law connectivity, commonly referred to as the scale-free networks, are an important class of complex networks. A heterogeneous mean-field approximation has been previously proposed for the Ising model of the Barabási-Albert model of scale-free networks with classical spins on the nodes wherein it was shown that the critical temperature for such a system scales logarithmically with network size. For finite sizes, there is no criticality for such a system and hence no true phase transition in terms of singular behavior. Further, in the thermodynamic limit, the mean-field prediction of an infinite critical temperature for the system may exclude any true phase transition even then. Nevertheless, with an eye on potential applications of the model on biological systems that are generally finite, one may still try to find approximations that describe the relevant observables quantitatively. Here we present an alternative, approximate formulation for the description of the Ising model of a Barabási-Albert Network. Using the classical definition of magnetization, we show that Ising models on a network can be well-approximated by a long-range interacting homogeneous Ising model wherein each node of the network couples to all other spins with a strength determined by the mean degree of the Barabási-Albert Network. In such an effective long-range Ising model of a Barabási-Albert Network, the critical temperature is directly proportional to the number of preferentially attached links added to grow the network. The proposed model describes the magnetization of the majority of the sites with average or smaller than average degree better compared to the heterogeneous mean-field approximation. The long-range Ising model is the only homogeneous description of Barabási-Albert networks that we know of.

cond-mat.dis-nn↗

arXiv2019

A Modified Ising Model of Barabási-Albert Network with Gene-type Spins

The central question of systems biology is to understand how individual components of a biological system such as genes or proteins cooperate in emerging phenotypes resulting in the evolution of diseases. As living cells are open systems in quasi-steady state type equilibrium in continuous exchange with their environment, computational techniques that have been successfully applied in statistical thermodynamics to describe phase transitions may provide new insights to emerging behavior of biological systems. Here we will systematically evaluate the translation of computational techniques from solid-state physics to network models that closely resemble biological networks and develop specific translational rules to tackle problems unique to living systems. Hence we will focus on logic models exhibiting only two states in each network node. Motivated by the apparent asymmetry between biological states where an entity exhibits boolean states i.e. is active or inactive, we present an adaptation of symmetric Ising model towards an asymmetric one fitting to living systems here referred to as the modified Ising model with gene-type spins. We analyze phase transitions by Monte Carlo simulations and propose mean-field solution of modified Ising model of a network type that closely resembles real-world network, the Barabási-Albert model of scale-free networks. We show that asymmetric Ising models show similarities to symmetric Ising models with external field and undergoes a discontinuous phase transition of the first-order and exhibits hysteresis. The simulation setup presented here can be directly used for any biological network connectivity dataset and is also applicable for other networks that exhibit similar states of activity. This is a general statistical method to deal with non-linear large scale models arising in the context of biological systems and is scalable to any network size.

q-bio.QM↗

arXiv2017

Perfect spike detection via time reversal

Spiking neuronal networks are usually simulated with three main simulation schemes: the classical time-driven and event-driven schemes, and the more recent hybrid scheme. All three schemes evolve the state of a neuron through a series of checkpoints: equally spaced in the first scheme and determined neuron-wise by spike events in the latter two. The time-driven and the hybrid scheme determine whether the membrane potential of a neuron crosses a threshold at the end of of the time interval between consecutive checkpoints. Threshold crossing can, however, occur within the interval even if this test is negative. Spikes can therefore be missed. The present work derives, implements, and benchmarks a method for perfect retrospective spike detection. This method can be applied to neuron models with affine or linear subthreshold dynamics. The idea behind the method is to propagate the threshold with a time-inverted dynamics, testing whether the threshold crosses the neuron state to be evolved, rather than vice versa. Algebraically this translates into a set of inequalities necessary and sufficient for threshold crossing. This test is slower than the imperfect one, but faster than an alternative perfect tests based on bisection or root-finding methods. Comparison confirms earlier results that the imperfect test rarely misses spikes (less than a fraction $1/10^8$ of missed spikes) in biologically relevant settings. This study offers an alternative geometric point of view on neuronal dynamics.

q-bio.NC↗