How Artificial Intelligence can explain its decisions

They have brought together the seemingly incompatible inductive approach of machine learning with deductive logic: Stephanie Schörner, Axel Mosig and David Schuhmacher (from left).
Credit: RUB, Marquard

If an algorithm in a tissue sample makes up a tumor, it does not yet reveal how it came to this result. It is not very trustworthy. Bochum researchers are therefore taking a new approach.

Artificial intelligence (AI) can be trained to recognize whether a tissue image contains tumor. How she makes her decision has so far remained hidden. A team from the Research Center for Protein Diagnostics, or PRODI for short, at the Ruhr University Bochum is developing a new approach: with it, the decision of an AI can be explained and thus trustworthy. The researchers around Prof. Dr. Axel Mosig in the journal "Medical Image Analysis".

Bioinformatician Axel Mosig cooperated with Prof. Dr. Andrea Tannapfel, head of the Institute of Pathology, the oncologist Prof. Dr. Anke Reinacher-Schick from St. Josef Hospital of the Ruhr University as well as the biophysicist and PRODI founding director Prof. Dr. Klaus Gerwert. The group developed a neural network, i.e. an AI that can classify whether a tissue sample contains tumor or not. To do this, they fed the AI with many microscopic tissue images, some of which contained tumors, others were tumor-free.

Scientists discover new ant species

Three-dimensional image of the previously unknown extinct ant species.
Illustration credit: Hammel/Lauströer

An international team of scientists has discovered a previously unknown extinct ant species encased in a unique piece of amber from Africa. Using the X-ray light source PETRA III at the German Electron Synchrotron (DESY) in Hamburg the researchers, from Friedrich Schiller University Jena, the University of Rennes in France, the University of Gdansk in Poland, as well as the Helmholtz-Zentrum Hereon in Geesthacht, Germany, had examined the critical fossil remains from 13 individual animals in the amber and realized that they could not be attributed to any previously known species. The name given to the new species and genus is †Desyopone hereon gen. et sp. nov. In this way, the scientists are honoring the two research institutions involved – DESY and Hereon – which contributed significantly to this find with the help of modern imaging techniques. Ultimately, it was only possible to identify the new species and genus through the combination of extensive phenotype data from scans and recent findings from genome analyses of living ants. The team reports on its discovery in the research journal “Insects”.

These mice grow bigger on the rainier sides of mountains. It might be a new rule of nature

Shaggy soft-haired mouse Abrothrix hirta (Order Rodentia, Family Cricetidae)
Resized Image using AI by SFLORG
Credit: Pablo Teta

Scientists studying mice from the Andes Mountains in Patagonia noticed something they couldn’t explain: the mice from the western side of the mountains were bigger than the ones from the east, but DNA said that they were all from the same species. The researchers examined the skulls of 450 mice from the southern tip of South America, and found that existing biological laws didn’t explain the size differences. Instead, in a new paper in the Journal of Biogeography, the scientists put forth a new hypothesis: the mice on the western slopes were bigger because that side of the mountain range gets more rain, which means there’s more plentiful food for the mice to eat.

“There are a bunch of ecogeographic rules that scientists use to explain trends that we see again and again in nature,” says Noé de la Sancha, a research associate at Chicago’s Field Museum, an assistant professor of Environmental Science and Studies at DePaul University, and the paper’s corresponding author. “With this paper, I think we might have found a new one: the rain shadow effect can cause changes of size and shape in mammals.”

The mice that de la Sancha and his colleagues examined in this study are shaggy soft-haired mice, Abrothrix hirta. “They’re very cute little buggers, they have soft white bellies,” says de la Sancha. “They live in the mountains, which makes them unique, but they’re also found in lower elevations. Overall, they’re not very well-studied.”

New methodology predicts coronavirus and other infectious disease threats to wildlife

The rate that emerging wildlife diseases infect humans has steadily increased over the last three decades. Viruses, such as the global coronavirus pandemic and recent monkeypox outbreak, have heightened the urgent need for disease ecology tools to forecast when and where disease outbreaks are likely. A University of South Florida assistant professor helped develop a methodology that will do just that – predict disease transmission from wildlife to humans, from one wildlife species to another and determine who is at risk of infection.

The methodology is a machine-learning approach that identifies the influence of variables, such as location and climate, on known pathogens. Using only small amounts of information, the system is able to identify community hot spots at risk of infection on both global and local scales.

“Our main goal is to develop this tool for preventive measures,” said co-principal investigator Diego Santiago-Alarcon, assistant professor of integrative biology. “It’s difficult to have an all-purpose methodology that can be used to predict infections across all the diverse parasite systems, but with this research, we contribute to achieving that goal.”

With help from researchers at the Universiad Veracruzana and Instituto de Ecologia, located in Mexico, Santiago-Alarcon examined three host-pathogen systems – avian malaria, birds with West Nile virus and bats with coronavirus – to test the reliability and accuracy of the models generated by the methodology.

Recycling Greenhouse Gases

Florian Schrenk (left) and Christoph Rameshan
Source/Credit: Technische Universität Wien

CO2 and methane can be turned into valuable products. But until now the catalysts required for such reactions quickly lose their effectiveness. TU Wien has now developed more stable alternatives.

Wherever the production of harmful greenhouse gases cannot be prevented, they should be converted into something useful: this approach is called "carbon capture and utilization". Special catalysts are needed for this. Until now, however, the problem has been that a layer of carbon quickly forms on these catalysts - this is called "coking" - and the catalyst loses its effect. At TU Wien, a new approach was taken: tiny metallic nanoparticles were produced on perovskite crystals through special pre-treatment. The interaction between the crystal surface and the nanoparticles then ensures that the desired chemical reaction takes place without the dreaded coking effect.

Dry reforming: Greenhouse gases become synthesis gas

Carbon dioxide (CO2) and methane are the two human-made greenhouse gases that contribute most to climate change. Both gases often occur in combination, for example in biogas plants. "So-called methane dry reforming is a method that can be used to convert both gases into useful synthesis gas at the same time," says Prof. Christoph Rameshan from the Institute of Materials Chemistry at TU Wien. "Methane and carbon dioxide are turned into hydrogen and carbon monoxide - and it is then relatively easy to produce other hydrocarbons from them, right up to biofuels."

Eight new species of tiny geckos tumbling out of Madagascar’s rainforests

 Seven of the new species of dwarf geckos described from Madagascar.
Credit: P.-S. Gehring, H.-P. Berghof, M. Vences & M.D.

An international team has discovered and named eight new day gecko species from Madagascar, and each of them is no longer than your pointer finger.

Researchers working in the rainforests of Madagascar have been studying the tiny brown Lygodactylus geckos in the subgenus Domerguella for decades. All this time they have been trying to understand their distribution and evolution, thinking that there were just five species. Now, based on analysis of their DNA and careful examination of their scales and proportions, an international team has discovered that there may be as many as seventeen! They have named eight new species in the journal Zootaxa.

In some places, the team found there were three or four different species found in the same place. ‘This was a remarkable discovery’ says Professor Miguel Vences of the Technische Universität Braunschweig, Germany, first author on the study, ‘On Montagne d’Ambre in the north of Madagascar we thought we were collecting just one species, but now we find there are four. Four different, closely related species that are almost indistinguishable to us, occurring together in the same place, apparently without interbreeding—this is exceptional, even for Madagascar.’

Indeed, Madagascar has remarkably high levels of reptile diversity and endemism, and over 150 new species have been discovered and named in the last thirty years. ‘These results highlight how important it is that we continue to collect samples across Madagascar, even of species we think we understand,’ says Dr Frank Glaw, Curator of Herpetology at the Zoologische Staatssammlung München in Munich, Germany, ‘There is still very much more to discover.’

Webb takes its first exoplanet image

This image shows the exoplanet HIP 65426 b in different bands of infrared light, as seen from the James Webb Space Telescope: purple shows the NIRCam instrument’s view at 3.00 micrometers, blue shows the NIRCam instrument’s view at 4.44 micrometers, yellow shows the MIRI instrument’s view at 11.4 micrometers, and red shows the MIRI instrument’s view at 15.5 micrometers.
Credit: NASA/ESA/CSA, A Carter (UCSC), the ERS 1386 team and A. Pagan (STScI)

For the first time, astronomers have used the NASA/ESA/CSA James Webb Space Telescope to take a direct image of an exoplanet. The exoplanet is a gas giant, meaning it has no rocky surface and could not be habitable. The image, as seen through four different light filters, shows how Webb’s powerful infrared gaze can easily capture worlds beyond our Solar System, pointing the way to future observations that will reveal more information than ever before about exoplanets.

The exoplanet in Webb’s image, called HIP 65426 b, is about six to eight times the mass of Jupiter. It is young as planets go – about 15 to 20 million years old, compared to our 4.5-billion-year-old Earth.

Astronomers discovered the planet in 2017 using the SPHERE instrument on the European Southern Observatory’s Very Large Telescope in Chile and took images of it using short infrared wavelengths of light. The Webb image, taken in mid-infrared light, reveals new details that ground-based telescopes would not be able to detect because of the intrinsic infrared glow of Earth’s atmosphere.

Scientists discover surprise anticancer properties of common lab molecule

Nobel laureate Dr. Aziz Sancar at an event in 2016.
Photo credit: Jon Gardiner/UNC-Chapel Hill

Scientists at the UNC School of Medicine have made the surprising discovery that a molecule called EdU, which is commonly used in laboratory experiments to label DNA, is in fact recognized by human cells as DNA damage, triggering a runaway process of DNA repair that is eventually fatal to affected cells, including cancer cells.

The discovery, published in the Proceedings of the National Academy of Sciences, points to the possibility of using EdU as the basis for a cancer treatment, given its toxicity and its selectivity for cells that divide fast.

“The unexpected properties of EdU suggest it would be worthwhile to conduct further studies of its potential, particularly against brain cancers,” said study senior author Dr. Aziz Sancar, the Sarah Graham Kenan Professor of Biochemistry and Biophysics at the UNC School of Medicine and member of the UNC Lineberger Comprehensive Cancer Center. “We want to stress that this is a basic but important scientific discovery. The scientific community has much work ahead to figure out if EdU could actually become a weapon against cancer.”

EdU (5-ethynyl-2′-deoxyuridine) is essentially a popular scientific tool first synthesized in 2008 as an analog, or chemical mimic, of the DNA building block thymidine – which represents the letter “T” in the DNA code of adenine (A), cytosine (C), guanine (G) and thymine (T). Scientists add EdU to cells in lab experiments to replace the thymidine in DNA. Unlike other thymidine analogs, it has a convenient chemical “handle” to which fluorescent probe molecules will bond tightly. It thus can be used relatively easily and efficiently to label and track DNA, for example in studies of the DNA replication process during cell division.

Soaking up the sun with artificial intelligence

Machine learning methods are being developed at Argonne to advance solar energy research with perovskites.
Credit: Maria Chan/ Argonne National Laboratory

The sun continuously transmits trillions of watts of energy to the Earth. It will be doing so for billions more years. Yet, we have only just begun tapping into that abundant, renewable source of energy at affordable cost.

Solar absorbers are a material used to convert this energy into heat or electricity. Maria Chan, a scientist in the U.S. Department of Energy’s (DOE) Argonne National Laboratory, has developed a machine learning method for screening many thousands of compounds as solar absorbers. Her co-author on this project was Arun Mannodi-Kanakkithodi, a former Argonne postdoc who is now an assistant professor at Purdue University.

“We are truly in a new era of applying AI and high-performance computing to materials discovery.” — Maria Chan, scientist, Center for Nanoscale Materials

“According to a recent DOE study, by 2035, solar energy could power 40% of the nation’s electricity,” said Chan. ​“And it could help with decarbonizing the grid and provide many new jobs.”

Corals pass mutations acquired during their lifetimes to offspring

The Elkhorn coral, Acropora palmata, grows into large stands via polyp budding and fragmentation so that many colonies belong to the same clone or genet. During growth, mutations can accumulate in its cells and new research shows that the Ekhorn coral is able to pass these mutations onto to their sexual offspring. This is unlike most animals that prevent such a transfer from the body to reproductive cells.
 Credit: Ilian Baums / Penn State. Creative Commons

In a discovery that challenges over a century of evolutionary conventional wisdom, corals have been shown to pass somatic mutations — changes to the DNA sequence that occur in non-reproductive cells — to their offspring. The finding, by an international team of scientists led by Penn State biologists, demonstrates a potential new route for the generation of genetic diversity, which is the raw material for evolutionary adaptation, and could be vital for allowing endangered corals to adapt to rapidly changing environmental conditions.

“For a trait, such as growth rate, to evolve, the genetic basis of that trait must be passed from generation to generation,” said Iliana Baums, professor of biology at Penn State and leader of the research team. “For most animals, a new genetic mutation can only contribute to evolutionary change if it occurs in a germline or reproductive cell, for example in an egg or sperm cell. Mutations that occur in the rest of the body, in the somatic cells, were thought to be evolutionarily irrelevant because they do not get passed on to offspring. However, corals appear to have a way around this barrier that seems to allow them to break this evolutionary rule.”

Since the time of Darwin, our understanding of evolution has become ever more detailed. We now know that an organism’s traits are heavily determined by the sequence of their DNA. Individuals in a population vary in their DNA sequence, and this genetic variation can lead to the variation in traits, such as body size, that could give an individual a reproductive advantage. Only rarely does a new genetic mutation occur that gives an individual such a reproductive advantage and evolution can only proceed further if — and this is the key — the individual can pass the change to its offspring.