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A data analysis method that borrows concepts from topology – the so-called “rubber-sheet geometry” – may soon find its way to a stock trader’s toolkit in analyzing market movements. This method, called Topological Data Analysis (TDA), uncovers patterns in large datasets, preparing them for deeper analysis.

In a study published in the Philippine Journal of Science, Ela Mae Riñon and Dr. Rachelle Sambayan of the UP Diliman College of Science Institute of Mathematics (UPD-CS IM) demonstrated that TDA can be used as an early warning signal for stock market crashes. Their study, which analyzed stock data of three Philippine companies from 2019 to 2021, successfully anticipated periods when the market was about to crash.

“The findings suggest that [TDA] can help identify industries most affected during economic downturns, such as the COVID-19 pandemic, aiding investors and policymakers in minimizing risks,” they said.

The T in Topological Data Analysis

To understand TDA, it may be helpful to compare it with how we observe stars. At first glance, the night sky appears as a seemingly random plot of stars scattered across the vast canvas of the universe. However, with extended observation, patterns emerge: clusters of stars, constellations, and voids become apparent the moment we recognize them. As we continue to gaze at the sky, the random stars fade into the background, while the clusters, constellations, and voids take the spotlight.

This effect is similar to what TDA does with large sets of data points. Essentially, TDA reveals hidden geometric structures within datasets, allowing insights to be drawn from what previously looked like an ambiguous clump of points. “TDA helps uncover patterns, such as clusters forming constellations, loops, or voids,” said the authors.

One tool in TDA, called persistent homology, follows a series of steps to systematically uncover patterns. First, researchers draw a small ball around the data points. Next, they gradually expand the balls until some of them overlap. When this happens, they connect the corresponding points. The balls continue to expand until the points form various figures, which are then classified into what are called homology groups.

Researchers classify the figures into three homology groups: connected components, which are open shapes like line segments; loops, which are closed shapes like triangles; and cavities, which are shapes that extend to the third dimension. As the balls expand, the figures can change from one homology group to another. A connected component, for example, might attach to a data point that closes it off, transforming it into a loop.

Swamp buffaloes (Bubalus bubalis carabanensis) are primarily used to assist farmers with tilling the land, transporting tools, and, alternatively, for meat, milk, hide, and manure, which is used as organic fertilizer. Riverine buffaloes (Bubalus bubalis bubalis), on the other hand, are mainly used in milk production. In the Philippines, crossbreeding and backcrossing these two breeds on a large scale helps create animals with improved potential for milk and meat production, despite their differences. Hybridization of swamp and river buffaloes has limited success, sometimes producing viable offspring that don’t achieve the desired traits.

A team of researchers conducted an investigation to clarify the taxonomic designation of swamp and riverine buffaloes in the Philippines. They discovered that the DNA sequences of the genes from both swamp and riverine buffaloes are distinguishable and that their chromosome numbers are different, affirming that they are two distinct species, not just subspecies of Bubalus bubalis.

The research team is comprised of Dr. Ian Kendrich C. Fontanilla, Nelvie Fatima Jane A. Soliven, John Gregor A. Roño, Francis L. Fontanilla, Emerson R. Servo, and Dr. Ernelea P. Cao of the University of the Philippines – Diliman College of Science’s Institute of Biology (UPD-CS IB) and Dr. Lilian P. Villamor, Therese Patricka C. Cailipan, Alexander M. Paraguas, and Aivhie Jhoy E. Cuanang from the Department of Agriculture – Philippine Carabao Center (DA-PCC).

“These results corroborate the observed differences in their appearances. Swamp buffaloes can be identified by the white or light gray markings on their lower jaw and brisket, known as a chevron, as well as their lighter skin and coat color compared to riverine buffaloes. They are also smaller, weighing between 325 and 450 kg, and have crescent-shaped horns. They are mainly used as draught animals,” said Dr. Villamor, citing data from her previous studies on buffaloes. “River buffaloes, on the other hand, are larger, weighing between 450 and 1,000 kg, and have curly horns. They are primarily raised for milk and meat production.”

In 1916, Albert Einstein theorized that two merging black holes create ripples in the spacetime fabric, similar to how a pebble creates ripples in a pond. These ripples, called gravitational waves, stretch and squeeze spacetime in amounts so minuscule that they were once believed to be too faint to detect.

But a century later, the Laser Interferometer Gravitational-Wave Observatory (LIGO) in the US, an L-shaped facility with arms spanning four kilometers each, detected minute discrepancies in how long lasers travel through each arm, signaling the first detection of gravitational waves.

Now, scientists are preparing to launch a more sophisticated observatory into space, aiming to detect even fainter gravitational waves or those beyond LIGO’s capabilities. This space-based facility, known as the Laser Interferometer Space Antenna or LISA, is a triangular observatory with sides spanning tens of millions of kilometers and is set to launch in the 2030s.

As preparation ramps up, scientists around the world are pitching ideas to improve LISA’s detection capabilities. Dr. Reinabelle Reyes and her former graduate student Marco Immanuel Rivera, from the UP Diliman College of Science’s National Institute of Physics (UPD-CS NIP) recently published a study identifying a set of parameters that could improve the analysis of signals coming from LISA and future gravitational-wave observatories.

Unlike LIGO, which mainly detects gravitational waves coming from two stellar-mass black holes, LISA hopes to detect a type of gravitational wave coming from compact objects – such as neutron stars, white dwarfs, and stellar-mass black holes – orbiting supermassive black holes. “When a stellar-mass black hole orbiting a supermassive black hole falls into it, an extreme-mass ratio inspiral (EMRI) gravitational-wave signal is produced,” Dr. Reyes and Rivera explained.

One complication with detecting EMRIs is that the environment where the compact object-black hole pair resides can considerably affect the EMRIs they emit. For example, supermassive black holes are often surrounded by glowing rings called accretion disks, which can modify the EMRI signal just as the Earth’s atmosphere distorts light from faraway stars.

By understanding how these environmental features affect EMRIs, astronomers can not only filter out noise from the signal but also learn about the environment itself. For instance, by studying the imprints of the environment on the gravitational wave signal, astronomers can infer the density of the accretion disk. 

Their study considered three environmental factors that may substantially influence the EMRI signal: accretion, gravitational drag, and gravitational pull. Their analysis determined the most measurable parameter combination, which is heavily dominated by these environmental effects. They also estimated how precisely these parameters can be measured—an essential factor for extremely sensitive detectors like LISA.

Their analysis is built upon a mathematical tool called the Fisher matrix, which evaluates how accurately an experiment can measure different observables. To illustrate, imagine a catch basin designed to collect water, rocks, and leaves. The Fisher matrix determines and quantifies how effectively the basin can catch each object separately, even before the experiment is set out.

“The Fisher matrix is used by astrophysicists to estimate the expected precision to which certain properties can be measured from a given signal to be observed in a future detector,” explained the authors.

While their study shows promise, Dr. Reyes and Rivera noted that modeling EMRIs is challenging due to strong gravity effects, and more accurate modeling is needed.  “It will be interesting to compare with calculations based on the newer waveform models which are adapted for EMRIs, as well as those which contain the effects of non-trivial environments,” the authors said.

“In the future, we hope to see how the parameter combinations we presented in this study can be applied directly in improving parameter estimation methods used in gravitational-wave astronomy, such as stochastic samplers,” the authors concluded.

For interview requests and other concerns, please contact media@science.upd.edu.ph.

Rivera, M.I. and Reyes, R.C. (2024) Measurable parameter combinations of environmentally-dephased EMRI gravitational-wave signals, New Astronomy, 112, p. 102263. https://doi.org/10.1016/j.newast.2024.102263

Dr. Pierangeli Vital, Donnabel Sena, Czarina Jay Catapat, and Ma. Christine Jasmine Sabio from the UPD-CS Natural Sciences Research Institute (UPD-CS NSRI), along with Dr. Windell Rivera of the UPD-CS Institute of Biology (UPD-CS IB) gathered 419 vegetable samples from three urban farms and four major wet markets in Metro Manila. The group detected E. coli in 13.60% of all the samples. The presence of E.coli in the samples from urban farms was also higher than in the samples obtained from wet markets.

According to Dr. Vital, high levels of E. coli in the samples from urban farms could be linked to various factors, such as lack of thorough post-harvest processing, unlike the samples from wet markets. “As observed in the urban farm sampling sites, they frequently use rainwater, pond water, and well water for irrigation, mainly for economic reasons, but this increases the risk of bacterial contamination,” she said.

Animals such as dogs, cats, and chickens often roam around urban farms, which raises the risk of microbial contamination in the irrigation water and soil where the vegetables grow. The researchers considered these as areas for improvement in developing urban farming practices.

“This research, together with our past research on agricultural food safety, is and was used in creating and adopting Philippine National Standards (PNS) on pre- and post-harvest microbial food safety in agriculture, with initiatives spearheaded by the DA – Bureau of Agriculture and Fisheries Standards (DA-BAFS),” shared Dr. Vital.

The researchers stated in their paper that the results could provide a factual basis for regulating, controlling, and eliminating food pathogen contamination in fresh produce, thereby helping policymakers implement regulations that ensure food safety. Even so, Dr. Vital mentioned that preventing foodborne illnesses such as E. coli can also be done by Filipinos in their own homes.

“Proper handling and cooking must be practiced at home, which involves simple steps such as thoroughly washing hands and kitchenware as well as disinfecting table surfaces when preparing food, using clean water when washing vegetables, effectively separating cooked and raw foods, and storing food the right way,” Dr. Vital added. “Following these simple steps can significantly help reduce the risks of foodborne illness at home and in the community.”

They plan to include more surveillance of relevant foodborne pathogens and conduct the study on a national level, in addition to investigating the antimicrobial resistance of the bacteria. These endeavors will provide significant data for analyzing trends in microbial food safety in the Philippines.

The paper, titled “Thermotolerant Escherichia coli contamination in vegetables from selected urban farms and wet markets in metro Manila, Philippines at the height of COVID-19 pandemic,” was published in the Asia-Pacific Journal of Science and Technology, a peer-reviewed journal covering research fields such as engineering, agricultural sciences, technology, and health sciences.

For interview requests and other concerns, please contact media@science.upd.edu.ph.

References:

Vital, P., Rivera, W., Sena, D., Catapat, C. J., & Sabio, M. C. J. (2024). Thermotolerant Escherichia coli contamination in vegetables from selected urban farms and wet markets in Metro Manila, Philippines at the height of COVID-19 pandemic. Asia-Pacific Journal of Science and Technology, 29(03), APST–29. https://doi.org/10.14456/apst.2024.44

To our guest speaker, National Artist Kidlat Tahimik, to our Chancellor, Chancellor Vistan, to our dean, Dr. Giovanni Tapang, academicians, university officials, institute directors, faculty, parents, guests and of course graduates, magandang gabi po sa ating lahat.

The theme for today’s commencement is “Science in the Service of Society.” Since I’m not particularly experienced in writing speeches, I’ll approach this topic the way we tackle complex scientific journals—by defining and discussing each term.

Let’s start with the word “science.” After spending at least four years immersed in this field, I believe its meaning is already familiar to us. However, I’d like to share a glimpse of the state of science in our country based on my experiences.

My adviser, Dr. Nathaniel Hermosa came back to the Philippines from his postdoctoral position as a Balik-Scientist fellow to establish his own laboratory in 2015. I was fortunate to be one of his first advisees. I witnessed firsthand the process of building a laboratory from the ground up, including the relatively tedious process of procuring equipment. I have seen how researchers, including my mentors, often have to justify their work as addressing pressing issues like poverty just to secure financial support in their projects. I, myself have experienced being disheartened with these circumstances. Last 2023, our work was selected as a finalist for the Best Student Research Award in Spain. Despite the university’s generous support, I was unable to attend the conference in person due to inadequate funding.

Let me be clear: our university is incredibly supportive and generous with research funding, but these challenges are part of the reality we face. Minsan nakaka-frustrate, madalas nakaka-lungkot. Yet, despite these obstacles, we continue to excel, producing great research papers and nurturing world-class scientists.

During one research meeting, I asked my adviser, “Why did you choose to return and conduct experiments here in the Philippines when it might be easier to do so abroad?” His response, in essence, was that while we might lack in resources and funding, we make up with ingenuity and resourcefulness. This may be an adaptive skill, but our lack forces us to think outside the box and come up with creative solutions to problems.

Next word is service. For this part, let me tell you a story.

Tungkol ito sa isang mag-asawang magsasaka na nagngangalang Ceasar at Aurora. Sila ay may tatlong anak: isang panganay na babae at dalawang lalaki. Upang mapagtapos ang kanilang mga anak, kinailangan nilang maghanap ng iba pang trabaho bukod sa pagsasaka. Nagsimulang mag-buy and sell si Ceasar ng mga baboy, at naging manininda naman sa palengke si Aurora. Ang kanilang panganay na anak na si Mona ang katulong ng kanyang ina sa pagtitinda sa palengke.

Sa murang edad, namulat si Mona sa hirap ng buhay at sa sakripisyo ng kanyang mga magulang upang mapag-aral silang magkakapatid. Sa buong apat na taon ng high school, mayroon lamang siyang isang pares ng uniporme at isang pares ng sapatos na pinilit niyang pinagkakasya sa kanyang lumalaking paa. Nakapagtapos ng high school si Mona, ngunit dahil sa hirap ng buhay, sinabihan siya ng kanyang ina na baka hindi na nya ito kayang suportahan sa pag-aaral nito sa kolehiyo. Pursigidong makatapos ng pag-aaral si Mona, kaya naghanap siya ng paraan upang tulungan ang kanyang sariling makapag tapos. Nag-simula syang magbenta sa kanyang mga classmates ng kanyang mga paninda. Nag tiis syang mag-meryenda sa isang pirasong muncher o tattoos habang pinapanood ang kanyang mga kaklaseng kumain ng softdrinks at piattos. Sa awa ng Diyos, nakakuha sya ng scholarship at tuluyang nakapagtapos ng kolehiyo.

This story is not mine but that of my mother’s and grandparents’. My mother was the first in her clan to earn a college degree. I am the first in our immediate family to graduate in UP.

We should remember that these diplomas and degrees are not solely the result of our individual efforts. We are here because of the collective support and sacrifices of those who stood by us throughout this journey. We are reaping the fruits of their labor and dedication.

Where does service fit into all this? Service and sacrifice go hand-in-hand. True service is never comfortable; it involves sacrificing something of our own and going out of our way to help others.

My grandfather Ceasar, who passed away during the 2020 pandemic, is not here to witness this moment. While we may never fully repay the debt we owe to those who came before us, we can certainly pay it forward. We can become mentors to the next generation of scientists. We can serve our community with our knowledge and skills. We can conduct research that advances science for the betterment of society.

Finally, let’s reflect on the word “society.”

I had a hard time concentrating on writing this speech due to the recent flood that has affected so many this week. In the middle of the typhoon last Wednesday, my husband had to rescue our pamangkins in Cainta because the flood is already approaching their second floor. It is really challenging to celebrate today however, I believe this is precisely the moment to reflect on the true meaning of this ceremony.

I took some time to research the meaning behind our UP Sablay. According to OUR’s website, the word “Sablay” refers to an indigenous loose garment that, though simple, is traditionally worn for formal occasions. As a verb (isablay), it means to drape a precious object, such as this garment, over one’s shoulder, symbolizing value and respect for that object.

Today, we are giving value and honoring not only our efforts but also the people who have paved the way for us—our seniors, mentors, and the entire community who helped us wear this Sablay with pride. We are showing respect for the dedication and service of everyone who made our journey possible.

Our UP Sablay represents more than personal achievement; it symbolizes our responsibility to contribute to society. As we wear our Sablays today, let us remember that our journey is a testament to the collective effort and dedication of our community. It’s a call to use our knowledge, skills, and achievements to serve others, to uplift those around us, and to address the pressing needs of our society.

As my call to action, I want to repeat what I said in our institute’s recognition this morning.

Pagsilbihan ang kapwa, pagsilbihan ang sambayanan. Gamitin natin ang pananaliksik bilang instrumento ng pagbabago.

Let’s use our education in paying it forward and may our legacy be one of bettering the next generation.

Thank you, and congratulations to the College of Science Class of 2024. Mabuhay ang mga siyentista ng bayan.

Maganda’t mabuting araw sa inyong lahat! Ako si Sean Brendan, mula sa Pambansang Linangan ng Pisika.

Tuwing iniisip ko kung bakit ba ‘ko nandito sa pisika’t agham, palagi akong walang depinitibong sagot. No’ng bata ako pinangarap ko maging astronot. ‘Di ko alam. Baka dahil ang astig ng kanilang damit, tapos sasakay sa ispeyship. Ang lupit din tingnan ng mga kemistri-kemistri. Pati ‘yang mga daynosor na ‘yan. Palaging paiba-iba ang gusto ko.

Bilang mga siyentista ng hinaharap, na minsa’y sinilaw rin ng mga bitwin, numero, palaka, o kung anumang dahilan kung bakit tinahak ang daang siyensya, kahit sa’n pa man tayo dalhin ng ating pagtuklas, alam nating madaling malunod sa angking ganda nito—sa sarap ng pakiramdam tuwing nakaka-solb tayo ng ekweysyon, sa pagpaypet ng kemikal, sa pagdila ng bato, o maging sa pakiramdam na, …, basta, “ang kul pakinggan”. Pero minsan, malungkot. Totoo ang mga nararamdaman nating kalungkutan sa “‘di tayo napili”, “‘di tayo nanalo”, “‘di tayo nakapasa kasi mababa ang gan’to”. “Kapag ba nagpatuloy ako sa
siyensya, magiging matagumpay pa ba ‘ko kung ngayon palang, ‘di na ‘ko magaling?”

Kadalasang ikinakabit ng mga pamantayang internasyual ang tagumpay sa agham sa ating h-index, o kung anumang iskolarling batayan sa bilang ng ating mga nailathala, kung ilang beses ito isinipi, at iba pa. Ang iba nama’y ikinakabit ang tagumpay sa kung ga’no kataas ang ating makakamit, sa rekognisyon at kasikatan na makukuha natin sa akademikong komunidad mula sa pagtuklas ng mga bagong resulta o pagbuo ng mga abstraktong teorya. Ang iba pa’y ikinakabit ang tagumpay sa kung ga’no kalayo ang ating mararating, kung ga’no kalaki’t maimpluwensiya ang mga prestihiyosong institusyong akademiko o industriyal ang ating mapupuntahan. Maraming pagsasalarawan sa iba’t ibang puntong pibotal na sumusukat sa kung ga’no tayo katagumpay sa ating mga larangan. Kung ngayon sa mga linangan, mga grado, sa akademya’t industriya, marami pang metrikong ginagamit para sukatin tayo. Bagamat nagagamit ito sa pagsukat ng kasanayan, pananagutan, pagpuna, pagdedesisyon, at pagpapabuti, ang mga ito rin ay nagiging kawnterproduktib.

Sa ganitong kapaligiran, ang presyur na umayon ay maaaring nakapaghihina sa pagkamalikhain. Ang mismong diwa ng siyentipikong pagdiskubre—ang pagsasaliksik at paghahamon sa istatus kwo—ay napahihina ng walang tigil na paghahabol sa mga paborableng sukatan. Gayunpaman, maging sa harap nitong mga mahihirap at ‘di magagandang realidad sa mundo ng agham na nagdudulot ng malawakang kumpetisyon sa trabaho at paghina ng produktibong gawa—sa mukha ng krisis sa edukasyon, limitadong akses sa impormasyon, kakulangan sa pondo, at sa kadiliman ng klimang pulitikal—hindi pa rin dapat na kalimutan ang mga mamamayan.

Habang nauunawaan natin na ang mga pananaliksik ay may kanya-kanyang kalakasan, sakop, at limitasyon—may direktang impak man sa mga komunidad at napapanahong isyu, o wala dahil ito’y abstrak at wala pa masyadong nakaiintindi—nais kong ipaalala sa lahat na ang ating pananaliksik, ang kabuuan ng ating trabaho, ay hindi umiiral isang bakyum. Ito’y isang intigral na bahagi ng mas malawak pang ekosistemang kinabibilangan din ng mga taong sumusuporta sa ating pananaliksik at ng publiko na ang buhay ay nais nating pagbutihin no’ng una pa lamang. Kaya kahit ano pa man ang sabihin ng mga
sukatan tungkol sa kakayahan at tagumpay natin, h’wag nating hayaan na magtabon ito sa tunay na pagkamalikhain, sa tunay na paghahangad ng kaalaman, at syempre sa integridad ng agham, dahil ang bayan ay nakasandal sa atin.

At habang naiintindihan din naman natin na ‘di makapagbubuhos ang walang laman na bukal—na tayo ri’y napapagod, nauubos, nalulubog sa kahirapa’t, nawawala ang pangarap para sa mamamayan dahil sa minsang pangangailangang unahin ang sarili—nais ko ring ipaalala na ang ating pagpupunyagi ay magkakaroon pa rin ng mas malalim na kahulugan. Kapag sumikat na muli sa wakas ang araw sa napakatagal at napakadilim nating gabi, makababalik din tayo sa pagpapanday ng landas para sa mga susunod na henerasyon.
At ‘di rin dapat natatapos ang siyensya sa papel at pagsasaayos ng mga metriko. ‘Di rin sa pagbuo ng mga aplikasyon nito.

H’wag tayong magtapos sa pagtutok lamang sa ating mga pag-uusap sa isa’t isa rito, sa pagbabahagi sa mga kapwa lamang na siyentista sa mga kumperensya’t kumbensyon, kundi iparating din natin ang ating mga natutuklasan sa mga lente ng mga nararanasang realidad na nakaaantig sa mga tao. Hindi sapat na alam lamang natin na ang ating ginagawa ay para sa tao, para sa bayan, naiuugnay din dapat natin ito sa adbokasiya’t aktibismo. Dapat naisasalin din natin ang mga kumpleksiting ito sa mga malilinaw at makabuluhang naratibong akesibol para sa mga bata, sa mga matatanda, sa mga taong nasa ibang larangan, sa mga taong may limitadong kakayahan, maging sa mga taong kinaaayawan—para sa lahat—dahil ang ating agham ay ang ating pagmamahal, at ang ating pagmamahal ay mapagbuklod at mapagpalaya.

Iparinig at iparamdam natin ang ating agham.