arXiv subjects

Simon Kasif

Publications and source records attributed to Simon Kasif.

5 recordsLinked to original sources

arXiv2024

Towards a Healthy AI Tradition: Lessons from Biology and Biomedical Science

AI is a magnificent field that directly and profoundly touches on numerous disciplines ranging from philosophy, computer science, engineering, mathematics, decision and data science and economics, to cognitive science, neuroscience and more. The number of applications and impact of AI is second to none and the potential of AI to broadly impact future science developments is particularly thrilling. While attempts to understand knowledge, reasoning, cognition and learning go back centuries, AI remains a relatively new field. In part due to the fact it has so many wide-ranging overlaps with other disparate fields it appears to have trouble developing a robust identity and culture. Here we suggest that contrasting the fast-moving AI culture to biological and biomedical sciences is both insightful and useful way to inaugurate a healthy tradition needed to envision and manage our ascent to AGI and beyond (independent of the AI Platforms used). The co-evolution of AI and Biomedical Science offers many benefits to both fields. In a previous perspective, we suggested that biomedical laboratories or centers can usefully embrace logistic traditions in AI labs that will allow them to be highly collaborative, improve the reproducibility of research, reduce risk aversion and produce faster mentorship pathways for PhDs and fellows. This perspective focuses on the benefits to AI by adapting features of biomedical science at higher, primarily cultural levels.

cs.CY↗

arXiv2024

A Trilogy of AI Safety Frameworks: Paths from Facts and Knowledge Gaps to Reliable Predictions and New Knowledge

AI Safety has become a vital front-line concern of many scientists within and outside the AI community. There are many immediate and long term anticipated risks that range from existential risk to human existence to deep fakes and bias in machine learning systems [1-5]. In this paper, we reduce the full scope and immense complexity of AI safety concerns to a trilogy of three important but tractable opportunities for advances that have the short-term potential to improve AI safety and reliability without reducing AI innovation in critical domains. In this perspective, we discuss this vision based on several case studies that already produced proofs of concept in critical ML applications in biomedical science.

cs.AI↗

arXiv2021

Interpretable Network Propagation with Application to Expanding the Repertoire of Human Proteins that Interact with SARS-CoV-2

Background: Network propagation has been widely used for nearly 20 years to predict gene functions and phenotypes. Despite the popularity of this approach, little attention has been paid to the question of provenance tracing in this context, e.g., determining how much any experimental observation in the input contributes to the score of every prediction. Results: We design a network propagation framework with two novel components and apply it to predict human proteins that directly or indirectly interact with SARS-CoV-2 proteins. First, we trace the provenance of each prediction to its experimentally validated sources, which in our case are human proteins experimentally determined to interact with viral proteins. Second, we design a technique that helps to reduce the manual adjustment of parameters by users. We find that for every top-ranking prediction, the highest contribution to its score arises from a direct neighbor in a human protein-protein interaction network. We further analyze these results to develop functional insights on SARS-CoV-2 that expand on known biology such as the connection between endoplasmic reticulum stress, HSPA5, and anti-clotting agents. Conclusions: We examine how our provenance tracing method can be generalized to a broad class of network-based algorithms. We provide a useful resource for the SARS-CoV-2 community that implicates many previously undocumented proteins with putative functional relationships to viral infection. This resource includes potential drugs that can be opportunistically repositioned to target these proteins. We also discuss how our overall framework can be extended to other, newly-emerging viruses.

q-bio.MN↗

arXiv2020

Artificial Tikkun Olam: AI Can Be Our Best Friend in Building an Open Human-Computer Society

Technological advances of virtually every kind pose risks to society including fairness and bias. We review a long-standing wisdom that a widespread practical deployment of any technology may produce adverse side effects misusing the knowhow. This includes AI but AI systems are not solely responsible for societal risks. We describe some of the common and AI specific risks in health industries and other sectors and propose both broad and specific solutions. Each technology requires very specialized and informed tracking, monitoring and creative solutions. We postulate that AI systems are uniquely poised to produce conceptual and methodological solutions to both fairness and bias in automated decision-making systems. We propose a simple intelligent system quotient that may correspond to their adverse societal impact and outline a multi-tier architecture for producing solutions of increasing complexity to these risks. We also propose that universities may consider forming interdisciplinary Study of Future Technology Centers to investigate and predict the fuller range of risks posed by technology and seek both common and AI specific solutions using computational, technical, conceptual and ethical analysis

cs.CY↗

arXiv2014

Logarithmic-Time Updates and Queries in Probabilistic Networks

In this paper we propose a dynamic data structure that supports efficient algorithms for updating and querying singly connected Bayesian networks (causal trees and polytrees). In the conventional algorithms, new evidence in absorbed in time O(1) and queries are processed in time O(N), where N is the size of the network. We propose a practical algorithm which, after a preprocessing phase, allows us to answer queries in time O(log N) at the expense of O(logn N) time per evidence absorption. The usefulness of sub-linear processing time manifests itself in applications requiring (near) real-time response over large probabilistic databases.

cs.AI↗