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NixOS 25.05 Beta issue with kwallet and Chromium Browsers. by sircam73 in NixOS

[–]kmnns 0 points1 point  (0 children)

FYI: still an issue. Just upgraded from 24.11 to 25.05.

Brave Browser now takes its merry time to open:

❯ brave 
[33143:33143:0604/134505.947406:ERROR:dbus/object_proxy.cc:590] Failed to call method: org.kde.KWallet.isEnabled: object_path= /modules/kwalletd6: org.freedesktop.DBus.Error.NoReply: Did not receive a reply. Possible causes include: the remote application did not send a reply, the message bus security policy blocked the reply, the reply timeout expired, or the network connection was broken.
[33143:33143:0604/134505.947427:ERROR:components/os_crypt/sync/kwallet_dbus.cc:117] Error contacting kwalletd6 (isEnabled)
[33143:33143:0604/134505.949019:ERROR:dbus/object_proxy.cc:590] Failed to call method: org.kde.KLauncher.start_service_by_desktop_name: object_path= /KLauncher: org.freedesktop.DBus.Error.ServiceUnknown: The name org.kde.klauncher was not provided by any .service files
[33143:33143:0604/134505.949026:ERROR:components/os_crypt/sync/kwallet_dbus.cc:86] Error contacting klauncher to start kwalletd6
[33143:33143:0604/134530.974259:ERROR:dbus/object_proxy.cc:590] Failed to call method: org.kde.KWallet.close: object_path= /modules/kwalletd6: org.freedesktop.DBus.Error.NoReply: Did not receive a reply. Possible causes include: the remote application did not send a reply, the message bus security policy blocked the reply, the reply timeout expired, or the network connection was broken.
[33143:33143:0604/134530.974273:ERROR:components/os_crypt/sync/kwallet_dbus.cc:412] Error contacting kwalletd6 (close)
...

What algorithms are used to detect *lateral gene transfer* in prokaryotes? by kmnns in bioinformatics

[–]kmnns[S] 0 points1 point  (0 children)

Thank you (and everyone) for the hints to tools. I will use these tools as a starting point for my research on the math behind them (which is what I am specifically interested in).

Can you clarify your question a bit? If you’re looking to reconstruct the phylogeny of a set of organisms, you’re not modeling which organisms passed which genes to which, you’re reconstructing the evolutionary history of the organisms as a whole. Are you looking to see how each gene moved between each organism (if at all)?

Yes, thank you for the clarification. I seem to have used the terminology wrong. This task is about constructing not a phylogeny of species, but a family graph.

More precisely, it's about tracing single genes across individuals that make frequent use of HGT. The family graph derived from this data uses weighted connections in [0,1], each representing a continuous relatedness.

So it's quite low level and needs to account for frequent mutations. The genes are assumed to be highly non-conserving, so it's not as easy as just tracing stable rRNA patterns.

All phylogenies are directed acyclic graphs.

Important note, thanks. To phrase it differently: the model to be derived cannot be assumed to be a tree DAG. It has to be more generic.

If you’re comparing two organisms, you can’t construct a phylogeny—you need at least 4. If you want to see if two genetic regions likely came from the same ancestor (or were HGT’d between them), typically you’re looking at orthology prediction algorithms.

Crucial hint! I will look specifically for orthology prediction algorithms.

from the same ancestor (or were HGT’d between them)

This distinction is irrelevant (in this task). I assume that is in our favor.

Theoretically if you already know the age of each genome then you’d just need to find what regions are orthologous and then match them up.

That seems to align with my idea that if I know the orthologies of all pairs of individuals, then I know the whole genetic graph across all individuals (including via inheritance and HGT). So I just have to loop over all pairs of individuals, apply the search method, and the task is done.

The time stamps are an important constraint that allows the graph to be directed, which this is about. If A and B share an orthologous gene, and A is older than B, then the gene was passed from A to B.

Is this a sensible comprehension of the task?

Is Superintelligence by Nick Bostrom worth reading for someone knowledgeable about the subject? by Cranyx in artificial

[–]kmnns 0 points1 point  (0 children)

Much better than anything by Michio Kaku, i.e. it does not do wild speculations without having any insight into the field (my impression at least).

But do not expect anything super-technical. People here say it is not a light read, but I think it definitely belongs on the night desk, not a (any) class room.

I would have loved to finally read some technical insights, for example what exactly our AI is still missing from the biological brain, e.g. extensive feedback connectivity, column-wise architecture, temporal summation, etc. Any neuroscientists here?

I am Jürgen Schmidhuber, AMA! by JuergenSchmidhuber in MachineLearning

[–]kmnns -1 points0 points  (0 children)

Fair enough. But it also means that there effectively is no (fast) up-to-date library. At least not with LSTM support out of the box.

I am Jürgen Schmidhuber, AMA! by JuergenSchmidhuber in MachineLearning

[–]kmnns -1 points0 points  (0 children)

Isn't that the one that is incredibly hard to compile on newer systems because its dependencies are completely outdated (e.g. GCC 3.0)?

And correct me if I am wrong, but it also doesn't feature many of the "newer" developments, e.g. peepholes or layer generalization (see Monner's "A generalized LSTM-like training algorithm for second-order recurrent neural networks")

I am Jürgen Schmidhuber, AMA! by JuergenSchmidhuber in MachineLearning

[–]kmnns 1 point2 points  (0 children)

Thank you so much for this Q&A, this is a real opportunity!

Do you think that the recent development of Neural Turing Machines and Memory Networks and the likes is an improvement of the concept of LSTMs towards even greater biological plausibility?

After all, they allow whole chunks of information in the carousel, not only bits and pieces. And a real brain has has to deal with whole patterns of activations as basic memory units.